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: BIODINAMICA: A TOOLKIT FOR ANALYSES OF BIODIVERSITY AND BIOGEOGRAPHY ON THE DINAMICA-EGO MODELLING PLATFORM
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors have developed a new software platform called BioDinamica, which encompasses more than 50 user-friendly functions related to biogeography and macroecology. I commend the authors for the integration of multiple biogeographical and macroecological analyses into one package, with a user-friendly interface. One aspect that deserves to be mentioned is the inclusion of recent novel techniques into the platform, such as geographic interpolation of endemism or species composition interpolation (although the latter simply consists in plotting ordination axes values in a map using an RGB composite, and thus relatively easy to code in R). Also, sufficient background in the references is provided, although more information on the platform in which BioDinamica is embedded (Dinamica-EGO) is needed. This is relevant in this context, as it seems not to be a widespread or widely known software. The manuscript is overall clearly written in professional, unambiguous language.

Some comments on tables and figures are as follows: Table 1 is fine, but please provide references for each method in a new column. The high number of functions make it virtually impossible to describe each of them in the text, so it is important to provide the user relevant information about each analysis. Figure 1 is poorly relevant in the context of the software, given it is a merely description of the interface, inputs and outputs. I suggest redoing this figure using a flowchart instead. There are many examples of this kind of figures in the literature related to software development. A numerical scale in Figure 2 should be included, at least for species richness.

Some minor spelling mistakes are as follows: The citation is 2018 or in press at line 103? It should be “Phylogenetic GDM” at line 108. At Table 1, correct the spelling in the SDM tool “Calculate area of Disdributions” and in the Statistica and Ordination tool “Gloabl Moran I” and “Unsupervisioned Classification by K-means”.
Experimental design: The research aim is well defined, and it is also stated how the research fills a gap in biogeography and macroecology. However, I am not fully convinced about including SDM tools, as there are several platforms that enable integrative analyses of species distributions. See, for instance, Guo & Liu (Ecography, 2010, V33, pp 637-642), Naimi & Araújo (Ecography, 2016, V39, pp 368-375) and Cobos et al. (PeerJ, 2019, V7, e6281). I think the authors should make an extra effort to stand out from the rest of software already available. The package could include some novel algorithms for model fitting, like random forests, support vector machines, neural networks, among others. See Naimi & Araújo (Ecography, 2016, V39, pp 368-375).

The methods described have sufficient information, but more detail is needed at some times, particularly for those methods recently developed. Could you describe this rarefaction technique in more detail at lines 77-78? It is not clear whether this is a new method or refers to classical rarefaction, because you have cited an unpublished study. I also suggest that you let the user to choose the ordination technique at lines 97-98, instead of constraining them to use only NMDS. Eigenanalyses are valuables per se, as they give the proportion of variance explained by the axes. In addition, using three axes sounds restrictive. Users should base their decision of the number of axes chosen on the stress.

I also suggest that you improve the description about k-means at lines 101-102. Although k-means is a supervised learning technique, the user can choose the optimal number of clusters a posteriori (using, for instance, the “elbow method”). Is this kind of implementation present or is the user restricted to a priori define the number of clusters? Please provide more detail about the SDMs implemented at lines 112-113. Moreover, indicate the algorithm used for spatial thinning at lines 117-119. The benefit of the technique presented at lines 119-121 is not clear. Indeed, how does this spatial bias could properly reflect the available environmental conditions? Is there evidence of a better performance relative to extracting random background points?

Lobo et al. (Glob. Ecol. Biogeogr. V17, pp 145-151) have shown that the AUC method you have described at lines 140-142 has several drawbacks that prevent its use in SDMs and may be misleading. Please warn about this, and consider including other model performance metrics, such as the AIC. See, for example, Warren & Seifert (Ecol. Applic., 2011, V25, pp 331-342) and Radosavljevic et al. (2014, J. Biogeogr. V41, pp 629-643). Finally, please justify why you considered only 3 dimensions at lines 147-148, as one or two could eventually suffice. Can the user select one or two components?

All the data, information and tutorials for a reproducible research are available at the link provided in the text.
Validity of the findings: Conclusions are, in general, well stated, linked to original research question and limited to supporting results. Sometimes, nevertheless, the authors should explain in more detail certain results. For instance, an explanation for the strong difference between both patterns are not given at lines 195-199. Besides, there is congruence between the pattern depicted in Fig. 2e and that of Fig. 2 in Oliveira et al. (Sci. Rep., 2017, V7, 2992). Fig. 2f, by contrast, also shows high endemism areas in the north and the south east. Authors should explain this difference at lines 200-204.
Additional comments: Overall, the manuscript, software and data are sound, and provide a user-friendly interface software with numerous biogeographical and macroecological analyses. After the authors have taken my comments into consideration, I believe the study merits publication. Thank you for letting me reviewing this manuscript and have a good review.


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: BIODINAMICA: A TOOLKIT FOR ANALYSES OF BIODIVERSITY AND BIOGEOGRAPHY ON THE DINAMICA-EGO MODELLING PLATFORM
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comments.
Experimental design: No comments.
Validity of the findings: No comments.
Additional comments: The paper presents an interesting toolkit for dealing with biodiversity and biogeography analyses based on an a user-friendly graphical interface. BioDinamica will certainly be a useful tool for the whole community of biogeographers, conservacionists, taxonomists and ecologists.
The text is straight-forward, and its goals are well defined.
In this sense, I recommend accepting the paper without modifications.


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: BIODINAMICA: A TOOLKIT FOR ANALYSES OF BIODIVERSITY AND BIOGEOGRAPHY ON THE DINAMICA-EGO MODELLING PLATFORM
Review round: 1
Reviewer: 3

Output:
Basic reporting: This paper introduces BioDinamica, a free package with a user-friendly interface that reunites algorithms for several spatial analyses for biogeography and macroecology. Such a package is very welcome, since many of these algorithms are already available but dispersed in different software, some of which lack a GUI or are paid. The package seems to be very complete and flexible. Each analysis has an associated wizard which guides the user through the analysis, which greatly facilitates the use of the program.

The manuscript itself is concise, well-written and clearly structured. I have pointed some suggestions for improvement directly in the text file. There are some main points that should be reviewed:

1) Introduction: before you introduce your own software, it would be enlightening to present a short review on already available packages and software. Surely most of the analysis included in BioDinamica can also be performed elsewhere (an exception is GIE). You should explain if those packages/software have any shortcomings, and how BioDinamica is a solution. Are they paid software? Are they all command-line-based? Are the needed functions dispersed in many different platforms and software?

2) You should include a section mentioning the utilities, such as "Extract values to points", which are very simple using BioDinamica compared with GIS software, for example. I also have a suggestion for future versions: including a simple "Join" function to extract names from polygon shapefiles to points (to recover names from administrative units, conservation units, etc). This would be useful to check the accuracy of the points.

3) I feel that the text lacks a biological “spin” when introducing the different analysis. For instance, your SDM section reads “Species Distribution models: Today, species distribution models (SDM) are one of the most widely used biogeographic tools.” This does not make clear why a biologist might want to estimate a SDM. The paper would be greatly enhanced if each section started with a short statement on what it is good for. There is no need to give too much detail nor to review literature, but just say what a biologist might gain from estimating SDMs, interpolating betadiversity, etc. This is especially true for the guidebook: it lacks biology altogether. I strongly advise that the next version of the manual includes a short statement for each analysis explaining what it is useful for.

4) Some of the methods used in the proof of concept are unclear and need further clarification, such as the generation of records from polygons, number of PCA axes used, etc. I have explained my doubts directly in the text.

5) One of the greatest strengths of similar software I am used to (e.g. MrBayes, Mesquite, BEAST) is the existence of an online group or email list which joins the community of users with the developers. As BioDinamica gets more popular, many end-users will undoubtedly have difficulties with running some of the more complex analysis, or even find bugs, and it would be great if they have something other than the manual to turn to. I advise you to set up and online forum or email list (BEAST use Google Groups, MrBayes uses SourceForge, Mesquite has a mail list) and already mention it in the paper.

6) Figure 2: this figure is already very informative but I think it can be substantially improved. First, it lacks a “column” with raw data: the non-interpolated values of e.g. species richness estimated from the points. Without seeing the raw data, I find it very difficult to evaluate if your interpolation makes sense or not. It was also annoying to compare it with Oliveira et al. 2017 because I had to go back and forth between the two papers. I suggest that you remake the figure with 6 columns (or maybe 2 figures with 3 columns): 1- raw species richness estimated from samples of polygons of Birdlife, 2- its interpolated values and 3- and its environmental prediction, 4- raw species richness estimated from museum specimens (not present in Oliveira et al. 2017!), 5- its interpolated values and 6- its environmental prediction.

Apart from the manuscript, I also tried downloading BioDinamica and running some of the analysis. I have some comments:

7) You should include links to the pages of Dinamica Ego 4.0.11 and Enhancement Plugin directly in the BioDinamica website, since you have to download both anyway.

8) At first, my input data had some errors in the coordinates, which made BioDinamica indicate an error. If possible, the next version should indicate the line containing the record where the error was found, otherwise it may be difficult to find the mistake.

9) GIE: I could run successful analyses with 5–7 classes (in a very timely manner – only a few minutes for a global dataset), but the analysis with 10 classes failed (“atributo ‘names[2] deve ter o mesmo comprimento que o vetor [1]” – by the way, it would be best if these error reports are displayed in English). I also had problems running an analysis into the same folder with output results. You should include an option for overwriting results or checking if the output folder already has data. This might be true for other analysis as well.

10) Minimum convex hulls: I got the message "Script X depends on submodels that could not be found in your system. Would you like to install and download from the Online Repository?". After I agreed to install the submodels, I could run the analysis, but the tiff files were empty – I’m not sure what went wrong.

11) Extract values per points: I got the error message: “wc2.0_bio_10m_01 is not a valid column name” but all values seem to have been correctly extracted. This analysis is much more straightforward and quick than using GIS software (the other way I would have done it).

12) SDM: after I input the occurrences I got the error "the functor "Sdm" functor cannot be executed. Its purpose is to replace a missing or incompatible submodel functor previously used in this script". I could not run this analysis.

13) Species richness interpolation: first I tried to interpolate using a world map as a mask and got the error “Error caught in R execution: ‘Topology Exception: input geom 0 is invalid: self-intersection at or near point xxx yyy at zzz www.” Then I tried to do the same analysis using an Argentina map as mask; this analysis advanced a little more, but then I got the error “the real value –nan(ind) is not valid”. I could not run this analysis.

I did not spend too much time trying to troubleshoot the errors I mentioned above – it could be something with my data or with the parameters I set. Anyway, this clearly demonstrates why it would be good to have an online group for this kind of situation.

The guidebook is welcome but needs several improvements. As mentioned above, each section should start with a quick practical/biological explanation of the purpose of the analysis. It also lacks appropriate references. For instance, each SDM should have its reference very explicitly included (e.g. the articles describing BioClim, SVM, MaxEnt, etc). This is also true for the Wizards: they MUST start with something like “Users using this analysis should cite papers X and Y” – for instance, the SDM Wizard currently cites a general review on SDMs). The guide could also include examples of successful outputs. Strangely, I could not use ctrl + F to search for words and navigate the PDF – maybe some problem with converting the file to PDF? Finally, the guide is in dire need of revision of the English – there are still many words and expressions in Portuguese and some portions are poorly translated. I strongly advise including all references in Wizards and preparing a revised version of the guidebook before the paper is published.

In sum, this is a nice and concise paper that presents a package which has the full potential to become one of the main tools in biogeography and macroecology. The software itself is easy to use, and although I encountered some problems while running some analyses, I am confident this can be solved with an online group for troubleshooting or addressed in future versions of the software. The functions that I could run were very easy and quick compared to other software that perform the same task. This seems like the start of a large project that has a great potential to be improved and expanded over the years.

Best regards,
Ivan L. F. Magalhaes
Experimental design: No comment
Validity of the findings: No comments
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: FUNCTIONAL PROPERTIES OF BACTERIAL COMMUNITIES IN WATER AND SEDIMENT OF THE EUTROPHIC RIVER-LAKE SYSTEM OF POYANG LAKE, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript entitled “Functional properties of bacterial communities in water and sediment of the eutrophic river-lake system of Poyang Lake, China” by Ren et al. discusses microbial functional potential in lake and river sediments and water column of the Poyang Lake, China. Authors offer new insights to the function of microbial communities in eutrophic waters and also explore the functional redundancies of the communities. I particularly enjoyed the breakdown of potential functions for each of the biogeochemical cycles, and the comparison between sediments and water column.

However, there are few parts of the manuscript that need expansion and clarifications.
The manuscript, particularly the introduction and discussion, is difficult to follow due to many grammatical errors and lack of proper punctuation. The standard of English needs to be improved and the paper requires a thorough editing for grammar, punctuation, word choice, etc. The language is too colloquial at times, and reoccurring grammatical mistakes make the manuscript hard to follow.
Experimental design: The manuscript lacks important data and details on sampling procedures. I listed most of the in the comments below. Main concerns include: lack of environmental data and analysis (temp, DO, pH, Chlorophyll, etc.), no information on the status of this eutrophic lake (cyanobacterial blooms? Turbidity? Sampling depths?). Please see detailed comments below and clarify.
Validity of the findings: I wish the authors expanded more on the association between functional redundancy and the vulnerability to environmental perturbations.
I understand the concepts of high and low functional redundancies, but the authors did not expand on these findings and what they mean for the ecosystem and microbial dynamics? What does it mean for biodiversity? Why is this important? This part of the discussion (and conclusions) needs more work.
Additional comments: More specific comments

Line 17: define PICRUSt

63: This first sentence sounds incomplete and confusing

67: Run-on sentence; confusing

103: No specific information on the lake, its tributaries, and sample collection. How deep is it? What’s the average depth of the rivers? How deep were the sediments collected? At what depth were the water samples collected?

110: I appreciate that all these nutrients were collected and analyzed but this manuscript is lacking environmental variables that are likely impacting biogeochemistry and microbial distribution. Providing env. variables like temperature, dissolved oxygen, pH, turbidity, and chlorophyll a concentration would be beneficial and including them in statistical analysis, along with nutrients, could reveal new and important relationships.

124: reference for the primers?

216: grammar; “This study showed”

224: defined OM in sentence 222, no need to do it again

225: “contributed” ?

227: “consistent of” seems incorrect here

240: Is the lake actually eutrophic? Is there any history of cyanobacterial blooms? This is important information that should be addressed in the discussion. Blooms can have a big impact on biogeochemical cycles and microbial communities in water column and sediments (i.e., Taihu).

250: Is this complete denitrification ending at N2? Or just N reductase genes (nas, nor, nir, nos) This is important as denitrification is a stepwise reaction and it can sometimes stop at N2O.

259: This goes along with the previous question. In the presence of oxygen, denitrification can stop at N2O because nos is oxygen sensitive. It is important to clarify here, whether this high potential of denitrification was in fact complete denitrification to N2 gas. Or just high potential of NO3- reductions.

256: This sentence is grammatically incorrect

272: Nitrification is also an important process in the N cycle, especially in the shallow lakes where it can be coupled with denitrification.

274: “can help us understand”

285-286: this sentence is confusing and awkward

295: I don’t see any mention of DNRA, which can be happening in the presence of sulfur as well. Did DNRA play a role in the sediments? Was there a functional potential for it?

307: This sentence is again confusing and grammatically incorrect


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: FUNCTIONAL PROPERTIES OF BACTERIAL COMMUNITIES IN WATER AND SEDIMENT OF THE EUTROPHIC RIVER-LAKE SYSTEM OF POYANG LAKE, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Ren Z et al. have reported the distinct compositional and functional difference of bacterial community between sediment and water samples from the river-lake system of Poyang Lake. The English language of this paper is adequate, and the structure conforms to PeerJ standards. I still concerned two points,
1, The nutritional status of Poyang Lake and its river-lake system is described as eutrophic in this paper, but actually it’s periodly eutrophic, and not appreciate to be called as eutrophic.
2, There is no evident difference between river and lake regions from the results of either water or sediment samples, this point is quite strange in such an estuary ecosystem, and I think some interpretation are needed in the discussion.
Besides, literature was well referenced, but the format was quite confusion in the list.
The authors have supplied raw sequencing data, but the sample name was inconsistent and hard to identify.
Experimental design: Although this paper seemed as a re-analysis of previous study by bioinformatics methods, it’s original and significative and worth to report, and within the scope of the journal.
The introduction part is not clear and coherent enough, and also the scientific issue and knowledge gap need carefully stated.
The statistical analysis section should be more carefully described, and supplement some exemplary literatures for the models.
The discussion section only focused on the metabolic function, while the sampling information such as the flow direction, environmental pollution, and river-lake interaction was not discussed.
Validity of the findings: The paper compared the functional redundancy of bacterial community by a linear regressions model, in which the functional composition dataset was based on the predicted metagenomes and their KEGG annotation, while the taxonomic composition was based on the whole sequenced community, and functional composition represented only a subset of the taxonomic composition. The author could try to eliminate the unidentified taxonomic groups, and then assess the function-composition relationship.
Additional comments: I think this study is of great significance for the research of Poyang Lake, and the function prediction give us some specific insight for a microbial community. However, I think the writing is too concise that many important details are overlooked (methods), and the introduction and discussion also should be improved.


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

Input:
Title: FUNCTIONAL PROPERTIES OF BACTERIAL COMMUNITIES IN WATER AND SEDIMENT OF THE EUTROPHIC RIVER-LAKE SYSTEM OF POYANG LAKE, CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The English was satisfactory although there were some typos and confusing sentences throughout. Many statements were not cited and need to be supported. Suggested improvements and specifics are posted below.
Experimental design: Methods need to provide much more details, especially within the statistical analysis section and the analysis of the sequence data.
Validity of the findings: Statistics definitely need to be reported and perhaps more rigorously tested. The importance or significance of the findings are not clear in relationship to the literature that was discussed nor to the greater overall question.
Additional comments: Line 63: this is a redundant sentence of the first in the intro.
Line 69: remove the word “all.”
Line 78: I would recommend this paragraph start with a comment on how there are many different ways to characterize functional capacity and then just discuss PICRUSt because I am left wondering why you wouldn’t use metagenomes over 16S predictions.
Line 97 and line 104: reference source not found ?
Line 103: is there a map somewhere indicating where these samples were collected?
Line 109: clarify how the sediment was homogenized
Line 139: quality?

Statistical Analysis: clarify what exactly was being compared. Abundances or presence absence? Was the data transformed? Etc.
Line 154: I don’t understand this
Line 162: Clarify what significance of nutrient variables means
Line 168: were these abbreviations defined earlier in the text?

There’s no reference to figure 1 in the text.

Line 169-170: report p values in text or reference to figures where this information can be found in text.
Line 201-210: I still don’t understand how you get redundancy information out of linear regression please clarify in methods or results.

Line 216: cite this statement… sediments can heavily influence the water column, are these truly distinct communiites?”
line 231: confusing sentence, please clarify and cite.
Lines 233: A lot of discussion of OM but how does this relate to your results? What about carbon fixation, methane production?
Line 238: I believe this is much larger, I would find a more recent citation.
Line 252: was OC defined earlier in text?
Line 259: Dynamics in environmental parameters in this lake is not discussed in the results and it is unclear if you are getting this info from new data collected in this paper or literature.
Line 276; but if there are high N loads, its probably not going to be occurring. If you think this is not the case, please support it in the discussion. Also support the significance of this more clearly. Nif genes are wide spread in make prokaryotes and archaea so it isn’t that surprising you see a lot of potential from this.

Lines 290 and beyond: need to support these statements with citations.
Line 301: again why is this important? What is the significance of these statements in relation to this system?
Line 317: again, what is the significance of this? What does this mean in the greater picture of lake poyang?

Figure 3. p values need to be reported somewhere. In 3A, it is hard to believe that there are truly significant differences between carbohydrate metabolism considering those error bars. Same with methane production. All the raw statistical data needs to be provided because it seems like B-D is also the case where the error bars are overlapping a lot and don’t really look different. If you are doing a lot of ANOVAs, corrections need to be made for multiple comparisons as well.

Figure 6. Should this just be a table?

Why was there not analyses done with just the 16S data? For example the abundances of 16S genes. I think this would be more convincing than using the PICRUSt information as this is all predicted.


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: IN SILICO ANALYSES OF CD14 MOLECULE REVEAL SIGNIFICANT EVOLUTIONARY DIVERSITY, POTENTIALLY ASSOCIATED WITH SPECIATION AND VARIABLE IMMUNE RESPONSE IN MAMMALS
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comments
Experimental design: No comments
Validity of the findings: No comments
Additional comments: The manuscript entitled ‘In silico analyses of CD14 molecule reveals significant evolutionary diversity potentially associated with speciation and variable immune response in mammals’ is well written and questions that are raised have been answered using various computational programs.
Following incorporation will improve the manuscript.
Table 1 and Table 2 show identity and similarity respectively, does not give much different interpretation/ information, should be merged in one table, keeping ‘similarity’ in bracket.
Author should construct a figure depict the gene structure indicating conserved domain, location of mutation/ substitution of amino acids or hotspots and whether deleterious or neutral etc.


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

Input:
Title: IN SILICO ANALYSES OF CD14 MOLECULE REVEAL SIGNIFICANT EVOLUTIONARY DIVERSITY, POTENTIALLY ASSOCIATED WITH SPECIATION AND VARIABLE IMMUNE RESPONSE IN MAMMALS
Review round: 1
Reviewer: 2

Output:
Basic reporting: - Overall, the paper is clearly written. A minor comment is that the word "the" is sometimes missing; e.g. *the* CD14 gene, *the* CD14 molecule, *the* CD14 protein, *the* evolutionary tree was constructed.
- I do not see a reason to abbreviate amino acids as aa on line 78 if you spell out the full word later (such as on lines 86, 115 and elsewhere).
Experimental design: - The authors layout the article in an easy to follow manner, and the provide an appropriate amount of detail in the methods section.
- I am curious as to why the particular 14 mammalian species were chosen?
Validity of the findings: Data is robust, and conclusions are supported by the results, but the authors should make the limitations of their study more clear in the Discussion.
Additional comments: - It would be nice to briefly define the amino acids properties listed on lines 114-118.
- I have also made a few minor comments in the PDF attached.
- Tables 1 and 2 could be easier to read if there was a colour-scale (in addition to the raw numbers) signifying the percents. However, if there are colour-charges involved, then this comment can be ignored.
- Is there a rationale for the row order in Tables 3,4,5? If not, there should be? Even if the reason is simply alphabetical.
- Figures 1 and 7 are too small/difficult to read.


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: IN SILICO ANALYSES OF CD14 MOLECULE REVEAL SIGNIFICANT EVOLUTIONARY DIVERSITY, POTENTIALLY ASSOCIATED WITH SPECIATION AND VARIABLE IMMUNE RESPONSE IN MAMMALS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article needs some English Language editing and i have identified and also suggested how to improve the wrong phrases
Line 26 -replace report with paper
Line 30 - replace ancient conservation with is conserved
Line 33 - replace this is important with this may be important
Line 63 is a repetition of line 50
Line 77 - change gather to glean
The objective statement is not obvious from this introduction. Authors should include the objective statement
Line 171-172 should be rephrased to reflect that CD14 protein sequence is not conserved
Line 176 - change show to shows
Line 249 - change eleven to 11
For the discussion section of this paper, there are many statements made by the authors that needs to be supported by citations
Line 273 - Citation should be included after disease condition
Line 278 - recast the statement because it appears something is missing here
Line 284 - Citation be included after viral infections
Line 293 - The number and conservation of LRR and delete the conservation of LRR domain in line 294
Line 316 - Citation should be included after pathway
Line 319- insert when between tolerance and compared
Line 327- Recast the statement here
Line 332 - Insert a citation after lipopolysaccharide
Line 347 - Citations should be behind protein activities
Genes and proteins were used interchangeably in this paper, authors needs to be more careful and use the terms where appropriate
Line 357 - change current statement to is important to decipher molecular and biochemical mechanism
Every where the authors talked about evolutionary event, they need to indicate whether it is divergent, convent or even neutral evolution

Overall, the authors needs to indicate that CD14 is a gene that encodes a protein and clear any confusion from the use of the terms interchangeably.
Experimental design: No comment
Validity of the findings: The authors should use the word may where they speculated in this paper.
Additional comments: See comments above


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

Input:
Title: GENOMICS ANALYSIS OF GENES ENCODING RESPIRATORY BURST OXIDASE HOMOLOGS (RBOHS) IN JATROPHA AND THE COMPARISON WITH CASTOR BEAN
Review round: 1
Reviewer: 1

Output:
Basic reporting: Abstract
Lines 36-38. Phrase is not clear.. no duplicate was identified in both.. corresponding to no recente whole... is a double negation..

M&M section
Line 90.. Arabidopsis and rice rboh genes were obtained ... that means this genes were amplified?, cloned?

Line 114..Gene expression analysis..
the gene expression was done in silico?,
under what conditions the plants were grown?

Results section
Line 133-134.. seems repetitive to 136-141.
Sube 166. and Isrbigd, And variation..

Lines 170-181,
after describir fig 2a and 2b, jumps to figure 3,
then Lines 182-188, is describing figure 2c,

Line 172. The average theoretical MW (molecular weight)
Line 174. average pI .. the I is the italic letter

Expression profiles jcrboh genes... what about castor genes?
this section is just in silico analysis?,
but conditions of experiments could change from experiment to experiment.? so you do not have control of expression profile?
IND, STD, PID are not defiende.

Line 214.. the response to drought and salt stress was investigase....
this experiment was carried out in the present work or was also in silico analysis?,
if was done in this work, information about the experimentos should be added in M&M section.

Line 227.. respondes to coletotricum.. was investigated.. no mention in M&M section
Line 233.. regulación by hormones.. not mention in M&M section.

Figures
Fig 2A. the three is mixing C,G, A sequences, H, B, sequences,
seems not a very good classification of groups
Describe in figure legend what means motif 1, motif 2 and so on

Fig 4. describe in figure legend the meaning of std, , pid, ind,
leaf age¿, which age?,
Experimental design: Needs to be more clear,
the work was an in silico analysis? experiments of gene expression analysis are not described
Validity of the findings: there is not a results supported by experimental design explained in the text.
Additional comments: The most concern is about the gene expression analysis,
no information about the experiments design are present,
then is not clear if presented data is also an in silico analysis reviewing all information deposited at databases.


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: GENOMICS ANALYSIS OF GENES ENCODING RESPIRATORY BURST OXIDASE HOMOLOGS (RBOHS) IN JATROPHA AND THE COMPARISON WITH CASTOR BEAN
Review round: 1
Reviewer: 2

Output:
Basic reporting: The MS is well written and presented. Please notice that R. communis common name id “castor bean” (not just “castor”).
Experimental design: Since data for expression analysis were taken from public data banks,how did authors make sure they were comparable? At present form,  I'm not totally convinced that differences noticed, both among tissues and conditions are really comparable and, therefore, representative. It would be advisable to confirm these trends with actual lab results (PCR analysis of transcripts abundance, for example).
Validity of the findings: See comments in the previous section.
Additional comments: My only reason to rccomend minor revisions appears above.


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

Input:
Title: GENOMICS ANALYSIS OF GENES ENCODING RESPIRATORY BURST OXIDASE HOMOLOGS (RBOHS) IN JATROPHA AND THE COMPARISON WITH CASTOR BEAN
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript “Genomics analysis of the respiratory burst oxidase homolog (Rboh) gene family in jatropha and the comparison with castor” attempts to presents a genome-wide comparative analysis of Rboh family genes in economically important non-food oilseed crop jatropha (Jatropha curcas) and castor (Ricinus communis). Overall, the manuscript conforms to the structure recommended by the journal viz. Introduction, Materials and Methods, Results, Discussion, and Conclusions. The findings of the study are well discussed and supported by existing evidence. The overall English comprehension and grammar of the article is good and attains standards of a scientific article. The phylogenetic analysis of jatropha and castor with model monocot and dicot provide insights into species-specific functions. However, below are a few suggestions that would be useful for the readers and make it scientifically thorough.

1.	Supplementary table S1 and S2 can be combined into a single excel file with information of S1 and S2 table as two separate sheets.
2.	Please improve the legend of Fig 1 by incorporating information for e.g. the scale of the bars etc.
3.	In the legend of Fig. 2, please provide the scale for the number of amino acid substitutions per site. Also, mention in the text what do the numeric values represented on the top of each clade correspond to?
Experimental design: 1.	In line 116, how did the author obtain clear reads from raw reads? Please specify exclusively in text.
2.	Usually, the average width of the transcription factor binding site is 10bp. Why did the author select such a wide range from six to 180 residues in line 113? Please justify.
3.	Please specify Bowtie2 parameters in line 117, unless used default.
4.	Please specify if authors have used either existing packages or in-house scripts for identification of differentially expressed genes (DEG) in line 120-121.
5.	In addition to DEGs, it would be great to provide a list of all the genes with expression and significance as supplementary.
Validity of the findings: The study is experimentally sound and well presented. For further comments refer section Experimental design.
Additional comments: No additional comments


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

Input:
Title: GENOMICS ANALYSIS OF GENES ENCODING RESPIRATORY BURST OXIDASE HOMOLOGS (RBOHS) IN JATROPHA AND THE COMPARISON WITH CASTOR BEAN
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript was improved,
Line 168... And variety.. An variety?
Line 176...pI was not corrected as p(italics I)
Experimental design: no further comments
Validity of the findings: no further comments
Additional comments: Review some typos alongó the text


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

Input:
Title: GENOMICS ANALYSIS OF GENES ENCODING RESPIRATORY BURST OXIDASE HOMOLOGS (RBOHS) IN JATROPHA AND THE COMPARISON WITH CASTOR BEAN
Review round: 2
Reviewer: 2

Output:
Basic reporting: I consider that my comments were properly adressed, therefore the MS could be now  published.
Experimental design: I consider that my comments were properly adressed, therefore the MS could be now  published.
Validity of the findings: I consider that my comments were properly adressed, therefore the MS could be now  published.
Additional comments: I consider that my comments were properly adressed, therefore the MS could be now  published.


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

Input:
Title: EFFECTS OF GUANYLUREA, THE TRANSFORMATION PRODUCT OF THE ANTIDIABETIC DRUG METFORMIN, ON THE HEALTH OF BROWN TROUT (SALMO TRUTTA F. FARIO)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors are assessing the impact of guanylurea on the health of early life stages of brown trout.  While the study’s main conclusions are a lack of effect, this information is still very important.

Introduction:
The literature references in the introduction and discussion are good, there is a sufficient amount of background provided.

Hypotheses need to be clearly established.
The hypotheses of the experiment are not stated and it is unclear why the authors picked the endpoints and life stages investigated.  Please describe why those endpoints were selected and what the hypothesis is.  The only endpoints that were explained briefly were Hsp70 and ROS. But even for these, it is unclear what the authors expected the effect of guanylurea to be.  For example, the authors can clearly establish why they expected hsp70 to cause proteotoxic effects by linking it to previous studies.  But why and how did the authors expect guanylurea to impact swimming behavior etc?

Methodology:
Overall the methodology is pretty clear but there are a few areas that need to be expanded upon.  The only section that is of concern is the larval growth which may be just a misunderstanding of the reviewer.

Sample size.
Are the authors counting the tanks as the n, or the individual fish?

Feed amount
Please define how much the fish were fed as a % bodyweight per day.  This is of particular importance for a growth and development study.  After reading the discussion it sounds like the authors fed the fish a ration weight.  Is this correct?  If so the growth data should not be included as the fish should not grow under those conditions.
This study is not particularly designed with growth as an endpoint, as the fish were only sampled at the end of the study and not throughout.  It would be better if the authors use the words weight and length rather than using the word growth.

Hatchery control fish.
It makes complete sense to use hatchery control fish.  What is not clear is why the hatchery control fish were 2-3 times larger (body weight) than the experimental fish.  Why is this, and what is the benefit or relevance of using them?  Does this mean the fish were being underfed and actually lost weight over the course of the study?  If so how did they also decrease in length?

Results/Discussion:
The discussion reads well.  The figures/tables are appropriate.
Experimental design: This is mentioned in section 1:

-Clarify the hypotheses
-Elaborate on the methods, especially with the larval feeding.  If the fish were fed at a maintenance ration, then the growth results are not relevant and should either be re-contextualized or dropped from the study.
Validity of the findings: As mentioned in the previous sections the growth aspects may not be valid.  However, the rest of the findings are novel and valid.  Of particular interest to this reviewer is the histopathological, stress protein, and lipid peroxide analysis.
Additional comments: The paper provides interesting information on the effects of guanylurea on a species of fish that is of relevance to European rivers.  The paper presents a substantial research effort with novel data analyzing the potential effects of guanylurea.  This paper could be strengthened by having a more clear direction in the endpoints measured and the expected outcomes.  Some of the endpoints measured such as survival, embryotoxicity, hatch success and swimming behavior the authors did not expect to see any significant effect on.  While other parameters such as hsp70, histopathology, growth, etc. the authors may have expected an outcome, but it is not clear what they were expecting to see.   For histopathology, the authors mention the livers of the larval fish were in better condition than the juvenile fish due to feeding them a maintenance diet.  It should be made clear why the fish were fed at maintenance, especially considering the authors were measuring growth and trying to deduce if the compound impacts growth.  The authors are correct in their statement that this data is of particular importance to risk assessment, and this paper makes a valuable contribution to the understanding of guanylureas effects in fish.


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

Input:
Title: EFFECTS OF GUANYLUREA, THE TRANSFORMATION PRODUCT OF THE ANTIDIABETIC DRUG METFORMIN, ON THE HEALTH OF BROWN TROUT (SALMO TRUTTA F. FARIO)
Review round: 1
Reviewer: 2

Output:
Basic reporting: See general comments for my review
Experimental design: See general comments for my review
Validity of the findings: See general comments for my review
Additional comments: This study examined the effects of a prolonged exposure of guanylurea on brown trout larvae and juveniles. The investigators measured internal concentrations of guanylurea, mortality, growth, movement, liver and kidney integrity, and two measures of stress, HSP70 and LPO.  Results from the study indicate that there was no statistical difference between guanylurea-exposed fish and the control. The methods employed in the study were sufficient and would not affect the results, though there is some question on why some of the molecular measurements were taken (See below).  Below are my concerns regarding the manuscript that I would like the reviewers to consider.

Major Concerns:

1.	Why did you measure HSP70 and LPO in the head? Why not measure it in the liver? Secondly, what was the hypothesis behind these measurements? Has metformin or guanylurea been shown to illicit lipid peroxidation? I would think LPO or HSP70 response in a common pharmaceutical to be counter-productive. You discuss the possibility of increased Phase II enzymes neutralizing ROS, yet one conclusion could be that guanylurea-ROS production does not occur in the head or anywhere for that matter. Then, the authors go on to say that phenformin reduced ROS of aging rats—albeit in the head—which it appears that this reference refers to phentermine. In that study it stated that “Rats treated with this antidiabetic drug showed intermediate values of ROS generation. Differences among the groups in total antioxidant activity were not obvious.” (Ansimov et al. 2015).

2.	Why wasn’t the vitellogenin data shown? That would be an interesting biomarker to compare to other fish studies.

3.	Since you have length and weight, consider giving a condition factor score. Again, others have used this as a measure of fitness with exposure to metformin, so it would be a useful comparison.

4.	It would be useful to have a paragraph in the Introduction on why some of these biomarkers were chosen. One could just take some of the discussion and move it to the introduction.


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

Input:
Title: EFFECTS OF GUANYLUREA, THE TRANSFORMATION PRODUCT OF THE ANTIDIABETIC DRUG METFORMIN, ON THE HEALTH OF BROWN TROUT (SALMO TRUTTA F. FARIO)
Review round: 2
Reviewer: 1

Output:
Basic reporting: See general comments.
Experimental design: See general comments.
Validity of the findings: See general comments.
Additional comments: The authors addressed the revisions suggested by both reviewers well and the article is acceptable 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: THE IMPACT OF IRRIGATION ON YIELD OF ALFALFA AND SOIL CHEMICAL PROPERTIES OF SALINE-SODIC SOILS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article deals with the Alfalfa and soil chemical properties response to irrigation in saline-sodic soil region. The writing is clear enough, however there are many grammatical and structural mistakes in the manuscript and I am not able to highlight/revise all of them. In addition, this paper needs quite a few places for professional editing. So, please revise the manuscript and improve it considerably in terms of these issues.
The literature is suitable for the purpose of the article, but the locations of researchers' first and last name is inappropriate (Line 357, 360, 381...).
Experimental design: There is insufficient detail in the soil sample collection section of the "Research method" section to reproduce the fieldwork and lab work.
How many plots are designed in your study? And the detailed geographic locations of them？You should add a clear statement and/or sketch map in the revision.
Which "soil types" determined your sampling densities? A detailed illustration of soil is necessary. Report soil types according to an international soil system, either the WRB or USDA systems.
You have listed the specifications of the pH and EC meter but not the specifications of the detailed glass electrode, if that's what you've used. What other properties of the soil did you measure? These are required for your conclusions.
Validity of the findings: Data is robust, statistically sound, & controlled.
Additional comments: 1.	The text is extensive and repetitive in many parts. Thus, I recommend rewrite abstract and introduction. The conclusions can be furtherly improved.
2.	Work on text clarification and formatting, improve figures, list of the abbreviations would be useful in this case to easily understand the text.
3.	The caption of Figure 1 seems to be wrong. Please double check.
4.	The units of X and Y axis are missing in the Figure 7. Please add them.
5.	In all the numbers with decimals, please consider to homogenize to only two/three decimal.
6.	The extensive and methodical experimentation proves the effectiveness of the selected methods. However, the paper would gain in clarity if the achieved results were correlated with the characteristics of the algorithms.
7.	The comprehensive discussion of effects of different irrigation treatments should be added in the revision.
8.	Lines 105-106: There were eight irrigation treatments …Need to justify why these different treatments were designed and used specifically.
9.	Lines 107-108 The equation numbers were missing. Please add them.
10.	Line 109-111 ETc, … calculated by Penman-Monteith method. The origin of essential parameters should be illustrated clearly.
11.	Lines 116-117 Five stems will be selected at random from each plot for measuring… which instrument was applied for these measurements.
12.	Lines 129-130; 154-157 Please rewrite these sentences, they are difficult to follow.
13.	Lines 177-178 The explanation given is hardly to understand.
14.	Line 183 “rainfall” should be “precipitation”.
15.	Description of Result and Discussion is not very professional. Several sentences in the Result section should be in the Method or in the figure captions. You don't need to say ....are shown in Figure X, simply put (Figure X) next to the sentences that describing the results. Paragraphs in the Discussion should start with a topic sentence instead of describing the methods again.
16.	The discussion is weak and unsatisfied, the author should make the best effort to modify this section. I want to see a considerable improvement in this regard.
17.	The conclusion was not well stated and written more as an abstract. A clear conclusion needs to be written.
Overall this manuscript adds practical values to agriculture management. I suggested authors to revisit this paper several times to make it more concise based on the above comments and comments from other reviewers.


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

Input:
Title: THE IMPACT OF IRRIGATION ON YIELD OF ALFALFA AND SOIL CHEMICAL PROPERTIES OF SALINE-SODIC SOILS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Title:
- "Alfalfa and soil chemical properties response to irrigation in saline-sodic soil region" uses incorrect English grammar. The response is possessed by the chemical properties, or the irrigation is something to which chemical properties respond. Therefore the title should read as, for instance, "Alfalfa and soil chemical properties respond to irrigation in saline-sodic soil region." Ideally, you would be more specific. The best titles state the results in 18 words or less (with correct English grammar).

Line 20: The description of the multifactorial can leave out the levels of all treatments and simply mention the number of levels and which factors were manipulated, possibly adding a sample number. Without sufficient description, words like "regreen" and "anthesis" are good parameters but difficult to understand out of context.

Line 46: "Nowadays" is too colloquial, and "have been considered as the most constrains limiting plant survival" has at least three instances of incorrect English grammar. The next sentence can be comprehended, but it also has numerous errors: "Moreover, the collaborative movement salts and water makes the water deficit and ineffectiveness, and threats to the sustainable yield of crop and forage and thus to the fragile ecosystems in the salt affected areas."

Line 51: "which is a C3" is an incomplete clause. "C3" refers to photosynthetic strategy.

Line 53: Please avoid colloquial contractions such as "it’s".

Line 54: "specie" must be "species", where "species" is both the singular and plural.

Line 56: A tilda (~) is used to signify an equivalence more approximate than an equals sign (=), unlike the dash (-), which is used to signify a range from one numerical value to another.

Line 58: "self-sufficient" is an adjective should be the noun "self-sufficiency".

Line 64: "There is huge gap" lacks the necessary article "a" and "huge" is a collquial adjective.

Line 67: "hard" is a collquilism; you should use "difficult".

Line 69: "maximum" is a noun; you should use the verb "maximize".

There are too many errors in English to continue my review.
Experimental design: There are too many errors in English to continue my review.
Validity of the findings: There are too many errors in English to continue my review.
Additional comments: There are too many errors in English to continue my review.

This could be a very good paper, given the impressive results of yield increase and your rigorous methods, but you must have someone sufficiently fluent in English revise this manuscript to become readable. Scientific papers need to be a permanent record, so readability is non-trivial. You do not have to use flowery language (e.g. beginning sentences with "thus" or "hence"), but you must minimize colloquial or ambiguous language. It is also very unusual to report ranges of values of measured physical quantities instead of means and standard deviations, which more accurately communicate central tendencies and errors to future readers.


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

Input:
Title: THE IMPACT OF IRRIGATION ON YIELD OF ALFALFA AND SOIL CHEMICAL PROPERTIES OF SALINE-SODIC SOILS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript addresses key issues (water scarcity and soil salinity) that are currently challenging agriculture around the world. However, the manuscript could be improved significantly with the help of a professional English editor or a native speaker. I strongly recommend assistance for English writing in order to convey this important research to a wider audience.
The literature references are supplied and relevant although more recent references could help to consolidate the old references. Adequate background to the problem in the region where the study was carried out was provided to put the study in context.
However, the introduction section can be revised and structured to improve the flow of ideas from presenting the context, identifying the problem and research gap and presenting the objectives.
The study addresses key issues and is relevant for modern agriculture and should be considered for publication provided the recommended revisions are attended to.
Experimental design: While water deficit and soil salinity have been widely investigated, the nature and complexity of plant and soil responses and their interactions with climate mean that local studies for different places still hold key answers to address these constraints. Therefore, the research fulfills the scope of this journal.
The research is well defined and relevant although the research gap was vaguely presented (possibly as a result of weak command of the English language). This can be rectified by soliciting professional help on language.
The methods and materials show that the study was rigorous enough and met ethical standards. The details provided in this section were enough to be replicated and I only suggested minor editorial editions.
Validity of the findings: The results are mostly valid and also adequately supported with literature. Minor revisions suggested include revisions of some arguments which do not change the structure of the manuscript entirely.
Only minor editions to the conclusions are suggested to align with objectives and research gap
Additional comments: Well done on carrying out the work for an adequate number of seasons.
However, please note that soil properties are usually difficult to deal with over short periods of time since most pedological processes are long term processes. They should be treated with caution.


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

Input:
Title: THE IMPACT OF IRRIGATION ON YIELD OF ALFALFA AND SOIL CHEMICAL PROPERTIES OF SALINE-SODIC SOILS
Review round: 2
Reviewer: 1

Output:
Basic reporting: As I can see from the previous review, you have corrected all of the reviwers comments. It is ready for publication.
Experimental design: no
Validity of the findings: no
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: THE IMPACT OF IRRIGATION ON YIELD OF ALFALFA AND SOIL CHEMICAL PROPERTIES OF SALINE-SODIC SOILS
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: All comments raised were attended to satisfactorily.


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: AN AVIAN FEMUR FROM THE LATE CRETACEOUS OF VEGA ISLAND, ANTARCTIC PENINSULA: REMOVING THE RECORD OF CURSORIAL LANDBIRDS FROM THE MESOZOIC OF ANTARCTICA
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a short note, which corrects the previous identification of an avian femur from the Latre Cretaceous of Antarctica, and for the first time presents a description of the fossil. As such, the manuscript is certainly a worthwile contribution to palaeornithology and I have only a few comments the authors may wish to take into account.
Technical details, such as the approariate use of the references, English grammar, etc. do not need to be improved except for the few minor instances listed below.
Experimental design: The paper follows current standards in palaeontological studies, but I wonder whether there should be a material and method section, in which institutional abbreviations are given and the used terminology is referenced. Certainly, this is not mandatory given the expected briefness of such a section and if it conforms with the journal standards, a material and method section can be omitted.
Validity of the findings: I full agree with the referal of the fossil to the Vegaviidae and have only a few minor comments the authors may wish to take into account (see below)
Additional comments: While I fully agree with the referral of this fossil to the Vegaviidae, the distal view of the distal end shows some differences to the distal femur of Vegavis in the depth of the patellar sulcus and the shape of the remaining lateral condyle (Fig. 4P, Q). I assume that these are due to the poor preservation of the fossil and it may be worth to add a specific note on this to the next (you already included some similar statements in lines 154ff).

You compare the new fossil with the holotypes of vegavis and Polarornis. What I miss, however, are comaprisons with the Vegavis/Polaronis material listed by Acista Hospitaleche in her paper on the putative gaviiforms from Antarctica. It would at least be necessary to state whether the new femur is also larger than the remains reported in this latter study.

Some minor comments:

- note that in avian terminology of the femur, the directions "cranial/caudal" rather than "dorsal/ventral" are used
- line 105: "is approximately 36" - add "mm" here
- line 152: "Additionally, the round proximoventral ligament scar of Vegavis is positioned near the midline in the new femur ... but is closer to the lateral margin in V. iaai." - as kit is, this sentence makes no sense, since you compare "Vegavis" with "Vegavis iaai". Is the new fossil meant here? In this case, it would be better to give the specimen number.
- caption of Fig. 1: "site" instead of "si te"
- caption of Fig. 3: "tendineus m. tibialis cranialis" - this should probably read "tendon of..."

As a side notes: Personally, I am not fully convinced that it is necessary and appropriate to keep Vegavis and Polarornis as two different taxa on the "genus"-level and I am not sure whether the differences between Vegavis and Polarornis are not the result of the poor preservation of the holotype of P. gregorii (e.g., concerning the absence of the distolateral scar). This question (synonymy of Vegavis and Polarornis) is certainly beyond the scope of the present manuscript, but it may ultimately bear on the affinities of the fossil within Vegaviidae, i.e., whether it is more closely related to Vegavis or Polarornis.

(Gerald Mayr)


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: AN AVIAN FEMUR FROM THE LATE CRETACEOUS OF VEGA ISLAND, ANTARCTIC PENINSULA: REMOVING THE RECORD OF CURSORIAL LANDBIRDS FROM THE MESOZOIC OF ANTARCTICA
Review round: 1
Reviewer: 2

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

The article is concise and well-written. It includes novel information about a very interesting and potentially important specimen. I congratulate authors for such interesting contribution.
Some minor comments are included in the attached PDF.
I think the article should be accepted after minor corrections.

All the best,

Federico Agnolin


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: TESTING RELATIONSHIP BETWEEN PLANT PRODUCTIVITY AND DIVERSITY IN A DESERTIFIED STEPPE IN NORTHWEST CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Study seems interesting and data are well publishable, but manuscript need minor correction. According to me Manuscript  fulfill journal standard.

The manuscript contains a multitude of typographical-, comma- and grammatical errors, sentence fragments and mixed use of capital and small initial letters. Most of these errors could have been easily avoided by using the spell check function found in commercial word-processing software.

Plagiarism is 35% I would suggest author to bring it down to 20%. Plagiarism report is attached.

Below are the Mistakes I found

51 should be “in the form of” insted “in form of”
29 should be “role in the controling” insted “roles in the control”
43 should be “the dominant” instead of “dominant”
58 should be “plant”  instead “plant plant”
63 should be “plant”  instead “plant plant”
64 should be “plant”  instead “plant plant”
65 should be “has” instead of “have”
91 should be “China” insted “China.”
96 should be “the desertified” insted “desertified”
131 should be “aluminium” insted “aluminum”
133 should be “the soil and levelled” insted “soil and leveled”
229 should be “These findings” insted “This findings”
224 should be “which” insted “whcih”
247 should be “strong” insted “strongly”
297 should be “pattern” insted “patterns”
314 should be “because of” insted “because”
315 should be “led” Instead “leaded”
317 should be “decreases” insted “decreased”
343 should be “similar” instead “similarly”
354 should be “ were dependent on the soil total’  instead  “was dependent on soil total”
359 should be “the soil” insted “soil ”
Experimental design: Experimental Design is ok.
Validity of the findings: Manuscript fulfill the AIM of the study.
Numerous studies have reported diversity patterns along natural productivity gradients. So there is no novelity of work.
Additional comments: No additional comments


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

Input:
Title: TESTING RELATIONSHIP BETWEEN PLANT PRODUCTIVITY AND DIVERSITY IN A DESERTIFIED STEPPE IN NORTHWEST CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: I find there are too many grammar mistakes in the text as follows, and substantial professional language editing should be used to improve the English used throughout the article.
L13 “different grassland” should be “different grasslands”.
L30 “played an important roles” should be “played important roles”
L37 “an ecological system” should be “an ecosystem”
L70 “most research” should be “most researches”
L103 “mean temperatures is” should be “mean temperatures are”
……
Experimental design: The experimental design description is rather vague. Six dominant plant species chosen in this study were selected. However, the authors did not mention what is the distance between the six plant species? Are they in the same community? They should clarified the experimental design.
Validity of the findings: 1. The results section needs to be more explicit, and grammatical errors need further modification as follows.
L219-220 What is the meaning of this comparison? If so, please move it the Discussion part.
L223-224 “by using model” should be “using model”.
L249-250 should be moved to the MMs part.
L254-258 is a very long sentence. It should be changed to several short sentences and clarified the meaning.
……
2. The conclusion is only a repetition of the results and is not highly summarized.
Additional comments: The authors tried to test the association of plant community productivity and diversity. Although I appreciate the effort of the work in the natural ecosystems, the conclusion presented in the manuscript is less surprising or novel.
1. The MS is not overall well written, and contains some unnecessary repeat and grammar mistakes. A professional English language editor following a restructure of the paper is needed.
2. The authors also analyzed the relationships between soil physi-chemical properties and plant diversity and productivity. I advise the authors should focus on the effects of soil physi-chemical properties on the relationships of plant diversity and productivity, rather than on plant diversity or productivity.
3. L93-94 What is the difference between Q1 and Q2? The authors should clarify the scientific questions.
4. L185-186 should be moved to the Discussion part.
5. L231-232 What is the internal mechanism of “that plant diversity inhibited AGB but did not affect BGB”?
6. The Discussion part have too many repetitions with the results section, and there is no further explanation for the reasons of the results.
7. L286-292 These three reasons should be clarified.


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: TESTING RELATIONSHIP BETWEEN PLANT PRODUCTIVITY AND DIVERSITY IN A DESERTIFIED STEPPE IN NORTHWEST CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: Literature references, sufficient field background provided
Self-contained with relevant results to hypotheses
Experimental design: Original primary research within Aims and Scope of the journal.
Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.
Rigorous investigation performed to a high technical & ethical standard.
Methods described with sufficient detail & information to replicate.
Validity of the findings: Data is robust, statistically sound, & controlled.

Conclusions are well stated, linked to original research question
Additional comments: The relationships between vegetation production and species diversity is a core question in ecosystem function. There are many different patterns were reported over global grassland, but lack of the related research in the desertified steppe. Thus, it is a valuable research, but there have some issues should be corrected moderately before publication.

ABSTRACT , I suggested that the author should re-write the it, the clear expression is needed
e.g. line 13-18, line 23-28.
Line 20-21, plant diversity inhibited AGB but did not inhibit BGB, why?   What is the mechanism ?
Line 29-30  Finally, the interactions among soil nutrients and their influence played an important roles in the control of plant diversity and productivity in desertified steppe, northwest China.
 I hold that this is the general phenomenon, we can conclude it without some research. Consequently, I hope the author can refine the important findings.

Introduction, Additionally, studies of the relationship between productivity and diversity in grasslands have been conducted primarily in Europe, Africa, and North America, and there are many potential problems associated with the data,  including  sample  sizes  and  the  surrogates  used  for  productivity  (Van  et  al.,  2001;  Bai  et  al.,  2012;  Cardinale et al., 2015; Trax et al., 2015). Understanding the interactions among resource availability, diversity and productivity is relevant for the preservation, management and restoration of native communities and may  be key in successfully restoring these species-rich ecosystems (Tilman et al., 2012; Cardinale et al., 2015; Trax  et al., 2015; Craven et al., 2016).
Line 82-88, How to link this sentence-there are many potential problems associated with the data,  including  sample  sizes  and  the  surrogates  used  for  productivity with next sentence? Please revise it.
In another word, what is the relationships between sample size….. and your topic?

Methods,
Line 115-117, these values  approximate  the  above-ground  net primary productivity (ANPP) in temperate grasslands. These values contained the AGB and BGB?

Line 114   2.2 Experimental design  might be changed into   2.2 sampling methods
Line 136 2.3 Methods might be changed into   2.3 Soil sample analysis?

Result
3.1 Occurrence frequency of all plant species and diversity indices
3.5 Relationships between soil factors and plant species on the basis of redundancy analysis (RDA)
Please re-write these sections, I hold that too long to express the most important result clearly.

4 Discussion
4.1 Species occurrence and diversity of different plant communities
4.2 AGB, BGB and R:S ratios of different plant communities
4.3 Relationship among litters, biomass and Shannon-Wiener index of different plant communities
4.4 Testing associations of diversity-productivity of plant communities

I suggested that authors should divide the DISCUSSION into two section;
4.1 The dynamics of community traits
4.2 The linkage of diversity-productivity in the  desertified steppe

References
Grazing enhances soil nutrient effects on trade-off between above and belowground biomass in alpine grasslands of the Tibetan plateau
Meta-analysis of relationships between the environmental factors and the aboveground biomass in alpine grassland, Tibetan Plateau
Some reports are about  the relationships between vegetation biomass  with soil properties, you can understand it.

Figures, tables and data are enough for this research.

Sorry, I am not the native English speaker, so ,I can not give you some grammar 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: TESTING RELATIONSHIP BETWEEN PLANT PRODUCTIVITY AND DIVERSITY IN A DESERTIFIED STEPPE IN NORTHWEST CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The study was well planned and executed. The paper is acceptable, but I have some concerns.

Abstract need to be rewritten, concluding section is missing and it looks more of introduction.

The manuscript contains some multitude of typographical-, comma- and grammatical errors, sentence fragments and mixed use of capital and small initial letters, I have corrected them see attached file

Although the plagiarism is 25% but some sentence needs to be a paraphrase. (see the attached plagiarism report)

I suggest accepting the manuscript after the above changes are made by the author.
Experimental design: Perfect
Validity of the findings: Manuscript fulfill the AIM of the study.
Additional comments: No additional comments


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

Input:
Title: TESTING RELATIONSHIP BETWEEN PLANT PRODUCTIVITY AND DIVERSITY IN A DESERTIFIED STEPPE IN NORTHWEST CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: There are still some grammatical problems, and the authors should carefully improve the language before further processing.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I am appreciate with the correction and clarification on the comments that previous raised. However, I find there are still some grammatical problems, and the authors should carefully improve the language before further processing.


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: TESTING RELATIONSHIP BETWEEN PLANT PRODUCTIVITY AND DIVERSITY IN A DESERTIFIED STEPPE IN NORTHWEST CHINA
Review round: 2
Reviewer: 3

Output:
Basic reporting: The revised MS is fine. The expression is smooth, reference is enough for supporting the field background. Besides, the structure has been corrected according to my comments.
Experimental design: The MS is fit for the aim and scope of Peer J
Validity of the findings: Data is robust, and conclusion is well proofed.
Additional comments: The MS has been revised well, thus, I recommend publishing this paper.


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

Input:
Title: A NEW PARAVIAN DINOSAUR FROM THE LATE JURASSIC OF NORTH AMERICA SUPPORTS A LATE ACQUISITION OF AVIAN FLIGHT
Review round: 1
Reviewer: 1

Output:
Basic reporting: summarized below
Experimental design: poor-summarized below
Validity of the findings: poor-summarized below
Additional comments: This is a frustrating paper. The dinosaur being described is clearly a new species, and looks to be quite important, as a Jurassic-aged paravian fairly close to the origin of birds. There are, however, several major issues with this paper.

First, why is the description so short? This specimen looks to be one of the best skeletons of a Jurassic paravian (at least from outside China), and has been CT scanned. There is so much anatomical information, and comparisons with other paravians, that could be presented. But the description reads like something that was prepared for Science or Nature and unchanged for this submission. This is PeerJ. There is basically unlimited space. The authors should describe this fossil so that nobody needs to ever describe it again.

Second, and most critical, the phylogenetic analysis is bizarre, and in my opinion unsuitable for publication. The authors in essence begin with an outdated version of published dataset, the Theropod Working Group dataset (TWiG is the proper acronym used by the workers in this group, not TWG as used by the authors here) and extensively modify it according to their own personal style, producing a highly unorthodox phylogenetic tree. The authors are also highly critical of the Theropod Working Group project—a 20+ year iterative study of coelurosaur phylogeny and evolution that has produced larger and more synoptic datasets over time—saying that including their new species in the latest TWiG dataset would ‘perpetuate problems’, and that the TWiG project does not ‘comply with modern ideals of data matrix construction.’ The main reason given is that the TWiG team has not ‘attempt(ed) to include all previously proposed characters and terminal taxa’ (i.e., has not included every taxon and every character published by other, non-TWiG studies). As a result, the TWiG studies are said to present ‘a false impression of confidence not earned by the data.’

These are bold statements. The authors seem to misunderstand the TWiG project. They say that TWiG analyses subsequent to the initial publication of Norell et al. 2001 ‘have not added characters and taxa in a single “lineage” of analyses, but instead have formed a branching tree of analyses that increasingly diverge in content’. In fact, the core TWiG team based at the American Museum of Natural History has produced a series of analyses that build on each other by adding characters and taxa over time, as is well documented in the literature (Norell et al. 2001 to Turner et al. 2007 to Turner et al. 2012 to Brusatte et al. 2014 to the more recent versions of Pei et al. 2017 and Gianechini et al. 2018).  Other authors, like Senter, have used the TWiG dataset as a template for their own analyses, but they are not part of the TWiG project. If Senter’s characters, or others, have diverged from the TWiG core team’s dataset, that is not because of shoddy work or sloppy divergence, it is a sign of a healthy field that is analyzing, reanalyzing, and building upon a standard dataset.

But all this is beside the point. Let’s look at what the authors have actually done with their phylogenetic analysis. This, not their sanctimonious tone, is where the real concerns lie.

The authors take a six-year-old version of the TWiG matrix (Turner et al. 2012) and then extensively redefine characters and change scores, based mostly on photographs and published literature. They have apparently seen very few specimens first-hand, which is an issue because the TWiG dataset was constructed almost entirely on two decades, and thousands of hours, of first-hand specimen study by the American Museum team. The version of the TWiG dataset they use is only about half the size of the most recent, updated version (Brusatte et al. 2014 and the small additions of Pei et al. 2017 and Gianechini et al. 2018), and thus is missing a wealth of key characters and taxa. The 2014 version has been out for four years—why haven’t the authors used it?! That makes no sense to me. The authors also extensively rewrite character statements to follow Sereno’s (2007) guidelines, seemingly unaware that Brusatte et al. (2014) reframed many of the characters in the same way. They justify revamping the dataset by cherry picking a few characters that they find problematic, namely one concerning the manual unguals that they find to be insufficiently quantified, and another few characters they consider to be non-independent. Fair enough: in a dataset of 800+ characters, not all of them will be written perfectly clearly, and some character non-independence will probably sneak through. These are small things that need to be revised, well within the norm for large datasets of morphological characters that have to be chosen and defined by a human brain and not a genetic sequencer. This is not some fatal flaw of the TWiG dataset. The authors’ new characters can suffer from same of the same issues.

So let’s be clear what they authors are doing: they are taking an outdated version of a standard dataset that has been poured over by a huge team of experienced researchers over the past 20 years, nitpicking about some small issues of character definitions, and then completely blowing it up and reforming it based on their own liking, mostly based on photographs, having seen very few original specimens.

Simply, for me, this just isn’t going to cut it. I don’t have faith in this approach, and I don’t have faith in the phylogenetic results, which are *highly* unorthodox.

This is a brief sample of some of the very unusual results of this analysis, some of which break with years of convention—not just in the TWiG analyses, but from numerous other studies by independent research groups. Pelecanimimus as an alvarezsauroid. Troodontids outside Eumaniraptora. Therizinosauroids more basal than ornithomimosaurs. Xiaotingia as a sinovenatorine. Halszkaraptor as an avialan. A non-maniraptoriform Haplocheirus. The list could go on. Maybe some of these relationships are correct. Maybe the authors are visionaries and everybody else—from Gauthier through to the TWiG team and dozens of other international teams—has been using badly-constructed characters or too-incomplete datasets. But I doubt it. It’s more likely that the authors’ analysis is flawed. I can’t in good faith allow the authors to blow up theropod phylogeny with this analysis, particularly as they are using their results to support a fairly unorthodox interpretation of the origin of flight.

It’s interesting that the authors dismiss some of their more unusual results by suggesting that these relationships may change as new characters are incorporated. Characters relating to alvarezsaurids outlined by Choiniere et al. (2010) were not included, characters relating to oviraptorosaurs published over 15 years ago by Maryanska et al. (2002) were not included, and of course, the enormous chunk of new TWiG data added by Brusatte et al. (2014), Pei et al. (2017), and Gianechini et al. (2018) were not included, much of which refers to tyrannosauroids and basal coelurosaurs, which have clear implications for the relationships of some of the clades found in unusual places in the authors’ analysis (ornithomimosaurs, therizinosauroids, alvarezsauroids). I agree, I think the exclusion of some of these characters may explain some of the weird results. That’s fine, not every analysis can include every single character that’s ever published. But it’s awfully brazen of the authors to heavily criticize the TWiG dataset for not including ‘all previously proposed characters’, when they themselves have excluded a bucketload of characters, including ones that they themselves admit are probably central to testing some of the weird results they find. Pot kettle black, I must say.

So what should the authors do? In my view, they cannot proceed with their current, half-baked attempt to blow up the TWiG matrix based on partial data and little examination of specimens. Clearly their new specimen is important and needs to be described, so I think there are two options if the authors want to retain a phylogenetic analysis in their paper:

1) Simply include the new taxon in the most recent version of the TWiG analysis. I suspect the authors won’t want to do this, because they seem to feel that the TWiG analysis is so flawed that it is useless. But this paper is primarily describing a new taxon. The authors don’t have to revise all of coelurosaurian phylogeny with it. They can save that battle for another day.

2) Step up to the plate and practice what they preach. Instead of taking an outdated version of the TWiG dataset and massaging it to their liking, start fresh and actually examine the many alternative datasets that are out there (TWiG, Senter, Cau, Foth & Rauhut, Agnolina & Novas, etc.), pool ALL of the characters and taxa together in the way they demand of others, come up with a proper comprehensive de novo phylogenetic analysis, and then publish a thorough revision of coelurosaur phylogeny and systematics.

It’s really only one or the other here.

I know my review seems harsh. But I’m trying to be fair and totally honest. Like many of my colleagues, I’ve been spending years (decades now even) slowly, gradually, carefully improving our knowledge of coelurosaur phylogenetics by working with other scientists to build ever-more inclusive datasets that are carefully vetted (by each other) and are based on meticulous observation of specimens. We probably are wrong about some things. Goodness knows the TWiG dataset has been producing different results over time as the dataset has grown. I’m not averse to change. But I am averse to disrespectful, incomplete efforts like the current bizarre phylogenetic analysis.

This new specimen is amazing. It deserves to be published. If done right, I could even see a Nature or Science paper here. But I’m sorry to say the authors are hitching their horse (and what a horse it is—a prize thoroughbred!) to a rickety wagon with rotten wheels.


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

Input:
Title: A NEW PARAVIAN DINOSAUR FROM THE LATE JURASSIC OF NORTH AMERICA SUPPORTS A LATE ACQUISITION OF AVIAN FLIGHT
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript presents a new theropod specimen from the Morrison Formation that represents a small coelurosaur, which is described as a new genus and species of dromaeosaurid. This would represent the oldest record of dromaeosaurids currently known. In general small theropods from the Morrison Formation are still very poorly known, but potentially have great importance for our understanding of early coelurosaur evolution. Thus, any new information on these animals is greatly appreciated.
The manuscript is generally well written and follows the usual scientific structure used in our field. The pertinent literature is included and has been used extensively.
Experimental design: As outlined above, the manuscript fits the aims and scope of PeerJ. The phylogenetic analysis includes a wealth of information and seems to be generally expertly carried out.
Validity of the findings: Although any new information on Morrison theropods is welcome, as stated above, the manuscript in its current form has some serious shortcomings that need to be addressed by the authors before it can be further considered for publication.
The first main problem concerns the description of the new taxon, which is so brief and poorly illustrated that it is almost impossible to evaluate the claims of the authors. The description basically consists of comments on a few selected characters and comparative statements, but it is not even clearly stated how much and which elements of the skeleton are preserved in the new specimen.
With the current description, I am not convinced that the specimen represents a paravian theropod, nor even that it necessarily is a new taxon. Please note that I am not saying that it is not, but the information provided is insufficient to verify these claims (none of the elements described or figured show clear maniraptoran synapomorphies, and the proximal part of the humerus actually seems to lack a previously proposed maniraptoran synapomorphy, a proximodistally elongate, rectangular internal tuberosity). A more thorough description of the actual morphology of the preserved elements (and not only some selected characters of a few elements) is necessary. Furthermore, I was surprised that basically no comparisons with other known small-bodied Morrison theropods, including Ornitholestes, Coelurus and Tanycoelagreus, are presented; as these would be the most likely candidates for a taxonomic identification if the specimen does not represent a new taxon, comparative statements of how this specimen differs from these taxa are absolutely necessary. This is especially the case for Coelurus, as the comparable elements (based on the description and few anatomical illustrations presented) actually show quite a few marked similarities. Thus, for example, the dentary referred to Coelurus is very similar to the dentary of the new specimen, as are the presacral vertebrae, and the humerus of Coelurus has a similarily extensive entepicondyle. Likewise, the skull shows similarities with that of Ornitholestes in having a pronounced lateral ridge at the lower boundary of the antorbital fossa and an anteroposteriorle elongate, kidney-shaped maxillary fenestra in the maxilla and a small pneumatic recess in the jugal. However, none of these similarities are commented on, nor are any characters mentioned that might help to differentiate the new specimen from these taxa.
Furthermore, in some instances, the description and the illustrations do not seem to match. Thus, in the description of the maxilla, the authors state that the maxillary fenestra is displaced dorsally if compared to other theropods. However, according to the figure, the fenestra is basically in line with the ventral margin of the antorbital fenestra, which is the same condition as in most other theropods. Another example is that the text states that a labiolingual constriction is present in the dentary teeth, referring to figure 6G. However, this figure shows a CT rendering of a tooth in lingual view, in which a labiolingual constriction would not be visible anyway. In their comparisons for this character, the authors furthermore refer to a figure that shows a tooth of Microraptor that clearly has a mesiodistal constriction, so I guess that they might refer to such a feature. However, a marked mesiodistal constriction between crown and root is clearly absent in the tooth figured in fig. 6G. Likewise, the description states that the presacral vertebrae lack external pleurocoels, but both the figure of the cervical vertebra in lateral view (fig. 8B) as well as the cervicodrosal vertebra (fig. 8F) clearly show large, matrix-filled depressions exactly in the position where I would expect an external pleurocoel.
Furthermore, in the absence of histological studies, I think the evidence that this specimen represents an adult is rather poor. The authors cite fused neural arches and partially fused cervical ribs as evidence for the adult status of the specimen. However, in small theropods, unfused, but largely closed neurocentral sutures can be difficult to identifiy (e.g. none of the known specimens of Archaeopteryx shows clearly identifiable neurocentral sutures, although basically all of these specimens are considered to be juveniles), and the two photos of presacral vertebrae provided do not only show unfused, but even slightly detached cervical ribs.
In summary, a much more detailed anatomical description and comparisons with other Morrison coelurosaurs are needed in this part of the manuscript.

For the phylogenetic analysis, the authors state that they evaluated all characters used in the different TWiG analyses over the years, reassessed them and recoded a vast number of taxa. This is certainly absolutely necessary and one of the strong aspects of the manuscript, for which the authors are to be commended! However, looking at the data matrix, I am somewhat unsure about the choice of including or excluding taxa from the analysis, and even though the authors briefly explain their rationale in the supplementary file, several aspects are left unclear.
One important aspect here would again be the phylogenetic comparison with other Morrison coelurosaurs. Of the three described Morrison coelurosaurs that are known from more than single elements (Ornitholestes, Coelurus, Tanycolagreus), only Ornitholestes is included in the matrix, and this taxon is used as outgroup, thus a priori excluding any closer relationship between the new specimen and this taxon. With the current taxon scope, the new specimen basically does not have any other choice but being a maniraptoran - which, as outlined above, is not obvious from the anatomical description.
Likewise, I am somewhat unsure why taxa such as Bahariasaurus (of which only short descriptions and some figures remain, and which was so far considered to be a non-coelurosaurian theropod by most authors) or Sciurumimus (described as a juvenile megalosaur) are included in an analysis focused on maniraptoriforms. The authors mention that they (as most iterations of the TWiG analysis) lack characters that would allow resolving the interrelationships of basal coelurosaurs, but as they would have to show that the new specimen actually is a maniraptoran rather than a more basal coelurosaur including such data would be crucial in this manuscript.

For more detailed comments please see the attached annotated manuscript.
Additional comments: In summary, I think this paper is potentially a very important addition to our knowledge of early coelurosaur evolution, if the authors provide a more detailed description and can clearly show that the specimen described is a new taxon and a maniraptoran (although even if this was only anew specimen of Coelurus or one of the other Morrison coelurosaurs, it has the potential to provide a wealth of new information on these generally rather poorly known taxa). I would thus strongly encourage the authors to do the necessary revisions and resubmit 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: A NEW PARAVIAN DINOSAUR FROM THE LATE JURASSIC OF NORTH AMERICA SUPPORTS A LATE ACQUISITION OF AVIAN FLIGHT
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I thank the authors for entertaining my comments in the first round of review. I still have some reservations about the phylogenetic analysis and am concerned about the many heterodox results. However, I am not one to stand in the way of publication. I've said my piece, the authors have replied, and now it's important to get this new taxon and the dataset out there.