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: MEASUREMENT ERROR USING A SEEMALAB STRUCTURED LIGHT 3D SCANNER AGAINST A MICROSCRIBE 3D DIGITIZER
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1. Authors carried out the detailed study on 'Measurement error using a SeeMaLab structured light 3D scanner against a Microscribe 3D digitizer'.
2. The English used is quite clear and technically correct. However, the proof reading of the manuscript need to be done while revising the paper.
3. The authors need to read and cite some more relevant and latest papers to improve the content of the paper.
Experimental design: 1. The Introduction section need to be improved further.
2. The research question in this present study needs to be defined in a better possible way.
3. The methods used to carry out the present study need to be more clearly stated.
Validity of the findings: 1. The discussion section must be modified and improved.
2. Include major finding of study in conclusion section.
3. The conclusion section should be precise and can be written preferably in bullet points.
Additional comments: 1. Authors carried out the detailed study on 'Measurement error using a SeeMaLab structured light 3D scanner against a Microscribe 3D digitizer'.
2. The English used is quite clear and technically correct. However, the proof reading of the manuscript need to be done while revising the paper.
3. The authors need to read and cite some more relevant and latest papers to improve the content of the paper.
4. The Introduction section need to be improved further.
5. The research question in this present study needs to be defined in a better possible way.
6. The methods used to carry out the present study need to be more clearly stated.
7. The discussion section must be modified and improved.
8. Include major finding of study in conclusion section.
9. The conclusion section should be precise and can be written preferably in bullet points.


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: MEASUREMENT ERROR USING A SEEMALAB STRUCTURED LIGHT 3D SCANNER AGAINST A MICROSCRIBE 3D DIGITIZER
Review round: 2
Reviewer: 1

Output:
Basic reporting: The revised article looks far better than the original submission.
Experimental design: No comment
Validity of the findings: Good enough. The article may be accepted for suitable publication in its present form.
Additional comments: The revised article looks far better than the original submission. All the comments are addressed properly. The article may be accepted for suitable publication in its present form.


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

Input:
Title: REELING THEM IN: TAXONOMY OF MARINE ANNELIDS USED AS BAIT BY ANGLERS IN THE WESTERN CAPE PROVINCE, SOUTH AFRICA
Review round: 1
Reviewer: 1

Output:
Basic reporting: This ms is clear, with a professional English used, even if the text is not always literary. This paper contains a lot of figures but they are all necesseray to illustrate the different results. Most of the figures are excellent but some of them should be improved (see specific comments in the document).
Experimental design: The experimental design is correctly explained, and the difficulty to sample and collaborate with fishermen highlighted. The different questions are well definied and relevant, provided answers about knowledge gap.

Methods are also well explained and rigorous.
Validity of the findings: The results are very interesting for the scientific community and this study should encourage scientists from other countries to check the species used as bait in their own waters.
Results are robust, illustrated both by molecular and morphological data. Some of the descriptions are relatively light but it's not really a problem as no new species is described. Please check my comments directly on the document.
Additional comments: The manuscript by Simon and collabs is a very important contribution to the knwoledge of South African marine worms, highlighted the presence of important diversity and presence of cryptic species among bait worms collected by fishermen.

In the introduction, I would like to have informations about the baits economy in South Africa: are there profesionnal bait collectors? exportation outside SA? Immportation of baits from other countries? Is it only a recreational activity? presence of bait shops?

I think that the discussion should be extended. In the current version, this part is not enough detailed, especially about the next step of these findings. Are you going to describe new species identified with molecular results? How management of these baits could be improved? Importance of correctly identifying the baits (life traits, biodiversity, habitats). Finally, use of live baits could widespread non-indigeneous species, please say some words abouth this situation in South Africa.


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: REELING THEM IN: TAXONOMY OF MARINE ANNELIDS USED AS BAIT BY ANGLERS IN THE WESTERN CAPE PROVINCE, SOUTH AFRICA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a very interesting work on the marine annelids used as bait in the Western Cape, South Africa. It is comprehensive in the sense that the authors are using morphological and molecular evidence to identify the species, in some cases, they even noticed that one single species is hiding at least two species. The finding that common names can represent more than one species is also relevant and it would have surely management implications in South Africa in the near future.

The manuscript is clear and references are sufficient for background and context, although I found many issues in the format and in some cases the rules of the ICZN have not been followed accordingly.

In general, I identified some main issues that the authors should improve. Therefore, I would like to strongly recommend to the authors the following:
1) To perform the description of Gunnarea gaimardi and Gunnarea sp. 1  separately, each with their own figures, instead of giving only one based upon G. gaimardi. The same goes for the two morphospecies found for Scoletoma cf. tetraura.
2) To compare in detail and provide more distinctions between Gunnarea gaimardi and Gunnarea sp. 1, since more morphological differences can be noticed by comparing the figures of both species.
3) To reconsider using the name Marphysa cf. corallina instead of M. corallina (Kinberg, 1865), to compare the M. cf. corallina specimens with descriptions of M. capensis also from South Africa, and to show the maxillary apparatus in figure(s)
4) To evaluate the possible usage of Lysidice atra Schmarda, 1861 over L. natalensis Kinberg, 1865 since they are apparently synonyms and the former claims priority
5) To improve the description of the species, legends of figures, and some figures themselves as suggested in the text.

Other things that the authors must meet is the standardization of the manuscript according to the format of PeerJ or that one they selected where necessary. For instance, lists of synonyms and figures order. All figures must be cited in order in the main text, therefore the figures in the plates must be rearranged.
Experimental design: All the experimental design is clear and well defined. No further comments needed.
Validity of the findings: The impact of the manuscript and novelty is well addressed by the authors. I think a few more details in the discussion on the management implications of their findings will be more meaningful in conservation terms
Additional comments: The authors addressed this relevant topic in a great manner. Systematics of the species using molecular and morphological data is greatly appreciated, although some corrections should be made. Please check my comments on the pdf attached. Best wishes


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: ASSOCIATION OF SERUM FETUIN-B WITH INSULIN RESISTANCE AND PRE-DIABETES IN YOUNG CHINESE WOMEN: EVIDENCE FROM A CROSS-SECTIONAL STUDY AND EFFECT OF LIRAGLUTIDE
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this cross-sectional study, with a preliminary 6-month interventional investigation, Xia and colleagues address the association of serum Fetuin B with Insulin Resistance (IR) and prediabetes in young Chinese women. Despite of an adequate sample size (127 healthy normal weight women, 80 insulin resistant but normal glucose tolerant women, 97 women with IR and prediabetes), and its interesting findings, unfortunately, the present article is overshadowed by several major flaws and complicated details, that make it difficult to fully appreciate the authors’ work.

-Title
“Serum Fetuin-B levels were elevated in young women with pre-diabetes”. There is no need of using past tense in the title, given that the effects of liraglutide intervention on Fetuin B represented a secondary analysis in a (very) small subgroup of patients. Something like “Association of serum Fetuin B with insulin resistance and pre-diabetes in young Chinese women: evidence from a cross-sectional study and effect of liraglutide” might be more appropriate.

-Abstract
Contrary to what has been stated, the aim of this cross-sectional study was not to analyze “the relationship of between the changes of Fetuin-B and the occurrence and development of IR” (line 28). For this goal, a large prospective observational study should have been designed. Lines 30-32 should be rephrased: “A total of 304 women were enrolled in this CROSS-SECTIONAL study AND SUBJECTED TO BOTH OGTT AND EUGLYCEMIC HYPERINSULINEMIC CLAMP (EHC). A SUBGROUP OF 50 (OR 26?) obese women….”
-Line 37: “independent correlation factor” these terms cannot be used together. Please check the statistical meaning. I would suggest “the M value was independently and inversely associated with serum Fetuin B”.

-Introduction
Lines 96-99 are misleading. The primary aim of the study was to address the association of serum fetuin B with IR, prediabetes and different metabolic indexes in young women subjected to both 2h-OGTT and EHC. Then, in a subgroup of overweight and obese women, according to reference BMI categories for the Chinese population, the effect of liraglutide 1.8 mg/once daily on fetuin B and glycometabolic homeostasis has been investigated, but this was a secondary aim.
In this respect, I would recommend explaining in depth the rationale behind the choice of liraglutide as the body weight-lowering pharmacological intervention (i.e. why not metformin?). Liraglutide is generally used worldwide at doses up to 1.8mg as antidiabetic agent, but higher doses (up to 3.0 mg) have been approved for weight loss in the US and Europe in obese individuals, irrespective of hyperglycemia. Similar to metformin, off-label use of Liraglutide has been also proposed for the management of PCOS in women with overweight/obesity-related IR. One could wonder if these young overweight/obese women were enrolled for intervention with liraglutide due to ovarian dysfunction and refractory menstrual problems.

-Methods
Lines 110-112: After looking at the metabolic indices in table 1, I believe that the Methods section would benefit of a better definition of the IR-NG study group. Actually, the IR-NG patients were those with insulin resistance at EHC (based on the M-value cut-off < 6.28) but with normal blood glucose levels. I would also suggest stating that the presence of prediabetes in this study was defined by the occurrence of IGT at 2h-OGTT. However, some of the enrolled women had also high fasting blood glucose levels (impaired fasting glucose - IFG).
Line 168: The abbreviation “PLSD” should be described in extenso. Was it a Fisher’s Least Square difference test following up to the analysis of variance?
Lines 170-171: Even though correlation and regression have many similarities, I would recommend using “linear REGRESSION analysis” in this sentence.

-Results
Lines 199-200: I do not feel that the range of serum fetuin B levels in 90.5% of healthy women contributes much.
Lines 204-205: I would suggest using BMI cut-offs that are specific for the Chinese population to define overweight/obesity, and then repeating calculation.
Lines 205-209: This paragraph appear tautological and redundant. It is common knowledge that most patients with prediabetes have IR. I would suggest deleting this paragraph or, at least, merging the IR-NG and IGT patients in single group as a supplementary material, exploring the association of IR with serum fetuin levels by regression analysis (adjusting for blood glucose status) and ROC curve.
Lines 221-224: The model was significant only after controlling for age, probably, due to (known) strong correlations between covariates (age, Fat %, BMI, WC, BP, and TG), that create collinearity problems. In regression analysis, how was multicollinearity handled?
Lines 226: Serum Fetuin B concentrations were divided into four QUARTILES, please revise throughout the manuscript text.
Lines 230-234: I do not feel that the use of row mean score and Cochran-Armitage trend test contributes much, whereas it apparently makes the lecture heavier. Also, “incidence” cannot be used in a cross-sectional context.
Lines 235-239: As anticipated in a previous comment, I would suggest presenting ROC curve analysis as a supplementary material, merging IR-NG and IGT women together. Otherwise, the paradoxical finding of a higher cut-off value of fetuin B in predicting IR-NG that the one predicting IGT (5.44 mg/dL vs 4.45 mg/L) need to be discussed. Indeed, IGT women and not IR-NG women presented the highest concentrations of serum fetuin B in this study.
Lines 247-248: This sentence is tautological, given that IR-NG women were arbitrarily defined by M values below 6.28.
Lines 255: 26 or 50 women? Please check and revise anyplace in the manuscript text/Table 5.

-Discussion
Overall, the discussion reads well. However, I would suggest revising line 279 according to the comments stated above (i.e. redundance of correlation with IR).

-Tables
Please, present the normally distributed data as Means ± Standard Deviations (in spite of standard error).
Table 2: Table title should be revised, given that this is not a Pearson correlation matrix.

-References
Literature review may benefit of two recent references on this topic (adipokines and effects of liraglutide in women, respectively):
- EBioMedicine. 2020;59:102912. doi:10.1016/j.ebiom.2020.102912
- Int J Environ Res Public Health. 2019;17(1):207. doi:10.3390/ijerph17010207
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: ASSOCIATION OF SERUM FETUIN-B WITH INSULIN RESISTANCE AND PRE-DIABETES IN YOUNG CHINESE WOMEN: EVIDENCE FROM A CROSS-SECTIONAL STUDY AND EFFECT OF LIRAGLUTIDE
Review round: 1
Reviewer: 2

Output:
Basic reporting: This article should be correct English.
This manuscript includes sufficient introduction and literature references.
Experimental design: This article got missing several positive controls and validation.
Validity of the findings: Authors should increased serum Fetuin-B levels in women IR and IGT patient groups. However, the totality of the results wasn’t enough to support their conclusions and very limited study.
Additional comments: The manuscript by Xia X. et. al. presents ‘Serum Fetuin-B levels were elevated in young women with 2 pre-diabetes’. This manuscript explored Fetuin-B as a biomarker in pre-diabetic patients. Some studies already reported function of Fetuin-B in metabolic diseases (Meex et al, 2015, Kralisch et al, 2017, and Li et al 2018). Otherwise, controversial papers also suggest (Ebert et al. 2017). In this study, authors investigated the correlation of serum Fetuin-B and human IR and IGT including BMI and lipid metabolism. However, some important data were missing like OGTT and ITT test data. And so, the totality of the results wasn’t enough to support their conclusions and very limited study. There are also some concerns and questions with this manuscript.

Comments
1.	In figures, authors didn’t
2.	Authors mentioned that most of the previous studies were cross-sectional and descriptive studies. They were merely a preliminary exploration of Fetuin-B on line 293~295. However, they didn’t suggest the reason why previous studies were cross-sectional and descriptive studies. Moreover, they said on line 332~334 like ‘Our research has some limitations, including that 1) our study is a cross-sectional study, so we can not infer the causal relationship between Fetuin-B and the occurrence and development of IR’. These suggestions were not consistent of their hypothesis.
3.	They suggest that hyperinsulinemia leads to increased circulating Fetuin-B. However, authors didn’t measure blood insulin levels in this study directly.
4.	And authors chose women as the research subjects to avoid the influence of sex hormone on insulin sensitivity in vivo. But generally, women get influence of sex hormone and other hormone compared to men. So, they should confirm those effects on men subjects.
5.	In figure 3A, authors measured Fetuin-B levels during OGTT. They suggest that Fetuin-B level is correlated with glucose level and IR level. However, OGTT data was not shown to show the correlation of Fetuin-B and IR or blood glucose level. Moreover, in NGT group, blood glucose level might be decreased after120 min. If Fetuin-B level is correlated with blood glucose level, Fetuin-B level should be decreased to the normal level. But serum Fetuin-B level was not decreased in 120 min time point.
6.	In table 1, HbA1c levels in IR-NG and IGT were in normal range below 5.6. So, their IGT and IR-NG patient groups should be validated again.
Minor comments
1.	This manuscript should be edited several spelling errors like Fetiun-B on line 322 and grammatic errors.
2.	Figure legends were duplicate.


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: ASSOCIATION OF SERUM FETUIN-B WITH INSULIN RESISTANCE AND PRE-DIABETES IN YOUNG CHINESE WOMEN: EVIDENCE FROM A CROSS-SECTIONAL STUDY AND EFFECT OF LIRAGLUTIDE
Review round: 2
Reviewer: 1

Output:
Basic reporting: Manuscript has been considerably improved according to this reviewer suggestion. I have only minor comments:

-Lines 169-171: Please delete this sentence, as the results of Cochran-Armitage trend test and Row Mean Scores analysis have not been included in the revised version.

.To improve readability of this manuscript, I would recommed to report in the introduction section that off-label use of Liraglutide has been proposed for the management of PCOS in women with overweight/obesity-related IR. Also, since women on Liraglutide in this study were affected by ovarian dysfunction and menstrual problems, it would be interesting to mention if there were any clinical improvement in menstrual cycles following pharmacological intervention.
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: WHERE IS MY ARM? INVESTIGATING THE LINK BETWEEN COMPLEX REGIONAL PAIN SYNDROME AND POOR LOCALISATION OF THE AFFECTED LIMB
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is an interesting study on an important topic. There are not many studies investigating self localization in chronic pain patients. Especially the difference between the affected and the unaffected had side as found here (hypothesis 3) is very interesting. But also the impact of the factors age and anxiety on error performance are important findings.
The language is correct-the writing very good. The Intro & background to provide a comprehensive overview about the  context and the literature is well referenced & relevant.  The Structure conforms to the standards. The Figures are relevant, high quality, well labeled & described. It might be interesting for people not knowing the DHT paradigm to include a methods figure illustrating this paradigm. As far as I could overview there were no raw data included. However, the data are plotted very clearly in the figures and additional raw data might not be necessary here.
Table 2 and Table 3 seem to be completely taken from the stat. software. I think it should be presented more user friendly. In addition please describe stat. values also in the Results section. It is quite difficult for the reader to find the stat. results in the table when not explicitly provided in the text.
Experimental design: The original primary research is within the scope of the journal.  The research question well defined, relevant and meaningful. The investigation was performed to a high technical and ethical standard. Overall, methods described with sufficient detail and information to replicate. The statistical comparisons are sound and described correctly.
Validity of the findings: The findings are highly informative and new. The assumptions made from these findings are justified. Replication of the paradigm possible with the information provided. Conclusions justified.
Additional comments: The following information might be provided:
A. Illustration of the experiment in a methods figure.
B. Improve readability of Table 2 and 3
C. Insert stat. values in the Results section.
D. Discussion (page 16, top): It is not comprehensible that the authors discuss distortion of somatosensory finger representation when addressing body matrix changes in CRPS. It would be more appropriate to address findings on the (right) intraparietal sulcus here.
Also on page 17: “…visually encoded data outweighs proprioceptively encoded data is greater for the affected than the unaffected hand in these groups…” The increased effect of the illusion in CRPS patients might well be related to proprioceptive impairment then? The same in elderly: decrease in visual function decreases then DHT effect since it is based on ten visual domain.
Might be also an issue for the limitations: visual and proprioceptive performance not explicitly tested here.
Conclusion: not very creative- just a mere repletion of main results.
Minor:
Citation error line 366: “First, Di Pietro et al (CITE)’s meta-
...“


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: WHERE IS MY ARM? INVESTIGATING THE LINK BETWEEN COMPLEX REGIONAL PAIN SYNDROME AND POOR LOCALISATION OF THE AFFECTED LIMB
Review round: 1
Reviewer: 2

Output:
Basic reporting: All good.
Experimental design: Some suggested improvement to analysis made in attached document. Otherwise, all good.
Validity of the findings: No comment (all good).
Additional comments: This ms describes using creating incongruence between seen and felt hand positions in order to test the implicit localisation of the hand in CRPS alongside non-CRPS and non-pain controls. The results do not bear out a particular localisation deficit in CRPS, but do suggest that the affected hand is not localised as accurately in CRPS and non-CRPS pain. The ms is well-written, although the authors fall into the trap slightly of not being able to put themselves in the shoes of someone who has never seen the DHT. Overall, this is publishable, but there are (as always) a number of points to consider/address. Most of these are entirely unproblematic, some require further thought, explanation or discussion.

Potentially problematic:

The introduction is clear, but the hypotheses are missing a step from the introduction. There is no discussion in the introduction around limb localisation in people with non-CRPS chronic pain. This is required in order to formulate the hypotheses involving the non-CRPS pain group. If no data exists, the this becomes more exploratory than hypothesis driven.

It is not clear whether error was absolute or directional. Which was it and why? It would seem from Figure 1, and supplementary figures, that error was coded as absolute, but is this fair? Presumably, in the static and hidden hand conditions, errors could be slightly to the left (say, -ve) and right (+ve) of the real hand, but in the DHT, the error could only ever be +ve (towards the visual representation (is that right?). If you do that, then you lose the characterisation of noise around the judgment that is made absolute in the Static and Hidden conditions, but remains directional in the DHT measurements. The upshot of this is that you reduce the variability in the static condition and not in the DHT. It might also disguise directional errors in your CRPS group that you might expect to see if you subscribed to the spatial neglect hypothesis.

Points needing further discussion:

The argument around usage and weighting is interesting. The results here suggest that proprioception itself is not the problem, but that it may be given less weighting is. That could help to explain why CRPS patients ‘lose track’ of where their hand is in daily living. Not using the hand fails to update representations and proprioception is (sort of) ignored. CRPS patients tend not to like looking at their affected hand either. Thus, without using the hand, looking at it or integrating proprioception from it effectively – how are you to know where it is? You only know by looking at it and they don’t do that if they can help it. I can imagine the mechanisms being similar to asomatognosia (which the DHT was designed to replicate according to the original) – failure to look towards the hand plus lack of proprioception and lack of motor updating = missing hand. Just a thought.

Is it interesting that pain ratings did not affect errors? Does this suggest that it is not pain per se that disrupts body representations, but the condition itself? Maybe not, if the affected hand is mislocalised more in both pain groups.

I am intrigued by the anxiety observations (more so than the authors, I suspect). If I have interpreted the results correctly, raised anxiety seemed to lead to greater errors. Why would this be? I think that the authors do not consider this point enough. Could increased errors, when anxious, be a result of even greater weighting on visual input? What could cause this? Is there something about the task that would make patients with CRPS (and fearful of coming into contact with anything) pay such close attention to their hand that reliance on visual input was increased? Their hands were in a ‘machine’ for starters. I wonder whether future studies could measure anxiety DURING the procedure. Or does anxiety disrupt integration in some way, helping to explain why patients lose connection with their affected hand?

I can’t help noticing that error for the unaffected hand (CRPS) in the Hidden condition seems to be larger than the affected. Is this in an interaction somewhere? If so, what is the explanation? I feel really mean, pointing this out because it’s probably nothing and not predicted at all (so why would you even look at it, right?), but it is there.

In a task that works through normal sensory integration processes, what is good or accurate performance? In a sense, being more ‘accurate’ could suggest poorer healthy integration. And this changes across time points. At T1, locating the hand close to the visual representation would suggest poor integration (total visual dominance); locating the hand close to the real hand would also suggest poor integration (total reliance on/ability to exclusively access proprioception). Somewhere in between (medium inaccurate) is good. At T6, locating at the last seen location is bad, locating at the true felt location is really good, locating somewhere in between is either ok or not being able to access proprioception. And the rate of change between T1 and T6 would tell another story. Anyway, just be careful about how you think about and describe performance and accuracy.

Things that are easy to fix:

Line 113: “importance of testing performance during implicit tasks is quite well established in studies with spatial people with neglect” In people with spatial neglect?

In parts of the paper (e.g. abstract) patients are referred to as having hand pain, but in the methods they are described as having upper limb pain. Can we have more details or more accurate descriptions of where the pain was located in the two patient groups?

When introducing the DHT, I think that it would be useful for the reader to explain that this leads to a localisation weighting that is biased towards the visual representation of the hand. This would help when, later, discussing re-weighting towards proprioception over time.

DHT procedure. If the participants move their hands outwards, why are they not aware of this? Ah, this is covered later in the manipulation check. Excellent. I wonder if it would be worth referring to, or signposting, this earlier.

Why is it called the Hidden Hand condition? When/how was the hand hidden?
Which hand were they asked to look at? How did it disappear?
It seems that the arrow always moved outwards. Would this bias localisation? In the Disappeared condition, the arrow would always pass over the real location of the hand, yes? Would this draw attention towards the real hand and/or boost the signal for its location due to congruent hand position and gaze direction? It actually makes little difference because it was the same for all groups, but in terms of future experimental robustness, I think that the arrow should start at different sides of the hand on each trial.

The methods seems to suggest that the hands always stayed in their own hemispace. Could a future manipulation be to have the hands appear to be in one hemispace, but actually be in another? (You can have that one for free!).

I think you need to explain why the error was measured in pixels. Presumably, this is because both the arrow and the hand were seen via a screen, but it can be confusing if you use terms like measuring the real position of the hand (end of self-localisation section).

What are T1-T7? These do not seem to have been mentioned before data analysis. Oh, right! These are the 6 arrow trials (perhaps call these Tx-Ty at that point), but where does the 7th come from?

It is not clear why Error over Time (T1-T7) was a factor for one hypothesis and average Error over the same time period was used for another hypothesis.

Some of the graphs in the supplementary materials refer to DHT, others to Incongruent. Please check all instances and be consistent. Although the DHT was used, incongruent (for DHT) and congruent (for Hidden) seem to make more sense here – although Static was also congruent…

Figure captions: These are not as helpful as they could be. Fig 1 – what are the individual dots? Are these individual participant scores? If so, why are there more dots than participants? Why can I not reconcile the 150+ blue dots in the CRPS group with the individual Hidden hand plots in Supplementary Figure 1? I don’t know what Figure 2 is showing. More explanation, please.

Anxiety AND CRPS seems to blow hand localisation. How interesting! I would consider changing the groupings for Fig 3. Supplemental figure 3 is much more compelling than the ms figure 3.

The first line of the discussion reads:
“This study aimed to evaluated hand-localisation …”
It either aimed to evaluate or it evaluated. I think you did evaluate, so I’d be happy with the latter, but I know that some people can get funny about that kind of thing.

The discussion claims that “people living with non-CRPS hand pain not only showed smaller difference between the DHT and control conditions – possibly indicating a smaller susceptibility to the illusion…” but this is not borne out by the statistics as far as I can see.

The tactile paragraph seems out of place here. How does it link to this experiment? Does it need to be in here at all?


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

Input:
Title: WHERE IS MY ARM? INVESTIGATING THE LINK BETWEEN COMPLEX REGIONAL PAIN SYNDROME AND POOR LOCALISATION OF THE AFFECTED LIMB
Review round: 2
Reviewer: 1

Output:
Basic reporting: Very good
Experimental design: Very good
Validity of the findings: Very good
Additional comments: Thank you for considering all of the points raised and giving a thoughtful and balanced response to each. I look forward to seeing this published.


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

Input:
Title: ASSOCIATION BETWEEN C-MAF-INDUCING PROTEIN GENE RS2287112 POLYMORPHISM AND SCHIZOPHRENIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: None
Experimental design: None
Validity of the findings: None
Additional comments: This paper conducted a genetic study that have evaluate the genetic association between CMIP gene and schizophrenia in a Han Chinese population. Although this is a positive study, which may provide valuable information, there are several major problems:
(1) Please provide the full name of CMIP in the title and abstract
(2) More background information about the relationship between CMIP gene variant and schizophrenia, latest progress and related mechanisms should be provided to tell readers why you exert the study.
(3) Please add related hypotheses in the introduction.
(4) Please provide a table for primer information.
(5) Authors should provide more demographic characteristics in the included subjects in order to further explore the interaction between gene and environment.
(6) Sex difference should provide the completed findings, such as alleles and genotypes distribution, model analysis, linkage disequilibrium and haplotype analysis.
(7) Please re-check table 3.
(8) Please provide a figure about linkage disequilibrium in total population.


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: ASSOCIATION BETWEEN C-MAF-INDUCING PROTEIN GENE RS2287112 POLYMORPHISM AND SCHIZOPHRENIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this research, Fu et al., conducted association analyses between 4 SNPs in CMIP with schizophrenia and found the allele frequency of rs287112 is significantly different between schizophrenia patients and healthy controls in female Han Chinese population. Further analyses showed that haplotype TTGT of rs12925980-rs2287112-rs3751859-rs77700579 had a lower risk for schizophrenia when compared to CTGA haplotypes. In all, the manuscript is clearly written except for some minor problems. However, whether such an association report is qualified to published in PeerJ needs to be considered. Here are my detailed comments:
1.	As this study is an association analyses, there is no one reference about the genome wide association study (GWAS) of schizophrenia. In recent years, many GWASs with more than 100,000 samples were reported, like [Pardinas et al., 2018, Nat Genet; Lam et al., 2019, Nat Genet; PGC, 2020, medRxiv]. Specially, the authors should read the Lam paper, which reported the largest study to date of East Asian participants (22,778 schizophrenia cases and 35,362 controls), and query whether the 4 SNPs (rs12925980, rs2287112, rs3751859 and rs77700579) were significantly associated with schizophrenia.
2.	If the rs287112 is related to schizophrenia, the authors should verify this result in large samples.
3.	About figure 1, there is no need to show D’, R2 is enough to elucidate the LD. In addition, the authors can add the structure information of CMIP gene above the figure to show the position relationship of 4 SNPs and CMIP.

About the writing:
1.	Line 37-38, “...in a Han Chinese female population” to “...in the Han Chinese female population”? Please consider it clearly.
2.	Line 89-90, “the threshold for MAF of all these four SNPs was set 90 greater than 0.05 in Chinese Han population (CHB).”, here, “set” may be not suitable.
3.	Line 96-99, a space in the primer sequences. Please check it carefully.
4.	Line 159, “...in CMIP was to be associated with...” to “...in CMIP was associated with...”
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: ASSOCIATION BETWEEN C-MAF-INDUCING PROTEIN GENE RS2287112 POLYMORPHISM AND SCHIZOPHRENIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: None
Experimental design: None
Validity of the findings: None
Additional comments: Thank you for your revision. But I still have some minor issues as follow:

1 please recheck the units and names to ensure the accuracy.
2. Some abbreviations such as GWAS, gene names should be presented full name when they first used.
3. Line 77. "...a Han Chinese population" to "the Han Chinese population".
4. Genetic models will give us more information. So I suggest authors to perform related analyses.
5.Line 192. "presented evidence" to "presented an evidence".
6 .Table 3. Please use “lower n” rather than "upper N"
7.Table 3 ,4 and 5. Please add the footnote about OR and CI.
8. Continuous Table 4 is same as Table 4. Please check them.
9. Figure 1. Please provide legend about A .B .C .D


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: ASSOCIATION BETWEEN C-MAF-INDUCING PROTEIN GENE RS2287112 POLYMORPHISM AND SCHIZOPHRENIA
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have addressed all of my concerns.


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: ASSOCIATION BETWEEN C-MAF-INDUCING PROTEIN GENE RS2287112 POLYMORPHISM AND SCHIZOPHRENIA
Review round: 3
Reviewer: 1

Output:
Basic reporting: None
Experimental design: None
Validity of the findings: None
Additional comments: None


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: PHYLOGEOGRAPHY OF HIGH ANDEAN KILLIFISHES ORESTIAS (TELEOSTEI: CYPRINODONTIDAE) IN CAQUENA AND LAUCA SUB-BASINS OF THE ALTIPLANO (CHILE): MITOCHONDRIAL AND NUCLEAR ANALYSIS OF AN ENDANGERED FISH
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well written, the tables and figures are adequate, but the methods, results, and discussion are not well done.
The objective of the work seems confusing since they propose to evaluate the phylogeography of Orestias, but then they say that the results will provide evidence of speciation. I suggest eliminating speciation from the objective since it cannot be evaluated with the methodology and data used.
Experimental design: The substitution rate of 6% used from the previous paper is wrong. First, this rate is coming from Burridge et al. 2008, but the rates estimates in this paper are <1%. Second, the rate estimated in Burridge et al. 2008 is for the Galaxiidae family a fish group belongs to another order, not related to Orestias.
I strongly suggest the authors calculate their own rate using geological and biogeographical information in the absence of fossils of the genus. Thus, the results and their re-interpretation could change the proposed scenario and be more striking to a wide audience.
Suggestion: Calculate the substitution rate in BEAST software using its D-loop sequences combined with those of Vila et al. 2013 and calibrate the split between the Titicaca clade (outgroup) with the ingroup clade. It is estimated that in 3 million years the appearance of the Titicaca or 5-2 the rise of the Andes Range.
Use the rate obtained for the clade of interest and make the demographic analysis again.
Validity of the findings: I find it an interesting manuscript since it generates new findings on the phylogeography of the genus Orestias in the Altiplano. However, the analysis and results are not original or new for a large audience. However, it could be if the authors improve their data analysis. All the evolutionary inference in the discussion is based on the demographic analyses based on a very high substitution rate for a fish population (6%). I strongly suggest the authors calculate their own rate using geological and biogeographical information in the absence of fossils of the genus. Thus, the results and their re-interpretation could change the proposed scenario and be more striking to a wide audience.
Additional comments: Dear Authors
To make your study more visible and novel, I suggest calculating a D-loop gene substitution rate and doing the demographic analyses again. This will not only generate a more accurate estimate but would also be very useful for other studies.


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: PHYLOGEOGRAPHY OF HIGH ANDEAN KILLIFISHES ORESTIAS (TELEOSTEI: CYPRINODONTIDAE) IN CAQUENA AND LAUCA SUB-BASINS OF THE ALTIPLANO (CHILE): MITOCHONDRIAL AND NUCLEAR ANALYSIS OF AN ENDANGERED FISH
Review round: 1
Reviewer: 2

Output:
Basic reporting: Abstract – The MS has two parts: phylogenetic analysis D loop and Microsatellite, reconstructed biogeographic histories. I think the readers would appreciate it if you add a sentence stating the aim of the study (mentioning the different parts) before presenting a summary of the results of each part.

My comments on the introduction are mainly on framing the study.

Materials and methods - Taxon sampling please make sure.

Reference - Please make sure about PeerJ format.
Experimental design: For research ethics purposes, cite (in acknowledgment), where applicable, permits acquired to conduct the field sampling.
Validity of the findings: - As mentioned in the previous section, give more context on current lit in the introduction.
Additional comments: - I enjoyed reading your MS but struggled to easily grasp the details largely because of how results were presented and having had to go back and forth from one figure to another. I think your figures are good but contain too much information and need to be explained for e.g. see sections of the discussion. With a little tweaking of how results are conveyed- I think the paper will be widely read and comprehended easily.


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: PHYLOGEOGRAPHY OF HIGH ANDEAN KILLIFISHES ORESTIAS (TELEOSTEI: CYPRINODONTIDAE) IN CAQUENA AND LAUCA SUB-BASINS OF THE ALTIPLANO (CHILE): MITOCHONDRIAL AND NUCLEAR ANALYSIS OF AN ENDANGERED FISH
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript was improved substantially, the tables and figures are adequate, but the methods, results, and discussion are not well done yet.
Experimental design: I do not agree with the substitution rate of 6% used from the previous paper (Guerrero-Jimenez et al.) because is wrong. First, this rate is coming from Burridge et al. 2008, but the rate estimates in this paper are <1%.
I strongly suggest the authors calculate their own rate using geological and biogeographical information in the absence of fossils of the genus. Thus, the results and their re-interpretation could change the proposed scenario and be more striking to a wide audience.
Alternatively, the authors could be using several rates 1 - 3 - 5 %(susbst./My) and compare results. Use these rates obtained for the clade of interest and make the demographic analysis again.
Validity of the findings: I find it an interesting manuscript since it generates new findings on the phylogeography of the genus Orestias in the Altiplano. However, the analysis and results are not original or new for a large audience. However, it could be if the authors improve their data analysis. All the evolutionary inference in the discussion is based on the demographic analyses based on a very high substitution rate for a fish population (6%). I strongly suggest the authors calculate their own rate using geological and biogeographical information in the absence of fossils of the genus. Thus, the results and their re-interpretation could change the proposed scenario and be more striking to a wide audience.
Additional comments: Dear Authors
I insist to make your study more visible and novel, I suggest calculating a D-loop gene substitution rate and doing the demographic analyses again. This will not only generate a more accurate estimate but would also be very useful for other studies.
I will not accept the manuscript until you calculate your own rate or use several (1-5%) and compare your results. I don't know why they don't do it if it is so easy. The discussion is very appropriate to the times obtained with the rate used and they could change. It appears the authors are trying to use a rate that fits a beautiful evolutionary history of Orestias populations, but it would be properly scientific to calculate a rate, get the results and look for a correct interpretation.
Best regards


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

Input:
Title: PHYLOGEOGRAPHY OF HIGH ANDEAN KILLIFISHES ORESTIAS (TELEOSTEI: CYPRINODONTIDAE) IN CAQUENA AND LAUCA SUB-BASINS OF THE ALTIPLANO (CHILE): MITOCHONDRIAL AND NUCLEAR ANALYSIS OF AN ENDANGERED FISH
Review round: 3
Reviewer: 1

Output:
Basic reporting: t seems to me that you have significantly improved the manuscript in your results and interpretation. However, I insist that the authors should include the new mutation rate calculation results in the manuscript or in the supplementary since they do not appear in either file.
The English should be checked by an English-native speaker, as there are incorrect sentences. For example, you cannot start a sentence with: And we perform certain analyses... Nor should you start a sentence with the abbreviated species name: O. ascotanensis is....
Experimental design: The methods are better, but I suggest making a Bayesian Skyline plot (BSP) for the demographic history using d-loop. The analyses that have been done to calculate the time of expansion have been criticized and do not consider the population genealogies. Also, neutrality tests and mismatch distribution plots are not conclusive, they only allowed to say that populations are not in Wright-Fisher equilibrium. As the BEAST analysis has already been done, it would be very easy to do BSP with the newly calculated rate.
Validity of the findings: There are no values for the estimated rate in the results, nor in the supplementary material. I insist that this is the opportunity for other researchers to make the same analysis, and for that, the methods and results should be clear and the article could be more cited.
I suggest that they should include in a table or graphs the values of the rates obtained with their confidence intervals. In the same way, the BSP estimates the expansion time.
Additional comments: Dear Authors
This is an opportunity to take your article to a higher level and clearly demonstrate how these fishes have evolved in such an extreme environment.
I urge you to improve the results of the work. They should show the results of the rate estimates, otherwise, it is not possible to know what they did. We do not need more obscurity in science.
It is an easy task and should not take so much time.
Best regards


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

Input:
Title: A POSSIBLE BRACHIOSAURID (DINOSAURIA, SAUROPODA) FROM THE MID-CRETACEOUS OF NORTHEASTERN CHINA
Review round: 1
Reviewer: 1

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

This is an extremely well-written and thorough MS describing a new sauropod specimen from the late Early Cretaceous of China, with an interesting and surprising identification. Based on the available data (both presented here and more broadly), the identification of this specimen as a brachiosaurid is as well-supported as possible. I’ve provided a small number of minor comments on an annotated version of the MS and have one slightly more substantial comment here.

Although I think the MS does a good job of exploring the possible alternative identifications, I think there is one possibility that is not fully covered and I would urge the authors to add some further caveats to their study. Firstly, we know very little about non-titanosaurian somphospondylan maxillary evolution (and arguably essentially nothing if Euhelopus lies outside of Macronaria). As such, it is conceivable that the presence of twisted maxillary teeth characterizes Titanosauriformes more widely (especially if Europasaurus lies outside of this clade). I’d strongly recommend highlighting this knowledge gap as a possible issue with a brachiosaurid identification, essentially saying that new materials of ‘basal’ somphospondylans are needed to ultimately test this, but that current evidence indicates that it’s a unique synapomorphy of Brachiosauridae. The second caveat is what do the rest of the sauropod specimens from the site indicate taxonomically? Is there any clue from (presumably) preliminary observations? Because if you ultimately identify a single somphospondylan taxon from these remains (or find no unequivocal evidence for taxa outside of that clade) and the maxilla is the only anomaly, it will perhaps seem increasingly likely that the maxilla belongs to that taxon instead and the twisted maxillary teeth reflect either convergence or a wider synapomorphy.

I think these caveats will strengthen your paper and somewhat ‘future proof’ it if we do eventually find an unequivocal somphospondylan with twisted maxillary teeth.

Best wishes,

Phil Mannion


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 POSSIBLE BRACHIOSAURID (DINOSAURIA, SAUROPODA) FROM THE MID-CRETACEOUS OF NORTHEASTERN CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The main structure of the manuscript is adequate, the tables provide useful data, and the figures are of good quality. The authors show an impressive knowledge of the previous references, and cite them correctly through the text. The English is professional and the sentences clear, which make the text easy to read and follow.
Generally, the content is really interesting, and provide interesting information about a cranial element found in the Longshan locality (mid-Cretaceous, China), which probably belonged to a brachiosaurid sauropod.
Experimental design: The research question and methods are well described, and properly developed in the manuscript.
Validity of the findings: The results are interesting, and provide new information on the Cretaceous sauropod faunas from China, and also sauropod teeth replacement generation and patterns. The authors also provide an updated phylogenetic analysis, and improve some previous palaeobiogeographical hypotheses, which help to explain the occurrence of a middle Cretaceous Asian brachiosaurid.
Additional comments: Generally, this work is of good quality and interest. However, I would suggest to address two points that could impove the manuscript:
- Although the authors provide references which describe with more detail the geology and location of the site, I would suggest including a map, at least for placing the site.
- I think the authors confused the antorbital fenestra with the narial fossa. I suggest checking this, and adapt the description, comparison and scoring of this feature in the matrix depending on the identification.


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

Input:
Title: ASSESSMENT OF METRICS IN NEXT-GENERATION SEQUENCING EXPERIMENTS FOR USE IN CORE-GENOME MULTILOCUS SEQUENCE TYPE
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this study, the authors performed benchmark tests of three major genome assemblers, SPAdes, CLC, and SKESA. They used Seqtk to simulate different read lengths and read depths from Campylobacter jejuni NCTC strains 11168, Escherichia coli IAI39, Listeria monocytogenes EGD-e, and Salmonella enterica LT2. They compared the number of the “completeness of core genes" and the time required for assembling simulated reads with several read depth among the three assemblers. As a result, the SPAdes assembler outperformed and required fewer read depths to recover original genes compared with CLC and SKESA. On the other hand, the assembly time increased according to the sequence depth, particularly when it was more than 100×. The assembly time required by SKESA and CLC did not change much even at a sequence depth of 500×.

The manuscript is written in clear English, but lacks in-depth discussions. For example, the authors should mention previous reports such as "Segerman B. Front Cell Infect Microbiol. 2020; 10: 527102.", "Molina-Mora JA, et al. Sci Rep. 2020; 10(1): 1392." and so on in Introduction or Discussion. In addition, this manuscript does not include raw data of simulated read data. Please add the data or more detail of Seqtk setting to allow other researchers to replicate.

More minor point; the image qualities of Fig. 1 and 2 are a little rough.
Experimental design: As stated above, the authors estimated the performance of three assemble programs using simulated read data. The comparative evaluation would be important for many researchers utilizing next generation sequencers.

However, the assemble details such as specified options were not provided. This information would be needed to understand the results concisely. And then, there would be some differences between the simulated data and real sequenced data. The authors would need to take into consideration the difference and explain it. Alternatively, the authors may be able to compare assembled data using public-deposited short sequencing data of bacterial complete genomes.
Validity of the findings: Although they compared completeness of core genes and the time required for assembling, they did not show whether there are significant differences among the three programs. If the authors could perform a statical analysis, the quality of this paper would be enhanced.

They also showed the number of core-gene differences between assembly and the three reference genomes in Table 2. Does the number mean unrecalled genes? I do not understand the reason that they exclude C. jejuni in this table. And then, there were several different genes in S. enterica and E. coli at even 100× read depth. Did these genes have any similarity? Why did L. monocytogenes show limited different gene number? Please add experiments or explanations concerning these questions to the discussion.

Souvorov et al. described "we showed that the quality of SKESA assemblies is better than both SPAdes and MegaHit" (Souvorov A. et al. Genome Biology 2018; 19: 153). Please explain the reason of this discrepancy.
Additional comments: I described my comments and questions above.


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

Input:
Title: ASSESSMENT OF METRICS IN NEXT-GENERATION SEQUENCING EXPERIMENTS FOR USE IN CORE-GENOME MULTILOCUS SEQUENCE TYPE
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this manuscript, the authors describe how a simple metric, the genes called by a cgMLST tool, varied in simulations of genome sequences with various coverage depth and read lengths. This is an interesting question, but the analyses done are very limited and the results are not always presented clearly in figures or tables, without enough information for the reader to understand quickly.

Use present tense at the end of Abstract (last two sentences)

Lines 88-92 Need to revise sentences structure, these are missing words or are not grammatically correct

Line 111 Not clear here what is considered a threshold “to recover original genes”. Do the authors mean all genes or some proportion are recovered at a certain coverage?

Line 145 What is meant by real data ?  The authors need to specific if these are raw reads or quality controlled reads (errors corrected) and indicate some information about average read length, etc.
Experimental design: The most important factor that has not been considered is the quality of reads and the potential of sequencing errors affecting read calling for cgMLST. Genes called is an important metric, but should be considered in conjunction with alleles called.
Validity of the findings: The findings are valid, but more care should be taken in explaining the data used in each simulation (quality of the genomes, level of assembly, raws read used or not, etc).

Figure 2 is superfluous, it contains information that can be summarized in a sentence.

Table 1. It is not immediately clear what metric is used to judge the performance of different assemblers with the two read lenghts
Additional comments: No additional comments


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

Input:
Title: ASSESSMENT OF METRICS IN NEXT-GENERATION SEQUENCING EXPERIMENTS FOR USE IN CORE-GENOME MULTILOCUS SEQUENCE TYPE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript by Liu et al. was improved, but some minor points need to be revised.

#1. Concerning Table 1 and 2, those right-side columns (probably x100?) were lost in the manuscript file. The authors would need to adjust the table or some settings of the file.

#2. (Fig. 1, Table 1, Table 2, and so on) Please add spaces between numbers and units (ex. "150 bp").

#3. The information of unrecalled core genes at depth 100x might be useful for some public health researchers, since the data indicated that there are some difficulties to be recalled in the genes. The authors showed the data in their rebuttal letter. I would like to suggest the authors to include the data in the manuscript or supplementary data.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I described my comments in "Basic reporting" section.


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

Input:
Title: ASSESSMENT OF METRICS IN NEXT-GENERATION SEQUENCING EXPERIMENTS FOR USE IN CORE-GENOME MULTILOCUS SEQUENCE TYPE
Review round: 3
Reviewer: 1

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: INHIBITION OF KELCH-LIKE EPICHLOROHYDRIN-RELATED PROTEIN 1 PROMOTES THE PROGRESSION AND DRUG RESISTANCE OF LUNG ADENOCARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: In the manuscript entitled “Inhibition of Kelch-like epichlorohydrin-related protein 1 promotes the proliferation and drug resistance of lung adenocarcinoma”, the authors illustrated that Keap1 knockdown promotes tumor cell growth, proliferation, invasion, metastasis and chemotherapy resistance in lung adenocarcinoma. There are a few comments that should be addressed to further improve the manuscript.
Experimental design: 1.	The authors should consider including the public database like the TCGA database to demonstrate the Keap1 level difference between patients and healthy control in figure 1.

2.	In figure 3, the authors demonstrated that Keap1 knockdown increased cell proliferation. However, in figure 4, Keap1 knockdown increased cell migration and invasion. Please clarify if the cell migration and invasion is in fact directly affected by Keap1 knockdown, rather than caused by the increased cell proliferation.
Validity of the findings: 3.	What is the rationale to choose A549 and H1299 cell lines for in vitro study? The authors should discuss this in the manuscript. Moreover, in figure 1, these two cell lines showed different Keap1 level, which seems as if these two cell lines have different cell capabilities. However, both cell lines have shown similar results in figure 2,3,4, and 5, which should be further clarified.
4.	There are no scale bars in figure 4A and 4C. Please update the figures with scale bars for clarity.
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: INHIBITION OF KELCH-LIKE EPICHLOROHYDRIN-RELATED PROTEIN 1 PROMOTES THE PROGRESSION AND DRUG RESISTANCE OF LUNG ADENOCARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors provide sufficient background and the article is well structured with detailed supporting data leading to addressing the questions asked in the hypothesis.
Experimental design: Experiments are detailed and address the aims of the proposed study. However, no data has been presented to understand some of the key aspects of Keap1 regulation. Some of the major questions/concerns I had while going through the manuscript:

1.	Loss of Keap1 expressions in H460 and H1299 cell lines (Fig 1E) are not robust. SE bar not shown in the HBE control data.

2.	The authors should verify if similar observations as shown in Tables 1 and 2 are found, and an inverse relationship exists between Keap1 expressions and LUAD in patient data from the TCGA database.

3.	What were the mutational states in the keap1 gene in the clinical LUAD tissues? Were any common mutational patterns observed in the high and low expression groups?

4.	What were the expression levels of Nrf2 in the (i) LUAD tissues compared to the non-cancerous tissues and  (ii) in the tested cell lines alone compared to those with Keap1 KD or OE? Can be assessed by Westerns/ IHC and mRNA levels. Correlations with Keap1?

5.	Did aberrant Keap1 levels affect Nrf2 nuclear translocation in the LUAD cells?

6.	Minor typing errors, for example line 189- replace “hanman” with “human”; line 317- “limitations” in place of “laminations”.
Validity of the findings: The experimental approach for the given hypothesis is straight forward, however the findings in this study lack novelty. The anti-tumorigenic role of Keap1 in lung cancer is well studied and established. Studies have also shown that loss of keap1 results in cisplatin resistance in lung cancer.

Discussion is more speculative and does not really connect the findings shown in the study. Reorganization of the discussion with major focus on the findings from this study is warranted.
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: INHIBITION OF KELCH-LIKE EPICHLOROHYDRIN-RELATED PROTEIN 1 PROMOTES THE PROGRESSION AND DRUG RESISTANCE OF LUNG ADENOCARCINOMA
Review round: 1
Reviewer: 3

Output:
Basic reporting: Gao and colleagues investigate the effect of Keap1 inhibition/overexpression on cell proliferation, migration/invasion and drug resistance providing some interesting findings in two lung adenocarcinoma cell lines (A549 and H1299). To support these claims authors use effective knockdowns and overexpression constructs and provide a series of functional experiments.

If the authors can address the following minor concerns I would support publication of this interesting concept.

Minor revisions:

1) In Figure 2, using the lysates of the Keap1 KD/OE cells could the authors test the expression levels of Nrf2 or some of its target genes? This should be also performed after treatment with H2O2. (oxidative stress conditions)
2) In Figure 4, the authors claim that Keap1 inhibition promotes invasion and migration but they do not show differences in the expression of EMT markers.
3) In Figure 5, can the authors extend their observations on cisplatin resistance using a second chemotherapeutic drug, for example paclitaxel?

Minor concerns/Suggestions

The authors should provide a concise and accurate background of the keap1-Nrf2 complex in the introduction section instead of the discussion, where they should summarize their main findings, emphasize their novelty, compare them with similar results from other experimental groups and discuss possible translational applications.
Example: lines 236-277 should be removed to the introduction section.

Lines 203-210: The authors should provide the specific number of the figure legend when they describe their results.

Line 311: the phrase “keap1 overexpression has a beneficial effect on chemoresistance” is confusing.
Experimental design: Some of the findings as mentioned in the basic reporting should be further confirmed with additional experiments.
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: INHIBITION OF KELCH-LIKE EPICHLOROHYDRIN-RELATED PROTEIN 1 PROMOTES THE PROGRESSION AND DRUG RESISTANCE OF LUNG ADENOCARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Authors have addressed majority of my comments. I would recommend incorporating the observations and figures generated from TCGA datasets either in the main figures or supplement with supporting text in the results section.
Experimental design: Sound.
Validity of the findings: No comments.
Additional comments: No additional comments


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

Input:
Title: INHIBITION OF KELCH-LIKE EPICHLOROHYDRIN-RELATED PROTEIN 1 PROMOTES THE PROGRESSION AND DRUG RESISTANCE OF LUNG ADENOCARCINOMA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have addressed all my concerns and therefore I support the publication of this manuscript.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: There are still some typo and grammatical errors in the manuscript that need to be corrected.


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 WHOLE-GENOME AND EXPRESSION PROFILE ANALYSIS OF WRKY AND RGAS IN DACTYLIS GLOMERATA SHOWED THAT DG6C02319.1 AND DGWRKYS MAY COOPERATE IN THE IMMUNITY AGAINST RUST
Review round: 1
Reviewer: 1

Output:
Basic reporting: WRKY transcription factors (TFs) are one of the largest gene families in plants, which can regulate a variety of plant processes and widely participate in the response of plants to biotic and abiotic stresses. Here the authors identified a total of 93 DgWRKY genes and 281 RGAs, including 65, 169, and 47 NBS-LRR, LRR-RLK, and LRR-RLP. Through analyzing the expression of DgWRKY genes in orchardgrass under different environmental stress DgWRKYs responded to both biotic stress and abiotic stress. DgWRKYs and RGAs may synergistically respond to the defense process of orchardgrass against rust. This study was useful for the study of the molecular mechanisms of WRKY gene in orchardgrass.
Experimental design: Many errors occurred in the text, it should be revised.
Line 44 References should be in order of years of publication
Line 67，76，98, 106, 167, 170, 171, 172, 189, 195, 214, 274, 361, There is a problem with the citing the reference formatting.
Line 206 two parens.
Line 60, (C T 2005) and Line 633, should be Thomas Eulgen 2005
Line 420, (C & C 2002) should be Devendra C, Sevilla CC. Availability and use of feed resources in crop-animal systems in Asia. Agricultural Systems, 2002, 71:59-73.
Line 713 The first word capital of the journal name in the reference, other small. In addition, some journals in the literature are full names, some are abbreviations, you should be modified in accordance with the requirements of the contribution journals.
Line  228， 237 , Note that there are some places to be spaced
Line 77，271 When a plant species first appears in the text, the Latin name should be full name. It should be short when it comes back later. Pay attention to Dactylis glomerata，Arabidopsis thaliana Line 119，123，261，139
Fig. 7, 11,12 Lack of differentiation significantness analysis.
some of the figs are not high quality.
Validity of the findings: It is OK.
Additional comments: On the whole, the paper writing is relatively rough, there are many small problems in the text, in addition to the literature reading is not enough, did not quote the literature of recent years (2019-2021), English writing is not standardized, there are many problems, it is recommended to find good Experts in English to promote.


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 WHOLE-GENOME AND EXPRESSION PROFILE ANALYSIS OF WRKY AND RGAS IN DACTYLIS GLOMERATA SHOWED THAT DG6C02319.1 AND DGWRKYS MAY COOPERATE IN THE IMMUNITY AGAINST RUST
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: The experiments of abiotic stress(heat,drought,submergence)  are all from the literature. Therefore, they don't have to be that specific.
Validity of the findings: No comment.
Additional comments: 1.The writing needs polishing.
2.All descriptions of abiotic stresses should be refined by reference.


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 WHOLE-GENOME AND EXPRESSION PROFILE ANALYSIS OF WRKY AND RGAS IN DACTYLIS GLOMERATA SHOWED THAT DG6C02319.1 AND DGWRKYS MAY COOPERATE IN THE IMMUNITY AGAINST RUST
Review round: 2
Reviewer: 1

Output:
Basic reporting: See general comments.
Experimental design: Did the authors studied the gene location?
Did the authors perform a genetic transformation and functional analysis of the gene(s) you cloned?
no
Validity of the findings: no
Additional comments: This study was carried out WRKY cloning and analysis of genesin Dactylis glomerata. 98 DgWRKY genes and 281 RGAs，GO and KEGG enrichment analysis of all genes showed that 78 DgWRKY TFs were identified in the plant–pathogen interaction pathway, with 59 of them differently expressed.
In fact, these genes studies have a lot of reports in recent years (about 800 papers in recent three years). Please see the following references. By studying this papers we can recommend some papers to let you know what has happened in recent years. You also can show some progress.
[1] Wang, X. Y., Song, J., Xing, J. H., Liang, J. F., & Ke, B. Y. (2020). Genome-Wide Identification and Expression Profile Analysis of WRKY Family Genes in Teak (Tectona Grandis).
[2] Yang, X., Zhou, Z., Fu, M., Han, M., & Xu, F. (2020). Transcriptome-wide identification of wrky family genes and their expression profiling toward salicylic acid in Camellia japonica. Plant Signaling & Behavior, 16(1), 1844508.
[3] Aguayo, P., Lagos, C., Conejera, D., Medina, D., & Valenzuela, S. (2019). Transcriptome-wide identification of wrky family genes and their expression under cold acclimation in Eucalyptus globulus. Trees, 33(10), 1-15.
[4] Villano, C., Esposito, S., D'Amelia, V., Garramone, R., & Carputo, D. (2020). Wrky genes family study reveals tissue-specific and stress-responsive tfs in wild potato species. Scientific Reports, 10(1).
[5] Shi, Y., Wang, G., Yang, X., & Cao, F. (2019). Analysis of codon usage bias of gene factors in Ginkgo biloba WRKY family. Molecular Plant Breeding.
[6] Wang, X., Li, J., Guo, X., Ma, Y., & Guo, J. (2019). Plwrky13: a transcription factor involved in abiotic and biotic stress responses in Paeonia lactiflora. International Journal of Molecular Sciences, 20(23), 5953.
[7] Wu, G. Q., Li, Z. Q., Cao, H., & Wang, J. L. (2019). Distributed under creative commons cc-by 4.0 genome-wide identification and expression analysis of the wrky genes in sugar beet (Beta vulgaris l.) under alkaline stress. PeerJ, 7(11).
[8] Yan, H., Li, M., Xiong, Y., Wu, J., & Ma, G. (2019). Genome-wide characterization, expression profile analysis of wrky family genes in Santalum album and functional identification of their role in abiotic stress. International Journal of Molecular Sciences, 20(22), 5676-.
[9] Li, Z., X Hua, Zhong, W., Yuan, Y., Wang, Y., & Wang, Z. , et al. (2019). Genome-wide identification and expression profile analysis of WRKY family genes in the autopolyploid Saccharum spontaneum. Plant and Cell Physiology (3), 3.

The authors should be revise the manuscript in the following ways:
The manuscript had showed too much about the function and description of the WRKY gene in the introduction section. The author should directly let the reader known what you should do.
Did the authors studied the gene location?
Did the authors perform a genetic transformation and functional analysis of the gene(s) you cloned?


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 WHOLE-GENOME AND EXPRESSION PROFILE ANALYSIS OF WRKY AND RGAS IN DACTYLIS GLOMERATA SHOWED THAT DG6C02319.1 AND DGWRKYS MAY COOPERATE IN THE IMMUNITY AGAINST RUST
Review round: 2
Reviewer: 2

Output:
Basic reporting: The  literature of recent years (2019-2021) must be quoted, and some old literatures should be deleted.
The introduction  requires refinement.
Experimental design: no comment
Validity of the findings: Fig.10 is lack of differentiation significantness analysis between highly resistant PI251814 and highly susceptible PI292589 lines, between treatment group and control group. And by now, the result can not verify if the up-regulated and down-regulated of the WRKY genes are truely.
Line346-Line361 should also discribe the result of the differentiation significantness analysis.
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: CONNECTIVITY IN SPANISH METAPOPULATION OF DUPONT’S LARK MAY BE MAINTAINED BY DISPERSAL OVER MEDIUM-DISTANCE RANGE AND STEPPING STONES
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This manuscript analysis the connectivity of the endangered Dupont’s lark metapopulation in its fragmented habitat in Spain, comparing different dispersal distances and the effect of accounting for unoccupied potential habitat patches as stepping stones. I think the topic is very interesting and the manuscript is nicely written. The methods are appropriate and the results highlight the key role that stepping stones habitat patches may play in the population viability of the species.

I only have some minor comments about the manuscript:

Abstract:
Although the main text is very nice to read, the abstract is somehow difficult to follow. I suggest rewriting it including some general background for the study in addition to the objectives; in methods, more specific information that includes how connectivity was assessed and the different dispersal distances that were used; same for the results.

Introduction:
-	Line 50. …isolation from the rest…
-	Line 84. …habitat area?...
-	Lines 93-97. This is a long sentence that is a bit difficult to follow. I suggest to rephrase it.

Materials and methods:
-	Subsection “Species habitat”: This section is a bit unclear to me. If I understood correctly, authors use the locations of the observed individuals to define the population locations in their analyses, and extract the stepping stones from an existing habitat suitability map. I’m not sure how they use the preferred land use categories on top of that map. I think this explanation needs clarification. Also, it seems to me that this is related only to stepping stone selection, in which case I suggest merging both sections into one to make the text easier to follow.

Results:
-	Line 291. I think in this sentence you mean only northwards?
-	Lines 304-306. The acronyms of the provinces might be confusing for an international reader. I suggest to include the full name of the province next to the acronym at least in the Table.
-	Lines 307-308. Actually, this sentence is not entirely correct. If you look at the top ten values in your table S3, there is one stepping stone with the same value of a subpopulation. It is only by chance that the subpopulation appears in the arbitrary top ten and not the stepping stone. Please, acknowledge this in your text.
-	Lines 354-355. This sentence seems to contradict the previous text. Do you mean that the western populations were still not connected to the big central population?

Discussion:
I appreciate the discussion. My only concern with it is that in my opinion is a bit restrictive. I think a comparison with other connectivity studies and the importance of stepping stones for population connectivity will support your results and provide a broader context.
-	Lines 415-419. I think this part needs to be more explained. I guess authors imply that changes in habitat quality come from vegetation succession processes. If so, the link between the two needs to the clearly explained. Additionally, I think the possibility of habitat destruction, should also be included here.
Do the habitat patches where the extinct populations occurred become stepping stones? That could mitigate the impact in the population somehow. I think authors could include some lines about that possibility and its implications. Or if that is the case, if those were used in the current analysis.
-	Nodes importance. Although authors acknowledge the importance of stepping stones may have in population viability, I think this is a key result and deserves to be highlighted even further. From a management point of view, it is easier to justify conservation measures where the species occur, but it is more difficult to implement those in areas where the species is not detected.

Figure 1. In this figure is difficult to see the difference between the black lines for provinces and populations. I suggest to redo it with the underlying map in grey. Also, the black dots for the stepping stones might be larger.
The names of the populations here are in Spanish, while they are translated to English in the main text. Please, keep the same throughout the manuscript.

Table 2. This table shows the results for only one of the dispersal distances. Please, include the three distances, as you do with table 3.


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: CONNECTIVITY IN SPANISH METAPOPULATION OF DUPONT’S LARK MAY BE MAINTAINED BY DISPERSAL OVER MEDIUM-DISTANCE RANGE AND STEPPING STONES
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1.	The manuscript should be thoroughly revised and corrected. I am not a native English speaker, but I feel that the manuscript could improve quite a lot with an additional (also linguistic) revision to improve its readability – even though the spelling is correct throughout the manuscript.
2.	The provided literature for the introduction and background is sufficient to see how the manuscript fits into the topic. However, the reference section should be carefully revised since at least one reference is missing (line 499: Rojas et al., 2016).
3.	The manuscript, the figures and the tables conform to an acceptable format of “standard sections” according to the provided instructions for PeerJ. The raw data is shared and available (including GIS maps).
4.	The manuscript represents an appropriate “unit of publication”. The outline is generally clear, and the study subject is especially relevant for conservation management. Hence it sounds interesting to me.
Experimental design: 1.	The manuscript topic is within the Aims and Scope of PeerJ.
2.	In the present manuscript, the authors did a connectivity modeling exercise with a large set of Dupont’s lark presence data coupled with potential stepping stones based on a MaxEnt probability of presence model. They explore the metapopulation structure (populations and subpopulations) of the endangered Dupont’s lark in Spain and identify critical nodes for the connectivity network. Also, they evaluate different connectivity scenarios according to potential dispersal capacity and the presence of stepping stones in the network.
3.    The manuscript deals with a well-defined subject. The objectives are clearly stated at the end of the introduction (lines 130-139). Hypotheses and predictions lack in the introduction. The specific aims of this article are to i) update the cartography of populations and subpopulations of the European Dupont’s lark range, ii) identify both vulnerable and critical nuclei from the connectivity point of view for the conservation of the metapopulation, iii) assess the role of unoccupied but adequate regions in the functionality of the whole metapopulation, iv) testing the effect of different dispersal distances evaluate the degree of isolation of each nucleus, and v) propose adequate conservation measures for the maintenance of the metapopulation.
4.	The investigation in this manuscript has been conducted rigorously and to a high technical standard. The research is conforming to the prevailing ethical standards as provided on lines 142-145.
5.	The applied methods are sufficiently described to be reproducible by another investigator.
Validity of the findings: 1.	First of all, I would like to acknowledge the effort made by the authors to transfer scientific knowledge to a management level. The outcomes of this work are of high relevance for the regional authorities in charge of biodiversity management as well as all stakeholders involved in Dupont’s lark conservation and promotion. Hence, I strongly support the publication of such work.
2.	All data on which the conclusions are based are provided. The data seems robust, sound and controlled to me.
3.	Some additional work on the conclusions (and other parts of the manuscript, see below) is required in my opinion. The authors should carefully revise the vocabulary involving e.g. metapopulation theory and dispersal. For example, a number of potentially identical terms are used, thus confusing at least me (subpopulation, patch, unit, nucleus).
4.	As stated in the review guidelines: speculation is welcome, but should be identified as such. I suggest check throughout the discussion, in particular lines 377-379 or lines 492-501.
Additional comments: 1.	The title “Medium-distance dispersal and stepping stones keep connectivity in Spanish metapopulation of Dupont’s lark.” (lines 1-3) is not precise enough in my opinion. I suggest: “Connectivity in Spanish metapopulation of Dupont’s lark may be maintained by dispersal over medium-distance range and stepping stones.” or similar.

2.	Be careful with your use of “dispersal” (lines 97-102, 109-120, throughout the discussion). Dispersal distances are usually described by a dispersal kernel that gives the probability distribution of the distances covered by a number of individuals of a given species, and not just one distance. Hence, you should (throughout the manuscript) be more carefully when talking about your applied criteria, which is namely a dispersal distance threshold (distance beyond which dispersal does not occur).

3.	Again (lines 451-458), use “dispersal” carefully. Dispersal is an ecological process that involves the movement of an individual or multiple individuals away from the population in which they were born to another location, or population, where they will settle and reproduce. I would therefore avoid mixing dispersal and movements to avoid adverse conditions (i.e. snow, storm etc.), cf "vagrants" in Supplemental Data S2!

4.	A crucial topic (in my opinion) is, however, not discussed in the article (e.g. lines 303-309). The connectivity model only includes information about the habitat surface, the habitat quality and the number of patches of each subpopulation and stepping stone (hence considering the presence and absence of the study species). However, the population size of the subpopulations (i.e. number of territorial males of the Dupont’s lark) is never accounted for in the connectivity model. To give an example: the subpopulation 12 “Pinilla del Campo” has a very high AVS value of 1090.66 (HS 4742, HQ 0.23, n° of patches 1), and is ranked as 6th most important node for intra-patch connectivity (dPCintra) with/without stepping stones. Nevertheless, it holds only 3 territorial males! Opposed to this example is the subpopulation 14 “Aranda de Moncayo” with an approximately 5 times lower AVS vale of only 203.39 (HS 4421, HQ 0.46, n° of patches 10), but holding more than 10 times more territorial males (34). This discrepancy should at least be discussed. The authors might as well reconsider the validity of their chosen approach if such differences between AVS values and the population size of subpopulations are frequent. An additional issue: I feel that the number of patches has a strong (and maybe unwanted) influence on the AHS value. How did you define a patch? How did you determinate the number of patches? Did you analyze the relation between n° of occupied territories and AHS?

5.	I think that the authors should discuss the values in Table 1 with regard to the different potential importance of dispersal threshold vs. considering stepping stones. The Equivalent Connectivity Index (EC) comparison in Table 1 shows following “ranking”: EC 5km dispersal threshold/without stepping stones (lowest value) < EC 20km dispersal threshold/without stepping stones < EC 5km dispersal threshold/with stepping stones < EC 100km dispersal threshold/without stepping stones < EC 20km dispersal threshold/with stepping stones < EC 100km dispersal threshold/with stepping stones (highest value)


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: CONNECTIVITY IN SPANISH METAPOPULATION OF DUPONT’S LARK MAY BE MAINTAINED BY DISPERSAL OVER MEDIUM-DISTANCE RANGE AND STEPPING STONES
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I am satisfied with the revised manuscript, which has clearly improved compared to the previous version – also due to the suggestions made by the second reviewer.
Almost all points made in my first review have been considered. I appreciate your effort to improve the readability of the text by correcting, reformulating, and shortening a series of sentences in the manuscript. You took in account my concern raised about the use of “dispersal” and your consequent change to “movement”. Although you unfortunately have chosen to not discuss the discrepancies between the AVS values and the population size of subpopulations, I am satisfied with your additional explanations regarding the AHS concept.
You have also resolved all other (minor) issues I had pointed out. I found just a few (mostly) spelling or format errors in the manuscript as noted in the attached pdf file.


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

Input:
Title: NITROUS OXIDE, METHANE EMISSIONS AND GRAIN YIELD IN RAINFED WHEAT GROWN UNDER NITROGEN ENRICHED BIOCHAR AND STRAW IN A SEMIARID ENVIRONMENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors use clear language throughout that is generally easy to understand. However, there are a few typos (e.g. "whiles" - ln. 87) that could benefit from a more careful proofread. Further some phrases are a bit confusing, or could be streamlined to improved reader comprehension, like the objectives and the first sentence of the discussion.

My biggest issue with this manuscript is the explanations of the potential mechanisms for biochar and biomass to reduce GHG emissions provided in the introduction and the discussion of these mechanisms in the discussions. Further, I think that the scientific literature is not particularly well utilized to support the hypothesis or the results. I believe at least one more paragraph is needed in the introduction to more thoroughly explain how biochar/ biomass might reduce GHG emissions. The discussion needs much more support and a check to ensure the references are correctly cited in relation to their overall findings and how they relate to the study at hand.

The figures were a bit hard to interpret with 8 different patterns. Perhaps a more hierarchical color scheme where similar levels of C and N share features to make them more distinguishable on different levels?
Experimental design: The study is well designed and data well reported, however, the knowledge gap being filled by this data is less clear. In lines 80-84 the authors say "Much effort has been spend..." and "The literature is replete...", then introduce their knowledge gap with what reads as a vague restating what was listed as well known in the literature. I do believe the authors have a point as to the utility of data regarding biochar compared with straw, but it is unclear what they mean by "without the confounding effects of crops...(ln. 85)". This would greatly benefit from more exposition of the information informing their central hypothesis.
Validity of the findings: Comprehension of these findings would be aided significantly by a reorganization of their presentation in the tables and figures.
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: NITROUS OXIDE, METHANE EMISSIONS AND GRAIN YIELD IN RAINFED WHEAT GROWN UNDER NITROGEN ENRICHED BIOCHAR AND STRAW IN A SEMIARID ENVIRONMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper entitled “Nitrous, methane emissions and grain yield in rainfed wheat grown under nitrogen enriched biochar and biomass in a semiarid environment” is submitted for publication as an original research article in PeerJ journal. The study aims to examine the effects of biochar and straw amendments coupled or not to different levels of N fertilizer on soil emissions of N2O and CH4 as well as on wheat crop productivity. The novelty of this work is that it contributes to a better understanding of organic amendments impact (biochar in particular) on GHG emissions by cultivated soils under arid conditions, which is not frequently studied. Authors concluded to a reduction in nitrous oxide and methane emissions (with a larger extent for biochar+ highest N dose), associated to higher wheat yields. These findings can contribute to guiding agronomic practices related to soil fertilization and mitigation of climate change.
The manuscript is well written in a clear and organized way. Results were well described and correctly discussed.The references used by authors are relevant and support the discussed ideas. Conclusions are well stated and reply to the objectives announced by the authors.
Experimental design: Comments are given in "General comments for authors"
Validity of the findings: Comments are given in "General comments for authors"
Additional comments: L 68 : « A number of mechanisms have also been proposed in literature to explain the effect of biochar amendment on soil N2O and CH4 emissions, with limited amounts of evidence to support them. » Authors are requested to give more details about these mechanisms and provide references.

L 75 : Authors explained that the effects of biochar vary depending on biochar type and soil conditions and concluded that « Such responses have limited widespread use of biochar in cropping lands. » I think this affirmation should not be announced this way because  there is a growing number of studies investigating the impact of biochar on soils and crops. Besides, this practice is becoming more and more encouraged in cultivated lands in many regions of the world.

It was mentioned in the background section, but it is also worth emphasizing in the introduction on the knowledge gap about biochar effects in arid environments. This is an additional source of novelty of this study, which avoids to the study to be of local interest. Authors can cite the following reference (https://link.springer.com/article/10.1007/s12517-018-4166-2) which shows that little is known about biochar application under arid conditions.

General comment : N2O and CH4 emissions as affected by biochar amendment were monitored during this study. What about CO2 ?

Study site :
L 106 : please  specify the aridity index used here.

Experimental design
L 125 : « The two C sources (biochar and straw) were applied at the same quantity of the material based on the straw returned to the soil every year. ». In my understanding, so that we would compare biochar and straw treatments, the amounts of biochar and straw applied to soil should bring the same quantity of carbon. But when I performed calculations, I found that biochar brings to soil 15t x %C  = 6 tons of C while straw brings 4.5t x 3 years X %C = 8 tons. Is this difference because you have taken into consideration straw C mineralization ? Please further explain that in the text.

L130 : please specify the nature of feedstocks used for biochar production and pyrolysis holding time if applicable. What’s the size of biochar granules applied to soil ?

Soil sampling and analyses
Were soil characteristics (other than Ksat) determined after straw or biochar amendment ? Bulk density (indicator of soil porosity) and pH for example are important parameters to be monitored, because they affect soil conditions, which affect in turn soil microorganisms development and activity. Why was Ksat the only soil property monitored during this study ?

L56 : Omit the e after CO2
L 244-245 treatments with s ans were instead of was.
L252 : the results were clear
L339 : reduce

Discussion
L 298 : Provide references supporting this first mechanism.

Were N crop content monitored ? This can help checking the hypothesis of higher uptake of nitogen by crops which leads to less N available for denitrification.