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: CHARACTERIZATION OF THE BACTERIAL MICROBIOTA COMPOSITION AND EVOLUTION AT DIFFERENT INTESTINAL TRACT IN WILD PIGS (SUS SCROFA USSURICUS)
Review round: 1
Reviewer: 3

Output:
Basic reporting: It is highly recommended to have the manuscript revised by an English speaker.  There are many run-on sentences that are difficult to understand. Certain statements need be supported by either data analysis or previously published papers, so please cite appropriate papers. Legends of some figures are incomplete or need to be rewritten. The experimental design and results are not good enough to make the conclusions in the manuscript.
Experimental design: The title of the paper was characterizing the bacterial microbiota composition and evolution in wild pigs, but more than half of the manuscript was comparing wild pig microbiome with domesticated pigs which is missing in the experimental design. The sample size is small. Also, the wild pigs were housed in specific area and fed with general feeds (such as corn/hay) and water before sample collection, which could impact the gut microbiome significantly.  These are major flaws in the experimental design.
Validity of the findings: The paper provides good information about the sequencing quality. Advanced statistical tools such as LEfSe were used for data analysis. Significant differences related to microbiome composition and metabolic pathways were achieved from the five locations of intestinal tract in wild pigs, but due to the flaws in experimental design, the findings were not trustable.
Additional comments: Abstract:
1.	Line 26. Remove “however,”.
2.	Line 28. Only wild pigs were mentioned. Need sample details of domestic pigs as well.
3.	Line 29. Delete “in these samples”
4.	Line 36. “in vivo” is redundant.
5.	Line 37. Conclusion related to intestinal microbial diversity cannot be supported by demonstrated results in the abstract.
6.	Line 39. Boars normally refer to male pigs and sows refer to adult female pigs. Please correct.

Introduction
1.	Line 55-58. Please rewrite this sentence.
2.	Line 65-66. Rewrite this sentence. A recommendation here: “Domestic pigs are now distinct from their wild counterparts in many ways such as phenotype, as evidenced by coat color differences.”
3.	Line 85-89. There is no logical connection in the big sentence. Please reword.
4.	Line 92-96. Cannot understand what the author tried to explain. Please reword.
5.	Line 107. The “female adult wild boars” needs to be corrected. The author needs differentiate boars and sows.
Materials and methods
1.	How long have you raised these three wild pigs with feeding corn soybean diets before sacrifice? They are no longer wild pigs once regular diet was introduced.
2.	Line 157. Spell out the whole words of “ACE” as the first appearance in the paper.

Results
1.	Line 191-194. Please clearly indicate the alpha indexes for each GI tract location with real numbers especially for OTU number. The p-values don’t provide enough information.
2.	The legend of Figure 2 is not complete. The x-axis labels of each location were not showing correctly in Figure 2 C and D.
3.	Line 191. It is better to present the observed OTU number/averaged OTU with other alpha indexes (Chao1, Shannon, Simpson and ACE) in the boxplot instead of showing them in a supplementary table. The OTU numbers are just as important as other indexes.
4.	In Figure 3, text in the legend “group” is not in an appropriate order. Labels “(A)” and “(B)” should be shown on corners of both sub-pictures in Figure 3.
5.	Line 214. How many phyla were detected in the pig gut and why do you only focus on the top 17? How did you pick this number? The abstract Line 30 depicted 17 phyla have been observed.
6.	Line 215. Rewrite the sentence “We found that Firmicutes were the most prevalent phylotype (52.35% of cecal microbes.......”. Be specific about the Firmicutes levels at each location or make it clear in which location that Firmicutes are the most prevalent phylum.
7.	Line 238. The statement “with more uniform distribution in the ileum” could not be supported by the composition profile directly. I assume you were trying to describe the ileum microbiome has a greater evenness than it at other locations, and that should be indicated by evenness index.

8.	Line 240-249. This is a three-way (three locations) comparison. Any statement saying specific strain level in one location being higher than both other two locations has to be supported by bar-charts or tables showing the relative abundances in all three groups. You can provide this data in the supplementary file.
9.	 Line 266. Legend of Fig 7 requires correction. This chart is showing pathways/functions instead of genus levels.

Discussion
1.	The first paragraph in the discussion needs to be refined. Most information has been depicted in the introduction.
2.	Line 312. Please add a citation to the sentence “During the evolution of pigs, the intestinal microbes in pigs has also coevolved.”
3.	Line 313-315. How did you get the statement “From wild pig’s Actinobacteria to the domestic pig Bacteroidetes …” Please clarify or cite the source of papers.
4.	Line 318. Please add citations to the statement in the last sentence of this paragraph.
5.	Line 321. Delete “overall”.
6.	Line 323-325. Rewrite the sentence. May need delete the “<” in the bracket.
7.	Line 326. Replace “>” with some words such as “over” and “greater than”.
8.	Line 362-366. Please separate the big sentence into 2 or 3 to make the statement clear. Try avoiding using big sentence when you are not comfortable with the language.
9.	Line 366. It is not appropriate to make this conclusion based on the current data. The author only sequenced the gut microbiome from three “wild” pigs and compare it with a bunch of previously published papers without truly downloading/analyzing any data of domestic pigs with similar age, gender or locations. There is an issue in terms of experimental design and data interpretation for comparison purposes between domestic and wild pigs.
10.	Line 367-371. Please cite the paper that relates to disease resistance in wild and domestic pigs.

Conclusions
1.	The conclusion cannot be supported by the experimental design because of two main reasons. First, the wild pigs were fed with specific diet (corn, soybean and hay) before sample collection, so they have been raised the same way as domesticated pigs. Diet and environment can have very significant effects on the gut microbiome and should not be ignored. Second, there is no comparable group of domesticated pigs with similar age, gender and other related background in the study so there is no way to compare the “wild” pigs with domesticated pigs directly.


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: CHARACTERIZATION OF THE BACTERIAL MICROBIOTA COMPOSITION AND EVOLUTION AT DIFFERENT INTESTINAL TRACT IN WILD PIGS (SUS SCROFA USSURICUS)
Review round: 2
Reviewer: 1

Output:
Basic reporting: Clear English was used throughout the article. Raw data has been uploaded and was available for reanalyse. The paper contains a description of the work that has been done independently, in a field that has been poorly researched so far.
In the first part of article, authors describes clearly why described work was necessary to develop and introduce the reader to the current state of knowledge. Article structure is good. Figures are well described in accordance with generally accepted criteria and complemented by supplementary data giving a full picture of the information presented. Nevertheless more findings about next generation sequencing methods would be appropriate in this section. Research question was appropriately formulated.
References were added correctly.
Experimental design: Original primary research was well proven and described, however the experiment was carried out with a relatively small number of unique samples. Methods have been described in sufficient detail to replicate according to generally used standards. Although the software for bioinformatic analysis has been used correctly, in the future I recommend using databases that are further developed (for ex Silva). 7 years is an extremely long time for the development of bioinformation databases. Statistical analysis was made correctly with widely used and described tools. Unfortunately, authors did not attach names and versions of used R packages, which would be more important to reproduce the analysis Manuscript contains necessary information about databases used in next-generation sequencing data analyse. Sequencing technical details have been correctly provided in supplementary files.
Validity of the findings: In the discussion section authors have correctly placed the subject of their research in a broad context. They carefully explained point by point obtained results and discuss its importance to the field. Nevertheless some facts about comparisons to human or other animals are confusing for reader. Conclusions were drawn with due caution. Findings described in the study are original and unique but more research is still needed to establish this, and the authors are aware of this right.
Additional comments: The authors have significantly raised the level of work by following the comments to the previous version of the manuscript. Explanations in the rebuttal letter were reasonable and clear. Errors from previous versions were corrected and contentious issues were clarified in the text. Scientific relevance of the article has been enhanced by the suggested amendments


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: CHARACTERIZATION OF THE BACTERIAL MICROBIOTA COMPOSITION AND EVOLUTION AT DIFFERENT INTESTINAL TRACT IN WILD PIGS (SUS SCROFA USSURICUS)
Review round: 2
Reviewer: 2

Output:
Basic reporting: Satisfactory
Experimental design: Satisfactory
Validity of the findings: Satisfactory
Additional comments: Revised manuscript should be accepted for publication.


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

Input:
Title: AN IMPROVED SIMILARITY-BASED APPROACH TO PREDICTING AND MAPPING SOIL ORGANIC CARBON AND SOIL TOTAL NITROGEN IN A COASTAL REGION OF NORTHEASTERN CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper evaluates several methods for mapping SOC and TN in an area in China. The paper is mostly well written. Methods are well-described. However there are some statements that cannot be generalised and not true. Those sentences need to be revised.
For example
L. 57: The classification is not meaningful and not true: decision tree is part of machine learning models.
L. 64 The statement i snot true. Geostatistics can be applied at any scale
L. 147. The apprach grouped the landscape into clusters and then samples were taken from each cluster. This is a stratified sampling, not purposive sampling.
Eq. 8 is called the confusion index or consistency of prediction. It has nothing to do with the model uncertainty.

There are also few English expression that can be improved, e.g.
L. 379 Less steady??
Table 1: "Description" not "describe"
Experimental design: The experiment is well conducted.
- Sampling
L. 142, It should start with the description of the area, covariates and sampling design. Please describe GMCC method
The data should be described later.
Eq. 7 What is m? How many m? How was m determined?
Why not use  Euclidean distance standardised by std. deviation of data?
Validity of the findings: The finding is applicable for the location in the area. I am surprised that the similarity method performed much better than regression methods. Since regression methods  are calibrated from the data while the similarity method has to assume that the classes are representative of the data. Does the clustering done after the sample was collected?
How was the actual sample determined? Maybe the sample was biased and not based on probability sampling. This needs to be discussed.
Additional comments: The paper is generally ok, but a major revision is needed to soften the statements and define limitation of the studey.


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 IMPROVED SIMILARITY-BASED APPROACH TO PREDICTING AND MAPPING SOIL ORGANIC CARBON AND SOIL TOTAL NITROGEN IN A COASTAL REGION OF NORTHEASTERN CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: I think the manuscript writing should be greatly improved. The manuscript is superficial or lacking information in some parts, especially the introduction and discussion. I suggest that English editing and proofreading by a native speaker.
Pay attention and avoid unnecessary repetitions.

INTRO
It would be important to briefly clarify how the auxiliary variables: elevation, climate (temperatures) and landscape units determine the C and N cycles (and variations), especially on a local scale.

R&D
I recommend comparing the results obtained (SOC - STN) with more previous research. Notably, because there were many previous studies on mapping & modeling SOC - STN in coastal ecosystems.

Figs.
Improve the quality of the figures.
Experimental design: The research project is within the aims and scope of the journal. The technique and methodology are reasonable, and the sample size is appropriate for the purpose of the project.
The results are sufficiently valuable and the methodological approach could be of interest to some future readers.

I suggest reading:
Spatial soil organic carbon (SOC) prediction by regression kriging using remote sensing data (Mondal et al., 2017) to improve RK paragraph.

Only few questions:
Why did you choose these auxiliary variables? And which conversion process has been used?

The NDVI calculation procedures have been drafted in an excessively concise manner.
Were Landsat atmospheric correction algorithms implemented? Average annual NDVI?
Validity of the findings: Data is sufficiently robust, statistically sound and cross validation controlled.

The conclusions are linked to original research question.
Additional comments: I believe it is appropriate to add the SOC and STN distribution maps drawn up through GWR & RK, at least in the supplementary materials.

Figs.
F.1 I recommend changing the color of the sampling points, and adding the coordinate grid labels.
F.5 Include the units of measurement in the two graphs.
F.6 The legends are not homogeneous, I recommend adapting their dimensions.
F.6c g kg-1 apex!


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 IMPROVED SIMILARITY-BASED APPROACH TO PREDICTING AND MAPPING SOIL ORGANIC CARBON AND SOIL TOTAL NITROGEN IN A COASTAL REGION OF NORTHEASTERN CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: This is a clear research paper with an acceptable storyline, it is well structured and discussed. There is sufficient information in the introduction.

The first table [line 164]was Table 5, Table 1 should be converted to a matrix of maps as one figure in the Field sample data [line 143]

[line 187:199] might be suitable for introduction, no need to talk about soil formation in the Model Development section.

Figure 3 has to be in the study area description, too weak finding to be in the results and discussion section. No need for Figure 4, table 1 has almost the same information!
Experimental design: This topic is well fit to the PeerJ aims and scopes. The research topic is very exciting and the objectives are promising.

The research questions are well defined, relevant and meaningful.

This is quite old fashion research, nothing new, the methodology is not that important nor the data, using just NDVI delivered from Landsat 5 which was March 1984.

It is clear that the authors didn't make the efforts to address these questions using adequate data and tools.

Example of a similar research topic and case study but with higher quality:

Zongzheng Liang, Songchao Chen, Yuanyuan Yang, Yue Zhou, Zhou Shi,
High-resolution three-dimensional mapping of soil organic carbon in China: Effects of SoilGrids products on national modeling, Science of The Total Environment, Volume 685, 2019,
Validity of the findings: The prediction modeling approach needs to be higher complex in order to map soil organic carbon and soil total nitrogen. The similarity-based approach, geographically weighted regression, and kriging are not enough to build this trust in your maps' reliability.

For example, Figure 7. You can't have a vertical prediction to SOC and STN, just impossible!!

The conclusion section is a reflection of how weak this research work.
Additional comments: This research is well written and structured, unfortunately, it needs a better scientific approach, data, and modeling.


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 IMPROVED SIMILARITY-BASED APPROACH TO PREDICTING AND MAPPING SOIL ORGANIC CARBON AND SOIL TOTAL NITROGEN IN A COASTAL REGION OF NORTHEASTERN CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The paper has been improved. Nevertheless there is still few awkward expression that would benefit from another round of edits.
e.g. (one of many)
L. 26 would help
L. 32  Soil samples from the depth of 0-20 cm were
L. 39 How much improvement compared to other methods?
L 220 there is only a matrix

Fig 7 a & b. please clarify what does the consistency mean,what do high values means?

 etc.. Please go through the manuscript carefully
Experimental design: The experimental design is well described.
It has been revised as sugggested
Validity of the findings: The authors need to add limitation of the study. As the samples were collected based on an assumed soil-landscape model, it may favour the ISA model.
Ideally, an independent probability sampling would be required. Limitations should be discussed.

L. 428-430, please do not compare R2 values with other studies, it is not valid. R2 values depend on the variance of the data.
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: AN IMPROVED SIMILARITY-BASED APPROACH TO PREDICTING AND MAPPING SOIL ORGANIC CARBON AND SOIL TOTAL NITROGEN IN A COASTAL REGION OF NORTHEASTERN CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: M Clean

The English editing has been significantly improved according with proposed corrections and suggestions, however, some imperfections persist.
Examples:
47 – 50 “And” was used four times in two lines of the same sentence (improve the editing).
57 Landsat TM imagery aren't environmental factors but tools to describe the spatial patterns.
86 Indicate soil properties
180 coordinates
181-186 The paragraph is confusing
Experimental design: OK

MM
also specify that the samples were collected in 2016 as previously done in the abstract
Validity of the findings: OK
Additional comments: OK

The Figs have been modified and 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: EFFECTS OF MINING ON THE MOLYBDENUM ABSORPTION AND TRANSLOCATION OF PLANTS IN THE LUANCHUAN MOLYBDENUM MINE
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1, The author make too simple and unclear conclusion at the end. This report warranted further study, but some specific guidance or suggestions for future strategy to solve Mo pollution problem should be provided.

5, The author should provide more clear definitions about mining area and unexploited area. For example, what is the scale of Mo production from the mining area? Does the molybdenum (Mo) ore both exposed to plants in both mining and unexploited areas?
Experimental design: 2, Mo concentration in soil might not be linearly correlated with Mo accumulated in plants. In that case, author should further refer or study Mo concentration in soil and make comparison with Mo in plants.
Validity of the findings: 3, “These previous studies suggest that mining gives rise to Mo accumulation 68 in soils (Qu et al., 2008;Huang et al., 2011)” should be ‘These previous studies suggested(demonstrated) that mining resulted an Mo accumulation of 68 in soils (Qu et al., 2008;Huang et al., 2011)”

4, “In this paper, we sampled indigenous plants growing near the largest molybdenum mine of Asia.” The term near is not clear, the author should provide exact distance.
Additional comments: The manuscript titled “Mining varied molybdenum absorption and translocation of plants growing in molybdenum mine area” by Yin et. al reported plants grown in mining area and unexploited areas and their Mo absorption and translocation at a community level. This study was meaningful for providing guidelines from relation of Mo concentration and their impacts on plants grown in mining area. The research was conducted in the Luanchuan Mo mine—one of the largest Mo mines in Asia and possible environmental factors were evaluated by the potential ecological hazard index. However, the author did not make strong and logical relations and some statements seems ambiguous to readers. Therefore, I suggest consideration for publication after the author revised the following parts:

1, The author should provide more clear definitions about mining area and unexploited area. For example, what is the scale of Mo production from the mining area? Does the molybdenum (Mo) ore both exposed to plants in both mining and unexploited areas?

2, Mo concentration in soil might not be linearly correlated with Mo accumulated in plants. In that case, author should further refer or study Mo concentration in soil and make comparison with Mo in plants.

3, “These previous studies suggest that mining gives rise to Mo accumulation 68 in soils (Qu et al., 2008;Huang et al., 2011)” should be ‘These previous studies suggested(demonstrated) that mining resulted an Mo accumulation of 68 in soils (Qu et al., 2008;Huang et al., 2011)”

4, “In this paper, we sampled indigenous plants growing near the largest molybdenum mine of Asia.” The term near is not clear, the author should provide exact distance.

5, The author make too simple and unclear conclusion at the end. This report warranted further study, but some specific guidance or suggestions for future strategy to solve Mo pollution problem should be provided.


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 MINING ON THE MOLYBDENUM ABSORPTION AND TRANSLOCATION OF PLANTS IN THE LUANCHUAN MOLYBDENUM MINE
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This manuscript by Yin et. al investigated whether mining of molybdenum (Mo) ore would affect Mo absorption and translocation by plants at a community level. This research was attractive and important, considering from environmental contamination and remediation. Undoubtedly, the researchers performed a complex and laborious work, however, there are some major issues that need to pay attention and reconfirmation.

1.	What about the soil conditions other than Mo concentrations for these two areas? Are they similar? From the list of plant species on these two areas, they are different. How are you sure they are comparable in the research?

2.	Mo is the main heavy metal pollutant in soil for both the mining and unexploited areas. However, Mo could also be formed in different salts with containing of other elements such as (S)Sulfur. What specific types of Mo adsorbed? Are there any other elements detected?

3.	It is ambiguous for conclusion that heavy metal (Mo) affected plants grown in mining areas with different mechanisms for Mo absorption and translocation. Since Mo is necessary for plant growth but only trace amount is needed, what is the tolerance range for Mo accumulation in plants?

4.	Community level is needed further clarification.

5.	Plants were mainly grown in 0–20cm soil, but is there representative depth (area) for the majority of Mo distribution?

6.	Rational analysis with comparison from data from other places (like other Mo mining areas) will be helpful and solidify the conclusion, because the tile does not restrict the mine area.

7.	The figure 3 is not cited in the paragraph. Please add it.

8.	Please discuss the reason why the translocation factor of wood growing in mining area and unexploited area is barely different for woody, compared with Herbaceous.


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 MINING ON THE MOLYBDENUM ABSORPTION AND TRANSLOCATION OF PLANTS IN THE LUANCHUAN MOLYBDENUM MINE
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This work is interesting and the authors have made this paper more readable and logic. Therefore, I suggest acceptance of this paper after all the necessary revisions.


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

Input:
Title: EFFECTS OF MINING ON THE MOLYBDENUM ABSORPTION AND TRANSLOCATION OF PLANTS IN THE LUANCHUAN MOLYBDENUM MINE
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: THE HIGH EXPRESSION OF MTH1 AND NUDT5 PREDICT A POOR SURVIVAL AND ARE ASSOCIATED WITH MALIGNANCY OF ESOPHAGEAL SQUAMOUS CELL CARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Wang et al. analyzed the prognostic value and in-vitro function of MTH1 and NUDT5 in esophageal squamous carcinoma (ESCC). Several points should be corrected.
1.  Abstract: “Protein expression were in ESCC cell lines were…” should be corrected to “Protein expression in ESCC cell lines were…”.
2.  Table 1: Alternating use of Chi-squared test and Fisher test looks arbitrary and is not favorable. Please use the same test throughout Table 1. Fisher test would be better. If the authors want use Chi-squared test, please explain the rationale.
3.  Table 2 and 3: HRs for vascular invasion are different between Table 2 and 3. Why?
4.  Table 2. The bottom row may be MTH1.
Experimental design: Experiments are well designed, and the methods are well described.

Minor point.
Line 129: The catalog numbers of antibodies for MTH1 and NUDT5 should be reported for reproducibility of the study.
Validity of the findings: It would be helpful if the authors discuss potential mechanism of how MTH/NUDT5 silencing causes cell cycle arrest and EMT inhibition.
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 HIGH EXPRESSION OF MTH1 AND NUDT5 PREDICT A POOR SURVIVAL AND ARE ASSOCIATED WITH MALIGNANCY OF ESOPHAGEAL SQUAMOUS CELL CARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Wang et al have a clear scientific aim and uses a sound methodological approach, using human tissue from the disease of interest, human cell lines, standard methods such as FACS, IHC, western blot, knockdown experiments et c to proof their hypothesis. The introduction and background are relevant, and a professional language is used. The literature references are relevant. I miss some explanation about the various stages of the disease that are then refered to in the result part (i.e. AJCC, T and N stage). It could useful to mention something about the disease stages in the background.

Figures:
1.	Figure 1A-I need some more clarifications. It states that A-H is representative IHC for MTH1 and NUDT5 expression in ESCC specimens. Is it from two different patients, where A and B comes from the same patient and C and D are adjacent normal vs tumor specimens from another patient?  Or is it four different patients? Please clarify. Figure 1I- is this data mean from 99 patients from IHC data or western blot? Please clarify in figure legend how many patients and method used to analyse the protein expression. The raw data for Figure A-I is missing.
2.	Figure 2. Please add number of independent experiments in figure legend. Raw data from figure 2F-G is missing.
3.	Figure 3. Please add number of independent experiments performed in the figure legend. Please improve font on FACS figures A, C. Very difficult to read legends.
4.	Figure 4. Please add the number of independent experiments performed in the figure legend. Looking at the raw data for fig 4A-B, and reading the text, it indicates that it is only one independent experiment, but 10 field counted per sample. Please clarify.  If n=1, it should be repeated to secure reproducibility and conclusion. Similarly, how many times have the western blot been performed in fig 4C-D? Is this a representative blot out of x experiments? If yes, please add the other blot as supplementary figure. If only one WB experiment, it should be repeated to make the conclusions stronger.

Minor lay-out/text/reference comments:
5..	 Lacking reference to figures in the result text. For instance, row 219-220 a result statement but no reference to data. Same for row 221 and row 226.
6.. Row 78: …”induced by ROS is 8-Oxo-7,…” should be …”induced by ROS is 8-oxo-7,…”
7.	Row 86: reference 13 should be formatted correctly
8..	Row 128, reference 20 should be formatted correctly
9..	Row 133: reference 20 should be formatted correctly
10..	Row 174: ….duration at 3 x 103 cells per”…, is it really 3 x 103 or is it  3 x 10000 ?
11..	Row 185, 186: ….”70% alcohol..”, please specify what alcohol, assume it is ethanol
12.	Row 197: …”8x104 cells”.., or is it 8 x 100000 ?
Experimental design: Row 121-124: Please clarify what you mean with paired ESCC specimens vs tumor tissues singly? (I guess it means 81 paired tumor and adjacent normal specimens and 18 ESCC tumor tissues singly).

Please add in the material and method section the ethical permit number showing that you are allowed to use the human tumor tissues and clinical data .
Validity of the findings: Missing some information on independent replicates of experiments (see above).
The authors should show that it has been repeated (n=3) and the same results are obtained.

The conclusions from figure 2F-G on row 351 : "..the depletion of MTH1 and NUDt5 remarkebly inhibited the proliferation of ..." is a bit strong when looking at the data. Suggest to change "remarkably" to significantly.
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 HIGH EXPRESSION OF MTH1 AND NUDT5 PREDICT A POOR SURVIVAL AND ARE ASSOCIATED WITH MALIGNANCY OF ESOPHAGEAL SQUAMOUS CELL CARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors correctly revised the basic reporting of this munuscript.
Experimental design: I see no problem in the Experimental design of this manuscript.
Validity of the findings: I have no concern about the Validity of the findings of this manuscript.
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 HIGH EXPRESSION OF MTH1 AND NUDT5 PREDICT A POOR SURVIVAL AND ARE ASSOCIATED WITH MALIGNANCY OF ESOPHAGEAL SQUAMOUS CELL CARCINOMA
Review round: 2
Reviewer: 2

Output:
Basic reporting: ok
Experimental design: ok
Validity of the findings: ok
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: COMPREHENSIVE ANALYSIS REVEALS A METABOLIC TEN-GENE SIGNATURE IN HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1.	I suggest the author improve the Introduction section by making a careful literature review about previous biomarkers associated with metabolism in liver cancer or metabolic classification for liver cancer.
2.	Besides comparing performance of different biomarkers, it is better to compare the subtypes classified by your biomarker with subtypes classified by TCGA group or other well-studied metabolic subtypes (e.g. PMID 30606699).
Experimental design: 1.	Adjusted p <0.05 was used when identifying DEGs. But P<0.05 was used when identifying prognostic genes. Why do not use same significance level (adjusted p <0.05) ?
2.	In Figure 4H, why not consider age, gender, grade and N in Multivariate Cox regression analysis? Same problem with Figure 5H, 6H and 7H.
3.	Since the risk-score-based biomarker is sensitive to batch effect, the cutoff set in training dataset may not work in independent dataset. It is better to validate this biomarker in more independent datasets if it is possible.
4.     The author should provide more details about the metabolic differences between two subtypes if it is claimed as a metabolic biomarker.
Validity of the findings: 1.	The result “Interestingly, subgroup stage I, stage 215 II, stage III in entire testing cohort were stratified into high risk group and low risk group, HCC patients in high 216 risk group had better OS than patients in low risk group (Figure S2 M-O)” is unreasonable, which is in conflict with the result when the samples were grouped by stage I-III and stage III-IV.
Additional comments: 1.	I suggest the author send the manuscript to language edit.
2.	The resolution is too low in Figure 8.


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: COMPREHENSIVE ANALYSIS REVEALS A METABOLIC TEN-GENE SIGNATURE IN HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: They wrote the report in an acceptable English language and can be understood in most cases. There are several areas that can be improved, especially on formulating the sentences to make it more concise and easier to understand (Minor) for example "However, ... still lacking" (line 88-89) can be rephrased to make it more understandable, since this is one of the main kick to explain the background. Another example is line 136-137, about the testing cohort, can be rephrased to make it clearer. My suggestion is that the authors can go through the paper one more time and start cutting complex and long sentences.

The background and context given is clear enough. Same with the references. Structures are clear.
Experimental design: Original primary research within the Aims and Scope of the journal: YES

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

Rigorous investigation performed to a high technical & ethical standard.: YES

Methods described with sufficient detail & information to replicate.: YES

Methods are clearly defined. Concerns:
1. What kind of normalization that was used in the paper? TPM, FPKM?  Raw counts are not acceptable.
2. I would suggest random partitioning to be used for the DEG calculation due to unbalance number of patients and normal. Otherwise, the result can be skewed.
Validity of the findings: The results were validated with an independent validation cohort (also publicly available data). All data are publicly available.

Regarding the result, several concerns:
1. About the testing cohort: The author mentioned 243 patients from external and 184 from the internal testing cohort, how can the total entire testing cohort be 608? The number doesn't seem to match. Except, if they included the training cohort as well, which doesn't seem necessary.
2. Line 179-182: The information is not clear. The summary is that high-risk subjects have poorer OS score. Not the case in 1-year. Comment?
3. Figure 5B, the stage has higher AUC. Comment?

Suggestion: Bidkhori et.al published a paper that was proposing 3 sub-types of HCC (they were using TCGA data as well). The authors can perform a simple analysis to see how their suggested genes perform for stratification of patients in each sub-type, or as simple as checking the expressions in each sub-type. I think this can add more value and validation to the paper.
https://www.pnas.org/content/115/50/E11874.short?rss=1

MINOR suggestions:
1. (MINOR) Figure 2: IMO, volcano plot should be enough for this. And it would be nice as well to mark the 9 proposed genes in both heatmap and volcano plot.
2. (MINOR) Figure 3: We can see that the proposed genes are higher/lower, but adding statistical analysis between high vs low risk (simple, t-test?) can add more power to the subsequent analysis
3. (MINOR) line 181: more poor --> poorer

In the discussion, each gene was discussed separately. Adding one paragraph to summarize all would be nice, can be with the help of the GSEA result (from the last part of results). My reasoning is that we know that each gene has its own function, but multiple genes can also affect a pathway/biological process, which would be interesting as well to be discussed. For now, the discussion is missing a connecting thread.
Additional comments: In this paper, Zhu et.al is proposing nine gene signature for HCC survival prediction. The analyses were done based on publicly available data (2 datasets). In their result, they showed that the nine gene signature performed better than any of the clinical or singular genes in predicting the low vs high-risk HCC patients.


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: COMPREHENSIVE ANALYSIS REVEALS A METABOLIC TEN-GENE SIGNATURE IN HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed my concerns adequately.
Experimental design: The authors have addressed my concerns adequately.
Validity of the findings: The authors have addressed my concerns adequately.
Additional comments: The authors have addressed my concerns adequately.


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: COMPREHENSIVE ANALYSIS REVEALS A METABOLIC TEN-GENE SIGNATURE IN HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The author has performed adequate language editing to an acceptable level.
Experimental design: Please include the use of FPKM value in the method part. Important for reproducibility.
Validity of the findings: No comment
Additional comments: Authors have made the required revision to make it as acceptable


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: ESTIMATING FOOD RESOURCE AVAILABILITY IN ARID ENVIRONMENTS WITH SENTINEL 2 SATELLITE IMAGERY
Review round: 1
Reviewer: 1

Output:
Basic reporting: Major comments (in order of importance)

1)	At many points, the sentence structure is very unusual (e.g. lines 180-182, 262, 275, 328), making it difficult to understand the content. Additionally, there are a considerable number of grammar/vocabulary errors (e.g. lines 55, 64, 107, 122, 190, 216) and punctuation errors (e.g. lines 65, 66, 162, 315) throughout the text. I have provided several examples for each of these issues, but since they occur frequently throughout the text, I am unable to highlight every single instance. I think the manuscript would greatly benefit from extensive editing, especially by any authors (or colleagues) that are native English speakers.
2)	The title is evocative and easy to understand but, in my opinion, does not fairly represent the work that is carried out in this paper. Specifically, I don’t think the work presented here integrates remote sensing with behavioural ecology – this implies that there is some integration of movement or other animal behaviour related data, which does not occur here. The work does, however, make an interesting contribution to the remote sensing of habitat qualities of particular species (namely, food resources), which I think ought to be reflected in the title.

Minor comments (in no particular order)

3)	I disagree with the use of “remote sensing” to refer to the satellite data-derived vegetation indices throughout the text, since “remote sensing” encompasses many more modes of data acquisition (e.g. camera traps, acoustic sensors, telemetry) that are neither used nor discussed in this study. I suggest this is replaced with “satellite remote sensing” instead.
4)	The authors use the term “barren” throughout the text to refer to bare ground. However, barren implies the that a patch of land is sterile (e.g. lacking a seed bank), but this cannot be directly deduced from low vegetation cover. I suggest the authors use “bare ground” instead.
Experimental design: Overall comments: The Methods section does not provide enough evidence that the statistical analyses were appropriate. Additionally, clarification is needed in some places to allow replication.

Issues which require re-analysis (in order of importance):

1)	In the Introduction, the authors state that their first aim is to determine whether “remote sensing data […] can be used to predict the spatial variability of Enneapogon seed-productivity [sic]” (line 132). However, the authors use Enneapogon seed productivity as an explanatory, not a dependent, variable in the models. This means that the goodness of fit measure (RMSE) describes how well spatial variability in Enneapogon seed productivity explains variability in the remotely sensed index, and not vice versa. It is not clear why the authors chose this approach. I suggest that the authors rerun their models using Enneapogon seed productivity as the dependent variable.
2)	The same rationale applies to the analysis of how well vegetation indices discriminate between the three main land cover classes (bare ground, grass-dominated and tree-dominated). Again, satellite-derived vegetation indices are treated as the dependent variable, whereas the study is interested in understanding “how Sentinel 2 information can be used to estimate habitat condition in a spatially heterogenous environment […]” (line 260-261), implying that their usefulness as an explanatory variable is of interest instead.
3)	The authors state that Generalised Least Squares (GLS) models were used to account for the “non-linearity of the natural spatial distribution of the vegetation” (line 208). It is not clear what is meant by this, given that GLS approaches do not relax the assumption for linear relationships between predictor and dependent variable (they do however relax the assumption that there is no correlation between residuals). Since the authors provided their raw data in a very accessible and very easy to understand format (thank you!), I was able to fit the GLS models myself. The diagnostic plots I obtained showed a worrying increase in the spread of standardized residuals for large fitted values for models using seed productivity as explanatory variables. I am not convinced, therefore, that the GLS models are currently an appropriate way to characterise the relationship between the satellite-derived vegetation indices and the vegetation parameters obtained in the field. I suggest the authors explore alternative models that fit the data better (e.g. Generalised Linear Models or non-parametric tests).
4)	It is not clear why the analysis of how much the satellite-derived vegetation indices differ between the three land cover types is limited to the five most representative plots for each type. If the question is to which extent vegetation indices can discriminate between different land cover types, this is likely to bias the results towards suggesting more successful discrimination. I propose that the authors rerun the analyses using all available vegetation plots.
5)	Currently, 18 separate Wilcoxon tests are run to identify which land cover types have significantly different vegetation index values, but no penalisation for multiple testing seems to have taken place. This could be rectified by using e.g. a Bonferroni correction, or consider a mixed ordinal regression model with a vegetation index as explanatory variable, and month as a random effect, to reduce the amount of statistical tests carried out.

Clarification needed (in no particular order):

6)	Please elaborate on your choice of study site, specifically why the vegetation quadrats were established close to an artificial water dam (see line 152).
7)	The description of how the Braun-Blanquet index was adapted is difficult to understand (lines 155-156). Specifically, could you clarify what criteria you used to determine the new threshold values?
8)	Please clarify whether the machine described in lines 169-170 is a scale.
9)	Please elaborate on the difference between atmospheric correction and removing absorption effects (line 193). Which algorithm was used for the latter?
10)	Were the GPS points of the quadrats (line 203) taken in the middle of the quadrants? Please explain how you ascertained that each 10m by 10m quadrant only overlapped a single Sentinel 2 pixel, given that the spatial error of the GPS was 5 m.
11)	The authors find significant Moran’s I values for both satellite-derived vegetation indices; however, the values were quite low, and though significant, are unlikely to be important. Given that the best models for each vegetation index were those without a spatial correlation factor, please add an explanation for why the inclusion of the spatial correlation in the final model was justified.
12)	The description of how the authors identified the 5 most representative plots for each land cover class (bare ground, grass-dominated, tree-dominated) is unclear (lines 228-231). I assume the five plots with the highest relative coverage of bare ground, grass and Acacia (respectively) were used, but I am not quite sure after reading the description.
Validity of the findings: The analyses and findings as presented in the Results and Discussion section do not clearly correspond to the stated aims of this study. I have four major comments, in no particular order of importance:

1)	The authors state in the Introduction that the present study has two aims: 1) find out to which extent Enneapogon seed productivity can be predicted by remotely sensed vegetation indices and 2) determining to which extent this relationship is robust over time. However, they then introduce apparently unrelated analyses in their Methods (the relationship between remotely sensed indices and total vegetation cover, the difference in vegetation indices between three broad land cover types). I suggest the authors either omit these analyses (and the discussion thereof), link these analyses more explicitly to their hypotheses, or revise the stated aims of this study.
2)	Additionally, they do not explicitly test to which extent the seed productivity-vegetation indices relationship holds over time. The Introduction should be amended accordingly.
3)	It is not clear, from the Discussion, to which extent the validity/generality of the results is affected by the fact that the year in which the study was carried out (2016) had exceptionally high NDVI values (line 267), given that the authors conclude that peak “greenness” was important in distinguishing between land cover types (lines 360-362). The discussion should be expanded accordingly.
4)	The conclusion states that “data generated by Sentinel 2 will provide a reliable estimation of habitat condition […] over time, with some limitation with respect to some components of the vegetation.” (cursive added for emphasis). There is however no discussion of what constitutes the limitations or the vegetation components in question; adding this would enhance the discussion considerably.
Additional comments: What interested me most about this paper was how field- and satellite-derived data were combined with an in-depth understanding of context-specific ecosystem processes to address a question of global interest – how can we measure habitat quality from space? Though the manuscript requires substantive revision (as detailed in my comments above), I believe a revised version has the potential to make an interesting contribution to our efforts to link satellite-derived data to estimates of habitat quality.


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: ESTIMATING FOOD RESOURCE AVAILABILITY IN ARID ENVIRONMENTS WITH SENTINEL 2 SATELLITE IMAGERY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper: “Integrating remote sensing and behavioral ecology in the arid zone is basically using a clear and unambiguous English language throughout the text”, though I found a few sentences difficult to read, which I marked in the specific comments. The introduction and background is well written and the paper structure conforms to the peerJ standards. I suggest to alter the title and to avoid behavioral ecology in the title. It might be misleading since no behavioral data set is included into the analysis, even though the connections are argued in the introduction and discussion. The figures might (I am unsure if a few comments are due to the pdf version) need some improvement which you can find in the specific comments. The submitted raw data to my opinion needs to be enhanced by the vegetation data.
Experimental design: The research topic is well within the scope of the journal and the statistical analysis is generally sound. Though the cluster analysis, as well as the NMDS are not well explained in the methods section.
Validity of the findings: Throughout the manuscript I did not see the functional link between MSAVI and seed productivity. Could you please provide a sound mechanistical link of why MSAVI should be able to predict seed productivity? Here I am also missing the results for the NDVI to compare with. You chose a linear model but actually from Tab.2 you can see that seed productivity is quite low in the green cluster. You determined the plants only on genus level, can you argue why?
Additional comments: Table 2: Check for significant differences.
Table 3: From which month is the NDVI, indicate level of significance in the caption.
Table S1: Please modify the caption, what is the meaning of numbers (indicator value, relative abundance or relative frequency)? Order the table and draw a box around each cluster. Here you specify only two clusters but in the rest of the analysis you have three clusters (are there no plant species in barren?). Here you use the word vegetation type to specify the life form, in the rest of the paper you probably mean vegetation composition types…. if so be more specific.
Fig. 1: This figure is difficult to read at 100% zoom, labels are too small and graphics are not eqally sized. Please specify the meaning of the point sizes in the map. Use crosses to indicate the location of genera in the ordination diagram. Check if you always use a space between number and unit 10 x 10 m. ESRI instead of ENSRI. Clusters are not always named coherently ( Acacia/trees /green)? You could also think of more meaningful names referring to vegetation types. I also suggest to add a small, concise description of the clusters to your results, since you argue that you researched vegetation composition.
Fig.2: R² and or RMSE values are missing in the figure, coordinates are not readable, no scale bar, and the legend at my computer appears rather blackish. Do not use your model abbreviations as labels “Enn. Seed productivitity” and add proper units to the axis label.
Abstract
Background: the last sentence is incomplete or needs rephrasing.
Methods: I suggest to move the research questions to the Background and add information about your design, GLS etc. in methods. More specific information
Results: change vegetation density to vegetation cover. Be more specific, add model quality parameters to prove your statement.
Discussion and Conclusion are missing in the abstract.
Text:
L35you did not specifically test for discrimination…change the wording.
L39: You did not include any animal ecological data and within the abstract the connection between behavioral studies and remotely sensed data remains unclear, so please rephrase L22-23 (include more specific examples or skip it) (like: remote sensing data offers the possibility to model important predictors for animal behavior).
L54: 20 km
L84:  rephrase clumped and dispersed at the time sounds funny
L94: spatial resolution-derived, sounds unclear to me
L115: be consistent either latin names or trivial names
L 188-190: Is the December belonging to the boom phase? Or did you select 2 images from arid summer to test model transferability? Please be more precise.
L194: Please briefly state, which technique you used for removing the absorption features to make your workflow also understandable to e.g. ARC GIS or R users.
L196: Sentence remains unclear: specify what you mean by high spatial resolution wavelength.
L213: You calculated the direction and amount of autocorrelation but for which model did you use it as dependent variables and why? Please add one more sentence to clarify.
L220: AIC, is it spelled out before?
L222: error or deviation? (RMSE /RMSD?)
L225: I suggest to rephrase since it does not match your research questions, since you never explicitly modelled vegetation composition, just Enneapogon abundance and seed productivity.
L226-233: Here, you could also apply the concept of distance (Jeffries-Matusita) that would fit more to the concept of discrimination.
L243: I am not familiar with GLS but I expected to see some sort of quality indicator for the relationship (R²), or the RMSE printed inside the figure.
L248: I suggest to use a more careful wording e.g. rephrase: the NDVI is significantly different between the three vegetation types (instead of distinguishes)
L250: rise?
L261: I suggest to use a more careful wording: instead of simply writing habitat condition I suggest to first of all state the seed productivity which you directly assessed and then argue why this implies habitat condition.
L313. High vegetation cover
L319: Could the capacity to discriminate between the classes be due to the selection of the five most barren / covered plots?
L328: Delete: that can browse on shrubs
L263: Did you really compare the MSAVI in October to the MSAVI in December and January? Please be a more specific in the wording.
L270: I suggest to stick to coverage, however I think you have a rather inhomogeneous vegetation pattern in your data with sharp contrasts between barren and green patches. Please be also more careful you did not directly assess the quality of your field estimations, so I would not argue that simply because my model is good my vegetation coverage estimates were good.
L274: So your data shows that Enneapogon is most abundant in the grass cluster. This sentence needs a little rephrasing to be sure in which cluster Enneapogon is most dominant.
357: satellite imagery
358: I propose: vegetation cover instead of density


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: ESTIMATING FOOD RESOURCE AVAILABILITY IN ARID ENVIRONMENTS WITH SENTINEL 2 SATELLITE IMAGERY
Review round: 2
Reviewer: 1

Output:
Basic reporting: All line numbers refer to “Manuscript with tracked changes”.

Major comments (in order of importance)

It is not clear to me, from the Introduction, how the vegetation cluster analysis contributes to answering the central question of the paper (namely, whether satellite-derived indices can be used to predict food resource availability in arid environments). I suggest either adding an explanation to the Introduction (e.g. before l. 162) or omitting this part of the analysis from the paper.

There are still irregularities and mistakes in grammar and vocabulary that sometimes make it difficult to understand the paper. There are too many instances to list all of them, but for examples, see e.g. l. 60, 130, 185-186, 198, and the caption of Figure 1. As a result, I would encourage a second round of thorough editing.

Minor comments

Figures 1 are 2 quite blurry, so I suggest making a more highly resolved version. Additionally, the points in Figure 1b would be easier to see if they were a bit larger. In Figure 3, I think using a lighter colour would be better for the middle bar, as it is difficult to see the lower standard error limit.

It is not immediately obvious to the reader that the top half of Table 2 refers to one satellite-derived index, and the bottom to another, so it would aid understanding if that was somehow made more obvious. I am also a bit confused as to the meaning of the chisquare test – could you add some explanation in the Table caption?

l. 41-42: It is not clear 1) which vegetation types differ from each other, and 2) in what quality they differ -- could this be clarified?
l. 45: Does this refer to “heterogeneity in seed production depending on vegetation type”? If not, how is vegetation heterogeneity relevant for predicting food resource availability?
l. 47: I am not sure to what “temporal unreliability” refers. There is also no mention of how useful satellite data-derived indices are for predicting food resource availability. Since this is a key question of the study at hand, I would suggest adding this to the Abstract.
l. 145: What does primary seed productivity refer to? Does this mean the grasses set seed once at the beginning of a given season, and then once again afterwards?
l. 147: I think this needs a little more detail about the hypotheses/predictions (I do not understand why vegetation type matters in this context for instance, see Major Comments). Essentially, I think this needs to answer the question: why is it relevant whether or not satellite-derived indices can discriminate between different vegetation types to predict food resource dynamics?
l. 176-179: Since the paper does not compare the relative utility of satellite remote sensing and rainfall data for predicting resource availability, or integrate said animal population dynamics, I am not sure why this motivated the choice of study area. Perhaps there are ecological characteristics that make this area interesting?
l. 182: It still is not clear to me why the transects were established close to the dam.
l. 188: Does this mean that each transect was sampled once per week, over a period of three weeks, in October? And then once again in December and January respectively? I think this needs to be clarified in the text.
l. 213: All vegetation types are used in the analysis, rather than a subset – I think the subsetting refers to the within-cluster replicates?
l. 246: I am not sure to what “October relative” refers – this is a problem when replicating the analyses because it is not possible to identify which observations were included in the analysis.
l. 252: I am not sure what “grass count” means here.
l. 253: The quadrats are 10 m by 10 m (i.e. refer to a single Sentinel 2 pixel), whereas the transects used to estimate seed productivity are 50 m long – I think this needs an explanation of why average NDVI and MSAVI2 values across the entire transect were not used instead.
l. 300: Repetition of Sentinel 2.
l. 303: I am not sure what aspect “variation” refers to.
l. 338: The word “satellite” is missing.
Experimental design: All line numbers refer to “Manuscript with tracked changes”

Bonferroni corrections have not been applied to Table 3, as far as I can see. These tests require a correction by 9 for each dependent variable (as there are 9 statistical tests per dependent variable), meaning the new alpha level is 0.0056; none of the pairwise comparisons are statistically significantly different after Bonferroni correction. The discussion needs to be amended accordingly (l. 319 -333).

Bonferroni corrections not applied to Table S3. This requires a correction by 3 (3 tests each per dependent variable), meaning the new alpha level is 0.017; none of the pairwise comparisons are statistically significantly different after Bonferroni correction.
Validity of the findings: All line numbers refer to “Manuscript with tracked changes”

Major comments, in no particular order

The results reported from the GLMM do not correspond to the Discussion – specifically, the effect sizes for both satellite-derived indices are negative (see Table 2) but are described as positive in the Discussion (l. 311) and appear positive in Figure 2. I suggest checking that the correct effect sizes have been reported, otherwise the Discussion has to be amended.

The effect direction of both satellite-derived indices does not correspond to Figure 2. For instance, the intercept is negative for both models but eyeballing Figure 2 indicates that intercept is positive. Could you double check that the correct effect sizes are reported in Figure 2?

The effect size of both satellite-derived indices is smaller than the standard error for these terms (see Table 2), implying that the link between seed productivity and these indices is highly variable and rather weak. In my opinion, the findings are not accurately represented unless these limitations are addressed, either in the analysis or the discussion.

I do not agree with the conclusion that the satellite-derived indices presented here “provide reliable estimates of both spatial and temporal vegetation cover“ (ll. 393), since only pure vegetation types were selected to test whether satellite-derived indices can distinguish between them (l. 263). However, if pure pixels are relatively uncommon across the landscape, this would imply that the satellite-derived indices are not useful for predicting vegetation type for a lot of the area. I suggest adding an explanation for why pure pixels are expected to be common across the landscape.

From the Discussion, it is not clear why and how distinguishing between vegetation types helps predict food resources (see also comments in Basic Reporting). The paper is primarily focused on grass seed productivity, and it is not obvious how being able to discriminate between shrub and bare ground helps map this food resource. I would add an explanation of this to the Discussion

Minor comments

l. 316-325: The discussion of what drives shrub distribution across the landscape is unrelated to the research questions set out in the Introduction. I’d consider deleting or explaining relevance to research question in more detail.
l. 326: This research aim was not mentioned in the Introduction. I suggest adding this accordingly.
Additional comments: Thank you for new revised version! There are, as you have seen, still several areas where I think significant change needs to happen for this paper to effectively communicate its message. However, I believe it will be very straightforward to carry these out, and I am looking forward to seeing the revised version.


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: ESTIMATING FOOD RESOURCE AVAILABILITY IN ARID ENVIRONMENTS WITH SENTINEL 2 SATELLITE IMAGERY
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript clearly benefited from the review process. However, I think the language is still complicated or grammatically wrong in some cases: L 326; Caption Fig. 3, L387; as well as there are some minor spelling mistakes, such as missing spaces: Caption Figure 1.; L45,

Moreover, it was difficult to catch the narrative of the paper easily: the research questions are framed very differently:
e. g.: Abstract:
Here, we aimed to test whether Sentinel 2 imagery were able to accurately assess the spatial and temporal variability of a minor tussock grass (Enneapogon spp.) in an Australian arid area.

Introduction:
1) whether satellite remote sensing data (i.e. spectral vegetation indices) can be used to predict the spatial variability of Enneapogon seed-productivity and
(2) whether this prediction holds over time.

Discussion:
Using on-ground measures of vegetation structure and Enneapogon seed-productivity we tested
the extent to which Sentinel 2 satellite images from Sentinel 2 can be used to indicate habitat
quality, and potential food resource availability (i.e. Enneapogon), in the spatially heterogeneous
Australian desert and semi-desert.

So in my opinion some careful minor editing is still necessary.

##Specific comments:

Your abstract, especially the methods and results section need more detail. The NMDS is not a method used for clustering, please be more specific. I expect to read a few measures of model quality (for the GLMMs) in the results section. As I guess from your analysis,  the relationship between seed  productivity and vegetation indices is only good in October, so the quality and the direction of the relationship changes.

For figure 2 the you used a best-case scenario, which I feel means you picked the most distinct plots and pixels for comparison. Thus the generalization that the indices differentiate well between the three clusters needs to be more cautious throughout the text.

The vegetation data (plant cover matrix) for the calculation of the NMDS is still missing, since one of the review points is to check whether all data is available please  ask the editor to decide if it is sufficient to submit the article without the plant cover matrix.

L205-209, thank you for adding the sentences, however, they are still difficult to understand to the NMDS as a clustering methods. Since basically you used two methods: clustering with gower distances and wards method? resulting in the colour of the dots in  the NMDS diagram, and a NMDS with gower distances.  For the NMDS you could also mention the stress level as well as the goodness of fit.  Please also state how you decided for the two clusters.

L106: Please reconsider this argument. Including many vegetation indices into a predictive model leads to over fitting. Your models are also only considering a single VI.

L226: Landsat? From the rest of the manuscript I thought you only considered Sentinel 2 imagery.

L237: are proxies of ….
L246: Please also mention the name of the test for spatial autocorrelation in the methods section.

L247: What do you mean by grass count?

L262: Which package did you use for the significance testing.

L 267-273: Please add a few indicators of model quality here. I am not very familiar with GLMM tables and could not figure out on which statistics you base your arguments.

L274: To be more precise you could consider calculating a normal indicator species analysis.

L278: Consider changing quadrats to plots.

L293: vegetation composition, or vegetation cover?

L372: Species name is one time in brackets and the other time without brackets,
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: ESTIMATING FOOD RESOURCE AVAILABILITY IN ARID ENVIRONMENTS WITH SENTINEL 2 SATELLITE IMAGERY
Review round: 3
Reviewer: 1

Output:
Basic reporting: Major comment

The edits in ll. 152-156, in my opinion, do not clarify how variation in the vegetation type is related to seed productivity, and hence food availability. I suggest that the authors consider moving the explanation they give in ll. 354-357 to the Introduction, and spell out this relationship between grass cover and seed productivity in the Abstract, Results and Discussion as well. I assume this linkage is very obvious to readers familiar with the study site, but I really struggled to understand the relevance of the vegetation cluster analysis for answering the research questions of the study.

Minor comments

Table 2: It is not immediately clear from reading the Methods why the significance of each model was tested by comparing the full model to a model lacking the interaction terms (rather than a null model). Could an explanation be added?
Results section in the Abstract: The results pertaining to the vegetation cluster analysis seem to be missing – could these be added for completeness?
l. 182-187: The authors mentioned they had added an explanation for why Fowlers Gap is a suitable study site, but I cannot find this in the new manuscript – as of now, my original comment (that since the paper does not compare the relative utility of satellite remote sensing and rainfall data for predicting resource availability, or integrate animal population dynamics, I am not sure why this motivated the choice of study area.) still stands.
l. 226: I think “identified by these clusters” should probably be “inside these clusters”.
l. 250: Could you please clarify whether, for the seed productivity analysis, vegetation indices were calculated for every pixel covered by the 50m transects? This is not immediately apparent from the text as it is currently written.
l. 258: Thank you for clarifying this – could the authors additionally clarify how they calculated the average (i.e. was it the mean or median, or the x most productive sites)?
l. 262: I think this should be “product of” instead.
l. 325: I am still unclear about what is meant by “cover variation” – does this mean variation of vegetation cover within in patches or between patches? And variation of what cover (grass, shrubs, …)?
Experimental design: Table 3: I really do believe that the Bonferroni correction is 9, and not 3 (as for each vegetation index the results of 9 separate tests are reported, implying 9 separate tests have been carried out). This means none of the differences are significant, and in my opinion this should be reflected in the Discussion.
Table S3: Similarly, a Bonferroni correction of 3 has to be carried out for each vegetation index, reducing alpha to 0.017 (meaning none of the differences are statistically significant).
Validity of the findings: No comments apart from the issues raised in 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: ESTIMATING FOOD RESOURCE AVAILABILITY IN ARID ENVIRONMENTS WITH SENTINEL 2 SATELLITE IMAGERY
Review round: 3
Reviewer: 2

Output:
Basic reporting: Dear authors,

I believe the manuscript greatly improved and is ready for publication. During the last reading I found a few very minor things, which I ask you to consider:

L52: under which conditions exactly?
Tab. S1 : In vegetation ecology indicator species analysis tables are sorted first by significance, and then by decreasing realative occurence per cluster.

Tab. S3. n=2 seems too low to generate meaningful results in statistical testing for my taste. Please consider to remove it from the paper.
Experimental design: ....
Validity of the findings: ...
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: GENOME-WIDE IDENTIFICATION AND CHARACTERIZATION OF THE FIBRILLIN GENE FAMILY IN TRITICUM AESTIVUM
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In this manuscript, using the reported FBN protein sequences in the wheat database, the authors identified 26 FBN genes and analyzed their biophysical properties and expression profiles of 3 TaFBN genes in different tissues and at different developmental stages and in response to abiotic and biotic stresses using the  GENEVESTIGATOR database, the results are informative. Overall, throughout the manuscript, the data used all came from database, there is no own experimental design, it`s simple, so the following problems must be solved.
1.	The FBN sequences for blast search should not be limited in only two species (Arabidopsis and wheat), more FBN sequences from other monocot plants should be added.
2.	The more detailed version of obtained wheat genome sequences should be noted.
3.	Line 202 mentioned ‘Gene structure analyses indicated that homologous genes had similar exon-intron distribution pattern’, but homologous genes, such as TaFBN2 and TaFBN10, TaFBN13 and TaFBN15, TaFBN6 and TaFBN21, TaFBN18 and 3, TaFBN17 and 25, TaFBN14 and 19, TaFBN22 and 26, TaFBN16 and 5, TaFBN12 and 20, seems have different gene structure.
4.	According to the ‘Fibrillin is a highly conserved family of gene’ in Abstract, the sequences alignments of conserved domain should be exhibited.
5.	The analysis results of TaFBN cis-regulatory elements, such as the indicated cis-regulatory element of TaFBN4, 5 and 6, should be associated with the results of expression profiles response to abiotic stress. If the two results were different, please explain the reasons in the discussion part.
6.	Line 255 described that at least 25 pairs of TaFBN genes underwent gene duplication arising from segmental duplications. However, the 25 pairs of TaFBNs were genetically replicated by tandem replication in Abstract. Please be consistent.
7.	Expression profile data used was 2015 and 2016 in which sequencing information of wheat genome was not newest and incomplete. So expression profiles of TaFBN families in different organs and stresses through RNA-Seq need to be analyzed based on the newest wheat database (2018).
8.	As get the results of expression profiles of RNA-Seq, validate it through qRT-PCR assay.
9.	The paper is full of grammatical errors, many discriptions are inaccuracy.


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

Input:
Title: GENOME-WIDE IDENTIFICATION AND CHARACTERIZATION OF THE FIBRILLIN GENE FAMILY IN TRITICUM AESTIVUM
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this study, Jiang and colleagues identified and analyzed the fibrillin gene family in wheat. The study is based on publicly available genomic and expression data. Although it could be of interest to better understand the evolution and molecular mechanisms of those proteins apparently participating in photosynthesis and involved in biotic and abiotic stresses, the authors failed to correctly interpret some of their results.
Moreover, there are multiple typos (e.g. line 261 “Tiussse”) and bad English formulations (e.g. line 257 “could be driven the evolution process”) all across the manuscript. Some paragraphs are relatively well written but others were not carefully edited. Therefore I would recommend the authors to get it proofed by an English speaking colleague or, at the very least, using an automatic spelling software (either the one directly provided in Microsoft Word or the one by Grammarly which performs pretty well, for example).

Availability of data: alignments of FBN genes/proteins in wheat and across the other species presented in Fig. 3 should be provided as fasta (or equivalent) format.

Citations are not always in the correct format: “Multiple references to the same item should be separated with a semicolon (;) and ordered chronologically.”
Experimental design: Phylogenetic trees must have bootstrap values like in Figure 4. Why showing three times the same tree but indicating only in the last one the support values?

Also, the references and accession numbers of all the sequences used should be mentioned.

Why not using the Wheat Expression Browser (http://www.wheat-expression.com/) to explore the expression patterns of TaFBN genes? All the genes are available and not only three.
Validity of the findings: The main flaw of this study is that the authors confused gene duplications and merging of genomes. The authors are apparently aware that wheat is a hexaploid species but they seem to ignore the mode of formation of this species and its implication for homologous genes. Indeed, they consider homeologs as duplications although they were brought together following inter-species hybridization and allopolyploidization. Those gene copies were completely homologous in the ancestral species. This is to distinguish from duplication as it can be seen in Arabidopsis or Zea mays, species that are diploids but known paleopolyploids and present sometimes a duplicated fibrillin gene. It is still possible that there are duplications especially on the chromosomes 2 but Figure 3 seems to indicate, if the node support values are meaningful, that the duplications are much older and shared by all the species included in the tree.
This also means that the values obtained in Table 2 do not reflect a duplication date but maybe the date of divergence of the progenitors of wheat. Also, I would have to criticize the method used. Indeed, the authors used a method and a value drawn from Koch et al. (2000) although this very same article describes and discusses different values of the synonymous substitution rate among which one that was estimated from grasses. Another article of high-interest discussing the uncertainty associated with those values is Senchina et al 2003.
Additional comments: Homeologs should be identified with their genome location (A, B or D) for example TaFBN22 and TaFBN26 could be named, due to their clustering with AtFBN1a and AtFBN1b in the Group 1, TaFBN-B1 and TaFBN-A1, respectively. The way the authors named the genes looks random and does not facilitate the interpretation of the results.


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

Input:
Title: GENOME-WIDE IDENTIFICATION AND CHARACTERIZATION OF THE FIBRILLIN GENE FAMILY IN TRITICUM AESTIVUM
Review round: 1
Reviewer: 3

Output:
Basic reporting: In terms of form, I did not find the figure captions.
Experimental design: This paper is an in silico analysis (there is no experiments) aiming at identifying Fibrillin genes in Triticum aestivum and studying their potential functions based on their expression, their structure, the prediction of their physical and chemical properties and ci-elements in their promoters.
As far as this family has not been studied in wheat, the paper is interesting but it has to be thoroughly modified, particularly by using the last version of the wheat genome to identify TaFBN genes (https://www.wheatgenome.org/Tools-and-Resources) and their expression (http://www.wheat-expression.com/). Of course, data extracted need to be treated to express the DEG according to the different conditions.
Validity of the findings: no comment
Additional comments: There are mistakes all along the text that I underlined in yellow. Also, I added comments throughout the text.

Introduction
The introduction needs to be improved in terms of the roles of fibrillins. Is there any review?
The overall introduction needs to be read carefully mistakes all along the text (ex: line 257 “could be driven BY”, line 261 “tissue “, etc…

Materials and methods
Did you check genevestigator results in real? It would have been great to run qRT-PCR on selected genes to validate the results.
Did you identify homeologous genes? In other terms, in your 26 TaFBN, do you have triplets? Can you precise?
You would need to use the last version of the wheat genome (https://www.wheatgenome.org/)
For gene expression, you may use www.wheat-expression.com platform (Borrill, P.; Ramirez-Gonzalez, R.; Uauy, C. expVIP: A Customizable RNA-seq Data Analysis and Visualization
Platform. Plant Physiol. 2016, 170, 2172–2186.), to retrieve more information

Results
Why did you analyze the expression of only 3 TaFBN genes? Moreover, you can not tell that line 322, that “you analyzed the expression patterns of TaFBN gene family”.

Conclusion
The last sentence is too global. I recommend to remove it.


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

Input:
Title: GENOME-WIDE IDENTIFICATION AND CHARACTERIZATION OF THE FIBRILLIN GENE FAMILY IN TRITICUM AESTIVUM
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Thank you for revising the manuscript. It looks better now, especially in the genome-wide identification and classification parts. There are still some suggestions for your responses and supplementary experiments.
1. The identification and homology comparison in these five monocot species should be compared in detail in the discussion. The analysis of gene structure, function domain and motif distribution of 26 TaFBN genes were good jobs, but the gene function from previous studies among different groups and different species should be introduced. This is important to the following analysis about cis-regulatory and gene expression pattern.
2. The cultivation condition should be more concrete, for example, the soaked “room temperature” in line 118 and germinated temperature should be a certain value. Some typos like the word “NaOCl” in Line117should be checked and revised.
3. The additional qPCR experiments were used to validate the expression profiles of RNA-Seq. The results in Figure 8a should correspond to the tissue special expression patterns of TaFBNs in Figure 6a. The results in Figure 8b, too, should correspond to the expression profile data downloaded from the website. If there is a deviation between website and experiment data, please explain the difference in the discussion.
4. The difference between PEG6000 and drought stress treatment methods should be listed in line 296. The obvious difference in expression profile of 26 TaFBNs between PEG6000 and drought stress should be explained in discussion. Based on the heatmap in Figure 7, the TaFBNs are more involved in cold stress and stripe rust stress. Please explain why you only chose drought stress for the validation of expression profile data.
5. The data of qPCR in Figure 8 were from three biological replicates in line 196, but the standard errors in figure were marked incorrectly, for example the standard errors in “DS-0h” should be 0.


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

Input:
Title: GENOME-WIDE IDENTIFICATION AND CHARACTERIZATION OF THE FIBRILLIN GENE FAMILY IN TRITICUM AESTIVUM
Review round: 2
Reviewer: 2

Output:
Basic reporting: In general the authors amended their manuscript with the recommendations of the reviewers.

However, although the authors mentioned that the text was carefully corrected by professional language company, I still think that some formulations could be omitted ("It must be fortunate that", "As we know"...). The authors can find my suggestions in the annotated manuscript. Some references are missing (wheat genome sequence)
Experimental design: It is good to compute the bootstrap but it is also important to show it! On Figure 3 please indicate the bootstrap support at least for the main clades, a tree without bootstrap values is meaningless!
The authors should provide the accession numbers of all sequences including the non-wheat sequences (Arabidopsis, Zea...)
Validity of the findings: Line 209, the authors find it interesting that all the sequences that they analyze contain a conserved PAP_FBN domain but one of their selection criteria was that to be considered in their dataset, a protein should have a PAP_FBN domain! Maybe that's what is in the Sup. figure S1 and S2 but the captions are missing.

There is still a paragraph misinterpreting the results ll. 313-317 with regards to the polyploidy of wheat and the number of genes identified. Here again you can find the full comment annotated on the manuscript.
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: GENOME-WIDE IDENTIFICATION AND CHARACTERIZATION OF THE FIBRILLIN GENE FAMILY IN TRITICUM AESTIVUM
Review round: 3
Reviewer: 1

Output:
Basic reporting: no
Experimental design: no
Validity of the findings: no
Additional comments: Thank you for the positive response to the previous suggestions. In this article, fibrillin (FBN) family genes were identified and characterized in wheat based on the whole genome of T. aestivum. The expression pattern of TaFBNs in different tissues, developmental stages and abiotic stresses were analyzed and verified by qRT-PCR experiments. It was useful for the research on the wheat resistance. After some modification, the article is better than before. More analyses of results data have been added in the introduction and discussion, and some words and sentences in language and figure format have been corrected. The inconsistent format in references are still obvious, for example, the absence of DOI, the italics of the journal names, the inconsistent paragraph format and so on, check and correct.


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

Input:
Title: GENOME-WIDE IDENTIFICATION AND CHARACTERIZATION OF THE FIBRILLIN GENE FAMILY IN TRITICUM AESTIVUM
Review round: 3
Reviewer: 2

Output:
Basic reporting: Manuscript amended according to the reviewers' suggestions. However, in the newly added parts the English needs some correction. I annotated the PDF wherever I spotted some problems, but again professional English editing would be necessary.
The reference section is weirdly formatted with words and numbers cut in between lines without dashes (for words).
Experimental design: The phylogenetic trees are now correctly displayed with support values but it is good practice to collapse low support nodes (< 50) and to use a symbol (*) for high support nodes (> 99). This should make the trees less crowded. For collapsing the nodes, if the authors don't know how to do it, I would recommend Newick utilities (Junier and Zdobnov 2010; http://cegg.unige.ch/newick_utils).
Validity of the findings: The interpretation of the phylogenetic results is just wrong in the way it was recently amended (please see the annotations on the manuscript). The authors should first check the literature, there is a large amount of studies on phylogenetic relationships, especially between crop species. The close relationship of barley and wheat is known for long and yet, the authors speculate that rice is closer to wheat based on this one gene family and their wrong interpretation of the results while this particular question is not the focus of their study.
Additional comments: Please consider taking on-board a phylogeneticist if you are planning to use evolutionary relationships in your work.


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

Input:
Title: GENOME-WIDE IDENTIFICATION AND CHARACTERIZATION OF THE FIBRILLIN GENE FAMILY IN TRITICUM AESTIVUM
Review round: 4
Reviewer: 1

Output:
Basic reporting: There was still some weird sentence structure and typos. I tried again to annotate on the manuscript the ones that I spotted but I ask the authors to also take care to clean up the maximum of typos, after a third revision I do not expect to see a "The" in the middle of a sentence (see line 91).
Experimental design: The authors made some changes on the Figure 3 as I recommended in the previous revision and reported in the rebuttal letter the method that they used but failed to add these modifications in the methods part and in the caption. Sorry, if I was not clearer previous time but I meant to replace bootstrap values > 99 with an asterisk. Also, I am not sure why the authors suddenly decided to make a phylogram (branch length relative to the amount of changes) instead of the cladogram (branch length meaningless) that they were showing earlier, this should also be possible with a consensus tree with collapsed nodes.
Validity of the findings: Please remove ALL mentions of duplication in wheat. The duplications that the authors are describing are not specific to wheat but common to all plant organisms (at least the ones on the figure 3), the only thing to mention would be that duplications happened a very long time ago. What about much more distant organisms (mosses, algae...).
Actually, the only peculiar thing for wheat is the loss of the FBN group 1 from the D genome, all the rest is in accord with the phylogeny (remember that wheat is hexaploid, so we expect at least three homeologs for each single-copy gene in a diploid species). Among the species included in the figure 3, many species are apparently showing a much more interesting pattern: duplication of group 7 in A. thaliana, duplication of group 3 genes in most dicotyledons, N. tabacum for group 2... but I am aware that it is not the focus of this study.
Additional comments: I strongly recommend the authors to correct all the annotations that I made. I realized that the authors did not necessarily understand the simple annotations so this time I took the time to provide them with full correction. The fact that some simple annotations were not considered by the authors was very upsetting!


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 NEMATODE SPECIES, CHROMADORINA TANGAROA SP. NOV. (CHROMADORIDA: CHROMADORIDAE) FROM THE HULL OF A RESEARCH VESSEL, NEW ZEALAND
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript contains new and original information: description a new species of free-living nematode from the turf algae on the ship’s hull. The species is new for science and properly described. Apart pure taxonomic interest the manuscript contains important ecological information, which drives attention to the role of meiofauna in fouling communities and to the question of invasive species in meiobenthos and how to recognize them.
Experimental design: Standard methods of material collection were used.
Validity of the findings: The paper is well written and contains all the necessary information. I have just minor comments and corrections.
Additional comments: Lines 57-58: C. epidemos not C. berzicki was reported from macroalgae by Hopper and Meyers, 1967. The last species is from periphyton of Danube River.

The author wrote that genus Cromadorina is “largely marine”. It is correct formally, but the presents of brackish and freshwater species is not mentioned in the text. That drives to confusion when reading lines 51-67. It is not clear, which species in the list are freshwater or brackish.

Line 101: Subfamily name is missed.
Line 157 (and several lines in “Diff. diagnosis”): it is better to put quotation on “a” and other indices.
Line 219: How can the nematode lives on microalgae? Do you mean here the specific life-form of diatoms (turf-like colonies) or else?
Lines 201-206 (or 70-73): Please, provide more taxonomic information about the algae that perform the habitat of the described species, if available, or give a description of the live-form (shape, length of filaments), if not. How this substrate looks like?

Figures are of good quality, and, I guess, the photograph of the head end (and probably, male anal region) will be appropriate here.


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 NEMATODE SPECIES, CHROMADORINA TANGAROA SP. NOV. (CHROMADORIDA: CHROMADORIDAE) FROM THE HULL OF A RESEARCH VESSEL, NEW ZEALAND
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comments
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Main remark: when describing a new species, the holotype should be illustrated. No holotype nor paratypes are indicated in the legend of the figures.  Minor corrections (e.g. on terminology, spicule description) are indicated directly on the manuscript.