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 RIGHT THALAMUS MAY PLAY AN IMPORTANT ROLE IN ANESTHESIA-AWAKENING REGULATION IN FROGS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Manuscript entitled: Evidence for a Key Role of the Right Thalamus in Anesthesia-Awakening Regulation in frogs
The authors have carefully addressed all major and minor comments; here please find some additional observations and suggestions.
COMMENTS:
1.	I would recommend a more cautious title, like the one in the previous version of the manuscript. In fact, results in this study about single area interactions are not conclusive and remain speculative, thus the title should reflect this aspect.
2.	Line 310, I would suggest to write marginally non-significant effect of the factor brain area (p=0.050). The effect is in fact significant when PE is used as variable instead of ApEn.
3.	Line 315 “However there was no significant interaction.” I recommend placing this sentence at line 311, before discussing the post-hoc analyses. Something like “, but no significant interaction between factors was observed.”.
4.	In paragraph 317-324 post-hoc analyses for the single brain areas are missing and should be reported since the ANOVA revealed a significant main effect of the factor “brain area”.
5.	Paragraphs starting from lines 346 and 368, please consider combining them in a single paragraph, since the second one consists of only 3 lines.
6.	Line 363 I believe something is missing in the brackets after “r=- […] the latter”.
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: THE RIGHT THALAMUS MAY PLAY AN IMPORTANT ROLE IN ANESTHESIA-AWAKENING REGULATION IN FROGS
Review round: 2
Reviewer: 2

Output:
Basic reporting: acceptable
Experimental design: acceptable
Validity of the findings: acceptable
Additional comments: no 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: ELECTROENCEPHALOGRAPHIC MODULATIONS DURING AN OPEN- OR CLOSED-EYES MOTOR TASK
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper would benefit from English language editing.
Please also include relevant references to other neural correlates of self-paced movement than the ERD/S that are represented over the motor cortex.
The figures have a good quality; however, all the figures are in the methods section. I would suggest to restructure the methods and the results sections.
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: ELECTROENCEPHALOGRAPHIC MODULATIONS DURING AN OPEN- OR CLOSED-EYES MOTOR TASK
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript discusses the impact of closing or opening one’s eyes when performing a finger movement task on the oscillatory components of the EEG signals. The well-written manuscript carefully explains the central research question, methods used and results. A sufficient literature background is also provided and the manuscript follows the professional article structure. However, the authors should address several points to improve the manuscript.

I would like to remark that the raw EEG data should be shared, too. The authors write that the EEG data is too large to be made available. This is hard to believe for me with the small number of subjects, short sessions and a moderate number of EEG channels and an invalid reason according to the PeerJ guidelines.
Experimental design: The research question is relevant, well-defined and meaningful. The methods were mostly well-explained. Concerning Figure. 5, a paired t-test was applied to detect significant differences in the ERD/ERS% changes for EO and EC. Regarding the validity of the tests, I believe that the repeated testing procedure leads to an unrealistic high number of significant differences. A correction for multiple testing should be applied here.

I also cannot match the results from Figure 5 and 6. In Figure 5, the ERD/ERS% values go up to 2.5 and 1.8, respectively whereas they go to 60 in Figure 6. Can you please explain the differences in the y scale?  I would also be nice to have the same color scale on both subplots in Figure 5.

Two more small comments:

line 122: It is unclear to me what you mean by “Laplacian processing”.
line 186: It is rather unusual to use three asterisks *** for p<0.01. Normally, one uses (* for p<0.05, ** for p<0.01, *** for p<0.001).
Validity of the findings: The conclusion of the work is sound and linked to the original research question.

As an addition to all the grand average result, I would like to see single-subject results. How many of the subjects showed a significant difference in the 10-13Hz band between EO and EC? Sometimes grand average results might be misleading when they are driven by individual subjects with very strong signals.
Additional comments: The authors discuss the meaning of motor imagery for BCIs used for assessing intraoperative awareness and motor rehabilitation after stroke. I believe that the authors can make an important contribution to the BCI community by comparing the information content of the motor imagery events for the EO and EC condition. Using machine learning methods from BCI, I would like to see a comparison of how well an MI event can be discriminated from a random time segment for both conditions. If there are any significant differences between the two conditions then the authors can comment on which condition gives better control commands in a BCI application. The stronger ERD in the alpha band of the EC condition makes me believe that the signals are more informative in that case.

Minor comments:

The abstract should focus more on the differences between the ERD/ERS changes in the EO and EC condition.
line 62-63: Grammar error: The structure of the sentence in brackets is wrong.
line 85: The use of the word “session” is slightly misleading. If I understood the experimental design correctly, then there was no (larger) break between the sessions/runs. Normally, the word session is used for whole recording units and sessions are separated by larger breaks.
line 93: Grammar error: “were takes”
line 107: Explain the abbreviations “CMS” and “DRL”.
line 216: You wrote OE instead of EO.
Caption of Figure 6: The authors should abbreviate both EO and EC or none of them.
line 270: “figure” should be written as “Figure”
line 282: Typo: “theses”.
line 296: A verb is missing in the sentence.
References 26-27: “EEG” should be written in capital letters


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: ELECTROENCEPHALOGRAPHIC MODULATIONS DURING AN OPEN- OR CLOSED-EYES MOTOR TASK
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article is generally well written although I recommend a further check with a native English (eg. page 2, beginning of the intro: Every day (I would omit comma); page 2, line 29 can appearS bilaterally..).

References to relevant literature investigating cortical excitability under EC condition is missing (eg. Boroojerdi ed al. 2000, Fierro et al., 2005, Cambieri et al. 2017) and could potentially improve the interpretation of the results.

The opening statement in the abstract "many studies have shown that EEG is modulated by the EC condition..." left me a little unsure: it is not only studies that have shown so, but rather it is a basic knowledge in neurophysiology that EEG reacts to EC/EO (alpha rhythm reactivity is probably the first notion any neurophysiologist learn).
Experimental design: The experimental design is clear and well described.

I am not sure that the performed analysis on EEG (erd/ers) is the most suitable instrument to evaluate differences in the two conditions, for the same reason mentioned above: a spectral analysis performed in the alpha and beta ranges (erd/ers) is greatly influenced by a MAJOR event which is known to occur in the EEG (alpha rhythm reactivity).
Validity of the findings: Regarding the findings, my concerns are mainly those expressed above: differences between EC/EO conditions were found only in alpha band (which is a major, visible event occurring in the EEG); I cannot prevent myself from questioning the novelty or interest of the finding.

I do question whether this type of analysis/instrument is suitable to investigate changes in the motor cortex in the two conditions (since others have shown that there is an influence eg. Boroojerdi ed al. 2000, Fierro et al., 2005, Cambieri et al. 2017).

I am also unsure of the speculative role proposed in the BCI domain: the first proposed setting is a BCI monitoring during general anesthesia, which is a VERY different condition with respect to an awake person with closed eyes (so many other factors other than EC/EO...). The second proposed setting is a BCI for motor rehabilitation, in which I do question the added value (concentration?) offered by an EC paradigm (an approach which is to my knowledge very far from the ecological approach to -motor- rehabilitation).
Additional comments: The article is clear and well written. I do question the interest and novelty of the findings, which are possibly limited by the chosen analysis method. I also fail to see the possible utility of the results in the proposed BCI settings.
I strongly suggest to the authors to conclude the article with an anticipation of their next steps (in terms of: further analyses and/or examples of application in the short term).


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: ELECTROENCEPHALOGRAPHIC MODULATIONS DURING AN OPEN- OR CLOSED-EYES MOTOR TASK
Review round: 2
Reviewer: 1

Output:
Basic reporting: Although, the authors addressed my concerns satisfactorily, I still have some suggestions for further improvement.

I believe it would be beneficial also for the future readers of this manuscript to understand the purpose of the recorded EMG signal and its relevance for the study. Therefore, I suggest to include your response to my previous comment also in the manuscript.

In Figure 1 I would recommend consistency with the rest of the text. Now, throughout the manuscript EC and EO are named "conditions"; hence, "sessions" should be replaced with "conditions, or even removed when redundant (e.g. inside the run boxes).
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: ELECTROENCEPHALOGRAPHIC MODULATIONS DURING AN OPEN- OR CLOSED-EYES MOTOR TASK
Review round: 2
Reviewer: 2

Output:
Basic reporting: The article still contains language errors, e.g.:

line 47/113: "Theses" - >These
line 179: "chosen" -> chose
line 280: didn’t -> did not
Experimental design: No comment.
Validity of the findings: The authors write in lines 186-188 that 'A surrogate permutation test (p< 0.01; 2000 permutations) from the EEGLAB toolbox was used to validate differences in terms of time-frequency and localisation of this ERSPs with a good alpha level (< 5%)'

What is a "good" alpha level? What is the different between the alpha level and the p level of the permutation test? For me, the provided information is not sufficient to reproduce the given results. Please clarify this by providing even more details.
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: ELECTROENCEPHALOGRAPHIC MODULATIONS DURING AN OPEN- OR CLOSED-EYES MOTOR TASK
Review round: 2
Reviewer: 3

Output:
Basic reporting: I am satisfied with the changes made in this aspect.
Experimental design: I am satisfied with the changes made in this aspect.
Validity of the findings: I am not entirely satisfied with the changes made regarding my last point (the BCI scenarios proposed as possible application of the results).

I would entirely remove the example of intraoperative awareness which, I repeat, has very little to share with an EC awake condition (please remove from lines 351 to 365 in the track changes version). You could eventually leave just the final sentence as introductory to the following example:
"The results obtained could be helpful for the Brain-Computer Interface (BCI) domain. Next step in this direction would be to verify that modulations observed for the EC condition are confirmed during an attempted movement - (in subjects with motor impairment)- or a motor imagery."
And then continue with the rehabilitation BCI example.
Additional comments: Overall, I am satisfied with the changes made except for the first BCI scenario proposed (intraoperative awareness) which in my opinion is out of focus and should be removed.


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: MEASURING SHORT DISTANCE DISPERSAL OF ALLIARIA PETIOLATA AND DETERMINING POTENTIAL LONG DISTANCE DISPERSAL MECHANISMS
Review round: 1
Reviewer: 1

Output:
Basic reporting: -	Well-written manuscript, clearly presented with sufficient literature references and relevant, interesting results presented
-	Please provide REF for lines 64-66
-	Line 82, unclear which untested assumption is being referred to here
-	Line 87, “untested observations” is a strange term – observations or untested assumptions?
-	It would be helpful to condense and re-order the information in lines 77-93 to avoid repeating statements and creating confusion
-	Lines 100 and 101 are slightly repetitive – could be combined or re-worded to simplify
-	Need REF and location for specific dates on line 164 – this is different in different places
-	Need location for seed mass and seed dispersal weights and dates provided
Experimental design: -	Research objectives are original and within the aims and scopes of PeerJ
-	Please provide climate data (MAT & MAP), soil types, as well as invasion history of sites if available
-	How shaded were the areas used for the seed trapping? Were they a certain distance from the forest edge? Unclear how they were they chosen besides having “minimal understory vegetation and nearly level topography”.
-	What was the understory vegetation? Other invasives present?
-	Including a diagram of the trapping experimental design (lines 194-217) would be really helpful – more helpful than Figure 1, which doesn’t seem to be necessary in my opinion
-	Were any tests done to confirm that seed dispersal was isotropic, as was assumed?
Validity of the findings: -	Although I am not versed in the specific kernel analyses that the authors did for this study, the findings appear statistically sound, controlled, and valid.
-	Conclusions are clearly stated.
-	Might be helpful to make a mention of species-specificity in the paragraph for lines 525-537.
-	How much variation in seed rain and dispersal distance happens within species – is this effect population-dependent or can it be applied to all A. petioltata?
-	Is there any work on A. petiolata for seed dispersal in its native range? Can you make any larger conclusions about why this animal fur seed dispersal may be (at least in part) responsible for its invasive success?
-	It would be helpful to work into both the Intro & the Discussion some larger picture scenarios. What does this mean for other invasive plants? How might this impact the spread of this species large-scale?
Additional comments: This is a well-written and ecologically interesting manuscript. It is a well-designed experiment and provides valuable knowledge to invasion ecology. My suggestions for revisions are within the above boxes.


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: MEASURING SHORT DISTANCE DISPERSAL OF ALLIARIA PETIOLATA AND DETERMINING POTENTIAL LONG DISTANCE DISPERSAL MECHANISMS
Review round: 1
Reviewer: 2

Output:
Basic reporting: All good.
Experimental design: Sound.
Validity of the findings: Data analysis was sound.
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: MEASURING SHORT DISTANCE DISPERSAL OF ALLIARIA PETIOLATA AND DETERMINING POTENTIAL LONG DISTANCE DISPERSAL MECHANISMS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Line 38-42, insufficient explanation of the experimental design (Mammal inclusion)
Lines 43-46, ditto for mammal fur test

Figures showing mammal inclusion treatments are not very informative and can be removed

Line 65-67 makes a broad statement about competitive & invasive ability with no citations

First paragraph not connected to main objectives of the study and could be condensed to 1-2 sentences or omitted.  Better would be a more general paragraph about seed dispersal life history strategies in plants in general, and how it might affect predictions about invasion.

More compelling would be to introduce the idea that dispersal distances used in modeling to date have been based on cursory field observations.

Lines 150-172 are a nice introduction to the study species, much better than the first paragraph

Lines 190-192 repeat information from above about the site

Methods on field measurement for dispersal kernel data are very vague.  Line 196 what is a point source and how many were there?  Were there 15 plants in total or multiple sets of 15, and if the latter, how was spatial variation considered?

Lines 233-281 description of the dispersal kernel modeling could be considerably condensed.  It is thorough and reasonably clear but the text needs to be tightened up.   Again, is this N=15 or were there multiple sites with 15 and if so, how many?

Figures 1 and 2 are not very helpful.  The description in the text is sufficient.

Line 349-357, more detail is needed to understand the design – I had to read this a few times and I am not sure if I understand:  there were 100 seeds per pelt and 10 trials per pelt?  Please revise for clarity of methods/design.

ANOVA’s –apostrophe inappropriate here
Experimental design: The experimental design is not clear and appears to be both under-replicated and to have some flaws.

Only 15 plants were used to estimate dispersal distance; intro sets the expectation of experimental data for dispersal distance but design falls a bit short on delivering this type of data.

Only one site was used, how might this affect the findings? i.e., genetic & envirionmental variation could select for different dispersal modes.

Design for attracting mammals to the seed trays is unclear and may influence the overall conclusions due to design flaw effects.  As I understand it food was placed as an attractant to mammals, correct?  If so, how might this affect overestimates of mammal interactions with garlic mustard, given an increase in mammal visitation rates to invaded plot?
Validity of the findings: The premise of the work is solid - we need better field and experimental data on garlic mustard seed dispersal.  However, while I agree that this study has the potential to contribute new data on dispersal distances and mechanisms in the study species, it is difficult to determine from the current version whether or not the design is sufficient to support the findings.
Additional comments: The goals of this paper are to quantify dispersal distances in garlic mustard and to test the potential for animal dispersal of its seeds, which are classically thought to be passively dispersed.  The authors use a combination of passive seed traps in the field, experiments to test for seed bank accumulation with and without potential animal traffic, and a simple test of whether garlic mustard seeds can attach to animal pelts (both wet and dry fur).

While such data are lacking for this invasive plant and may be useful for making better predictions about its spread, the manuscript as written is unclear as to whether the design is sufficient for such interpretation.  In general it appears that the sample sizes are very small, that some aspects of the design (i.e., phenotypic and environmental variation; attracting more animals than would be normally found in the field in garlic mustard patches) and that each element of this paper requires additional replication and development.


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: ANTICIPATORY POSTURAL ADJUSTMENTS AND KINEMATIC ARM FEATURES WHEN POSTURAL STABILITY IS MANIPULATED
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is very interesting and the meanly suggestion is to review the English because some words is not clear for manuscript language.

In the abstract is the first time that appears the acronym APAS should be written in full

Improve the description of the methodology because it is very succinct

Conclusion: not clear

Introduction is too long
Sample size calculation was done?
I suggest completing the information on the approval of the institution's ethics committee
The results are described in a very extensive way and with many values that I suggest that they come only in the tables and only those that are most relevant to the study are described.

What is the contribution of this study to clinical practice?
Experimental design: The methodology is well described and with details that allow to replicate the study
Validity of the findings: The findings is interesting for clinical practice
Additional comments: The manuscript is very interesting and the meanly suggestion is to review the English because some words is not clear for manuscript language.


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: ANTICIPATORY POSTURAL ADJUSTMENTS AND KINEMATIC ARM FEATURES WHEN POSTURAL STABILITY IS MANIPULATED
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript was written in professional english language.
There are few typos the authors should correct:
- Line 122: there is a double parenthesis in the references
- Line 152: "30% of the tight length" should be corrected to "30% of the thigh length"
- Line 216: I believe "man" is mean.

It is suggested to avoid abbreviations in the discussion, such as "mvt" line 350.

The authors should be consistent with the number styles according with journal requirements, decimal mark is sometime with point or comma.
There is an error to report APA timing: the values unit is in ms which is physiologically unlike for APAs (e.g. line 270, SOL 0,08 ms). Also, line 311 for ankle displacement, i.e. 1.3 ms.

The introduction and the references are relevant to introduce the background for the study

Figures and tables follow the conform to the journal requirements.
Experimental design: Since the biomechanical characteristics of the experimental tasks, the trunk muscles, such as erector spinae and the rectus abdominis, should have been recorded. They represent a critical group of muscles that would properly discriminate the APAs features among the 3 task conditions.
Why did not the authors record these muscles?

It is not clear how the acceleration time of kinematic data was calculated?

In the EMG data section is not described how the deactivation of muscle activity was calculated.

Please, indicate the software used for the statistical analysis.

The method to quantify the APA (in terms of integrated EMG signal) was specified in the methods. However, the results were not reported in the results sections
Validity of the findings: The aim of the study was to disentangle the conflicting role of APAs during a upper-limb motion using different postural stabilities (standing and sitting).
The results show different kinematic features among the 3 conditions mostly due to different postural constraints. Different task demands showed a different modulations of APA timing, which is in accordance to previous findings (e.g Bertucco & Cesari, 2010), and it supports in part the hypothesis of the authors of APAs role as postural strategies to facilitate the upcoming movement.

However, the 3 postural conditions influenced the kinematic performance in term of movement time and acceleration time. I am wondering whether the self-selected motor execution imposed by the subjects may have influenced, as a consequence, the APA magnitude and timing parameters, which in part would support the classical paradigm of APA as strategies to counteract the expected mechanical effect of the focal perturbation. In other words, since the subjects modulated the kinematic of the movement due to different postural constraints and difficulty, the APA therefore were differently modulated by the CNS to minimize the perturbing affect of the dynamics of the movement. The authors should reason this in the discussion.

While the quantification the APA (in terms of integrated EMG signal) was specified in the methods, this is completely missed in the results sections. The magnitude of the APA is a very critical feature that explains how the CNS generates these feedforward strategies to respond to the postural demands. This would better clarify, together with timing, the role of APA during the movement preparation. I anticipate that while APA timing reflects more the difficulty of the task and provide the underlying mechanics to facilitate the movement, on the other hands the APA magnitude would preparare the mechanical basic to counterbalance the disturbances arising from the volitional movement.
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: ANTICIPATORY POSTURAL ADJUSTMENTS AND KINEMATIC ARM FEATURES WHEN POSTURAL STABILITY IS MANIPULATED
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have made all corrections suggested by the reviewers and the article may be accepted for publication.
Experimental design: Suitable
Validity of the findings: The findings are interesting
Additional comments: The authors have made all corrections suggested by the reviewers and the article may be accepted for publication.


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

Input:
Title: ANTICIPATORY POSTURAL ADJUSTMENTS AND KINEMATIC ARM FEATURES WHEN POSTURAL STABILITY IS MANIPULATED
Review round: 2
Reviewer: 2

Output:
Basic reporting: The Authors properly responded to my comments

minor comments:
line 114: typo, it should be thigh length NOT thight length
Experimental design: The Authors properly responded to my comments
Validity of the findings: The Authors properly responded to my 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: ASSESSING SOIL BACTERIAL COMMUNITY AND DYNAMICS BY INTEGRATED HIGH-THROUGHPUT ABSOLUTE ABUNDANCE QUANTIFICATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: Lou et al have found that relative abundance and absolute abundance show opposite trend, and they proposed the iHAAQ method to quantitatively measure the absolute abundance. While I acknowledge the importance of combing the qPCR and high-throughput sequencing, some issues such as experimental design, figures and statistical analyses should be assess clearly. Please see the comments below. In addition, there are some small grammatical problems throughout the manuscript, especially in the results. There are also some long sentences that are hard to understand.
Experimental design: The molecular methods are well presented. However, no information about the number of replicates in each treatment was given in the methods. The power and significance of statistical tests are hard to asses if the replicates are missing. In addition, some analyses were not demonstrated in the methods, such as the cluster analysis.
Validity of the findings: The findings are meaningful and the conclusions are well stated. However, a lot of results about comparisons on relative and absolute abundance should be assessed in a statistical way. Any statistical comparisons on these values? Especially in Fig. 4, Fig. 5 and Fig. 7.
Additional comments: There are a lot of sentences in the results are actually the description of methods, such as how to calculate the absolute abundance. I think this type of information should be moved to the methods section.

In the discussion, a lot of results are repetitive. Please focus on discussing what you found and avoid repeating presenting your results.

Line34-35: It is for sure that, any advantage for this study?
Line47-48: The question about “who are they” is not assessed in community ecology. Community ecology is about the abundance and distribution of species, community assembly, species interactions, etc. In addition, you seems like talking about microbial species richness here, but you are assessing the abundance of microbes in this study.
Line57: Development of specific target genes? Please try to rephrase this sentence.
Line61: Again, I don’t think “community ecology” is used appropriately here.
Line193: Sequenced with primers? Please try to rephrase this sentence
Line220: ANOVA was used with SPSS
Line245: Please cite the figures in an appropriate way.

Table1: Are these values are mean values in different treatments? How about the standard errors? In addition, I think the test is based on post-hoc multiple comparisons? Which type of multiple comparisons were you using?
Fig.1: I think the “introducing the internal reference strain (IRS)” should be placed in the first row of this figure.
Fig.2: Can you provide the error bar here?
Fig.4: “Minor” is missing in this figure, although you mentioned in the legend. The phyla names should be italic.
Fig.4, Fig.5 and Fig.7: A lot of results about which one is higher or which one decreases are presented in the text. But are these comparisons statically validated? It is more appropriate if you can provide the error bars and statistical comparisons on these values.


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: ASSESSING SOIL BACTERIAL COMMUNITY AND DYNAMICS BY INTEGRATED HIGH-THROUGHPUT ABSOLUTE ABUNDANCE QUANTIFICATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The present manuscript described an iHAAQ method, which combined the high-throughput seq with qPCR (ideally V4 region of 16S rDNA), to reveal the absolute abundance of microbial community. Although such combination has been noted previously (Props, R. ISME J, 2016; Stammler, F. Microbiome, 2016; Zhang Z. Scientific reports, 2017), the study has its own merits: Validation of the reliability and accuracy of iHAAQ by an internal reference strain EDL933 and a strain WG5 with PAH degrading ability. The study is well designed and conducted, and obtained data are sufficient to support the conclusions. Overall it is an interesting paper.
Experimental design: The study is well designed and conducted, and obtained data are sufficient to support the conclusions.
Validity of the findings: -It has been widely admitted that template-specific Illumina sequencing artifacts may lead to biases in the perceived abundance of certain taxa, that is, the wide range of experimental variables may introduce bias at all steps of a typical 16S-seq workflow. Did authors take any measure to minimize the bias effects?
-The discussion needs to include some comments about synthetic spike-in standards (Nucleic Acids Research, 2017, Vol. 45, No. 4 e23 doi: 10.1093/nar/gkw984)
- 16S rRNA is variable in copy numbers in bacterial genomes, more specific information should be given in Line 210-212.
-Lots of phrases not sufficiently concise, for example, the redundancy in Line 69-74, is it really necessary to apply detailed data for illustration?
-The information in line 94-97 was contradictory to that in line 90-92.
-Line 126, PHE, full name should be given on its first appearance.
-Readable, but does need some grammer and misc corrections throughout.
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: CHARACTERIZATION OF THE BASIC HELIX–LOOP–HELIX GENE FAMILY AND ITS TISSUE-DIFFERENTIAL EXPRESSION IN RESPONSE TO SALT STRESS IN POPLAR
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In this submitted manuscript, Zhao et al. analyze the salt stress response of bHLH family TFs on poplar. The bHLH family TFs are not only crucial for the embryonic development of many fundamental organ systems but also important for cell reprograming, i.e. Ascl1, NeuroD1 and Myod1. They are very flexible in terms of regulating transcription in that they can either promote or repress transcription, and do so in many different ways. The manuscript is technically solid. I have some minor comments.
1, There are some concepts don’t have clear definition, i.e. bootstrap values. Authors should give some interpretation before using these concepts. My suggestion is modifying the sentence in abstract “According to their protein sequence similarities and the bootstrap values, the genes can be classified into 25 groups with specific motif structures each.” as “According to their protein sequence similarities, we classified the genes into 25 groups with specific motif structures.”
2, Please explain why the number of samples in raw 65 (we selected 20 plants) is not consistent with the number in raw 74 (profiling from the 12 samples…).
3, Why don’t use the gene symbol in Figure 1? I have no idea on PtrbHLH41 and PtrbHLH41 are similar on protein sequence.
4, Authors should give some description on which clustering method and which distance matrix are used in gene expression clustering in Fig. 4 and Fig. 5.
5, The raw data in supplemental files is not the whole data. Authors should upload the whole gene expression data of 202 genes on 12 sample, not only the differential expressed genes’ data.
6, The author should improve the readability.


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

Input:
Title: CHARACTERIZATION OF THE BASIC HELIX–LOOP–HELIX GENE FAMILY AND ITS TISSUE-DIFFERENTIAL EXPRESSION IN RESPONSE TO SALT STRESS IN POPLAR
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English in this manuscript need to be improved.
Experimental design: no comment
Validity of the findings: With only two biological replicates, the statistical analysis is under power. This should be stated in the analysis.
Additional comments: The author should expand subsection "Validation of the DEGs by RT-qPCR" by comparing RT-qPCR and RNA-seq result in more detailed and quantified way.


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

Input:
Title: CHARACTERIZATION OF THE BASIC HELIX–LOOP–HELIX GENE FAMILY AND ITS TISSUE-DIFFERENTIAL EXPRESSION IN RESPONSE TO SALT STRESS IN POPLAR
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is written well, except minor grammatical mistakes e.g. at line 24.
Experimental design: Analyses are relevant in the context of bHLH transcription factor family. However, most of the manuscript is descriptive without much discussion of mechanistic basis of the biology of bHLH family genes.
Validity of the findings: The findings, particularly RNA-seq data may be useful for the researchers interested in bHLH transcription factor in poplar.
Additional comments: - Authors should include a representative structure of the consensus bHLH domain.

- The grouping of bHLH in 25 groups seem to be arbitrary (Fig1, S1). It is unclear what constitutes a group, and in many cases group divisions seem random. For example, Groups W, X, Y can be classified as a single group. And  group A can easily be divided into 3 groups or more.
      Authors should make the criteria to define a group absolutely clear and discuss the unique properties of each group in detail.  Also, there does not seem to be a pattern in Fig 2 in gene structure and motifs belonging to different groups.

- Is the phylogeny constructed by fitting the best model. It is unclear how the optimal parameters for phylogeny were obtained. Authors should evaluate best parameters using a model selection tool.

- Fig 1 is better described as dendrogram and not phylogenetic tree, because there is no information about  distance measure and branch lengths in this tree.

- Subcellular location prediction is interesting. However, authors should discuss more about why a transcription factor will be located to Golgi? And if there is any difference in function, motifs, gene structure etc among the bHLH located in different cellular compartments.

- Authors should discuss the source of functional diversity of HLH transcription factors. It seems that the
functional diversity would be attributed primarily to domains and motifs other than HLH domain. But
nothing has been discussed on this front in the paper. The implications in the diversity of HLH motifs are also unclear.

- What are the other up/down regulated genes in stress RNA-seq? Authors should discuss how the target genes of bHLH are affected by stress.

- RNA-Seq data should be deposited in the public databases and accession numbers should be included in the data accessibility section.

- It will be informative to include the phylogenetic groups for the motifs in Table S3.


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

Input:
Title: CHARACTERIZATION OF THE BASIC HELIX–LOOP–HELIX GENE FAMILY AND ITS TISSUE-DIFFERENTIAL EXPRESSION IN RESPONSE TO SALT STRESS IN POPLAR
Review round: 1
Reviewer: 4

Output:
Basic reporting: The paper focuses on studying bHLH class of genes in poplar plant.

The language in the paper needs clarification or grammatical correction. Specifically,
- line 19: "Besides" should not be used
- line 84: "standards" is actually referring to thresholds applied to filter the gene list

Legends of the figures need to be further clarified. Specifically, figure 3 description is confusing with reference to sub panel A-D more than once. Figure 5 legend needs to clarify which heatmap corresponds to URG and which one to DRG.

The RNA-Seq data should be uploaded in SRA and the SRA ID specified in the paper.
Experimental design: The Abstract needs to clearly define the objective/aim of the study.

The authors seem to set out to study the bHLH gene family however it is not well defined on why the author choose salinity to study genomic responses under abiotic stress.

Methods need some clarifications:
- Line 71 talks about doing sequencing with GENEWIZ. This should be in the "gene expression analysis based on RNA-Seq" section or a separate section describing library prep and sequencing.

- What were the parameters for sequencing in terms of read length.

- Why was the analysis done with DESeq (2010 release) instead of DESeq2 (2014 release)

- In differential expression analysis for salt stress vs no salt, it is not defined what is upregulation and downregulation. Does upregulation mean upregulated in stress samples vs non-stress samples?

What was the sequencing depth or other read stats like total reads per sample and alignment rates.
Validity of the findings: In the results, the paper characterizes the gene structure of the selected bHLH genes. Are those characterizations similar to other classes of genes in poplar?

Is the uneven chromosomal distribution independent of the size of the chromosomes?

The between-pair comparison is confusing. For example, when comparing leaf-root and stem-root, the differences identified should be the differences between leaf and stem (since root is the same dataset). However, lines 174-175 say - "gene expression are different in roots relative to both leaves and stem" which suggests something is different about root. This analysis needs to be explained better.

What is the objective of selecting the 19 genes that are deferentially expressed in the 3 sets of tissue pairs? What does it mean that these genes would be predominately deferentially expressed in both - tissue differential gene expression and differential expression due to salinity? Does it mean the genes are irrelevant for stress "tolerance" in this case?

Cluster 3 characteristics in line 182 needs to be further clarified instead of saying "opposite pattern of cluster 1".

The conclusion in line 282 about major stress responses are induced in root was also discussed in line 257-258. This seems a repetition of the result/discussion.

The paper tires to characterize a set of bHLH genes in poplar. They also try to do some functional genomic studies and validate the results using qPCR. However, the paper falls short of clearly describing the methods as well as results which makes the interpretation of the results and conclusions hard. Hence, I would recommend not accepting the paper in its current form.
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: A GENOME-WIDE INVESTIGATION OF MICROSATELLITE MISMATCHES AND THE ASSOCIATION WITH BODY MASS AMONG BIRD SPECIES
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a well written article and represents a nice extension to our knowledge of microstatellites.  I have listed a variety of suggestions and issues below.  Most of these should be easy for the authors to fix.

lines 15-18:  This sentence reads awkwardly perhaps change "except for" on line 17 to "besides".

line 22: should probably cite this paper:
Adams R.; H. Blackmon; J. Reyes-Velasco; D. Schield; D. Card; A. Andrew;
N. Waynewood; T. Castoe. Microsatellite landscape evolutionary dynamics across
450 million years of vertebrate genome evolution. Genome 59:5, 295-310.

They documented abundance for all types of 2-6mer SSRs in 5 species of birds. Actually might be nice to say whether your finding on totals match up with these numbers from their supplement:

Species	Loci per Mbp	2mer	3mer	4mer	5mer	6mer	All 2-6mer
Gavialis gangeticus 	 65.41 	 46.32 	 89.44 	 28.12 	 9.26 	 238.54
Taeniopygia guttata 	 33.06 	 49.15 	 86.86 	 31.30 	 9.78 	 210.14
Ficedula albicollis 	         33.96 	 49.36 	 113.22 	 37.60 	 16.97 	 251.11
Gallus gallus 	                 42.35 	 59.52 	 121.68 	 39.09 	 9.09 	 271.74
Meleagris gallopavo 	 36.92 	 51.82 	 112.43 	 31.76 	 8.38 	 241.31

line 24-32 This may be a bit confusing some readers may think that SMM is an alternative to replication slippage.  Maybe avoid this by changing your text on line 29-30 to: "Several mathematical models of microsatellite evolution have been proposed to represent the mutation processes...."

line 34 should cite the Adams paper above here as well

line 58 provide a citation for this software

line 82 you give a link to the website for the avian phylogenomics project as the source of your tree that many of your analyses depend on.  I was unable to locate or find this tree to evaluate its appropriateness for your study.  Please provide the tree as supplemental material or provide a doi to the data that you are reusing for instance at Dryad.  This is concerning especially with regard to PGLS analyses since the tree structure can have large impacts on the significance of your results. Furthermore, since you did your work in R please provide a script that performs the analyses you describe.

line 114 I am not sure what this sentence is communicating.

line 138 This should be tested statistically

line 146-147:  This is one example of a phrasing that I found difficult to keep straight:

"The correlation analysis revealed that microsatellites harboring more mismatches than expected are significantly related with that carrying fewer mismatches than expected"

At first read, this seems as though your saying something not possible.  Upon further reading and reflection, I think that maybe a better way to say this would be:

"The correlation analysis revealed that microsatellites harboring more mismatches than expected are present in far fewer copies than expected"

If this isn't what you mean then I don't understand it and I think readers may have similar troubles.  This applies later when you discuss this result in lines 183-184.

More broadly throughout the paper I found it difficult at times to keep track of the meaning of the measures that you are using.  I would recommend putting a parenthetical reminder to the reader in a few places for instance in the discussion when you start talking about some of the measures like average mismatch.

line 166-167 I am not sure what is you think is propitious (using the defaults, using SciRoKo,..) regardless please explain more explicitly.

line 215-216 This should be tested rather than stated based on a visual examination.  Some of the slopes look very similar and seem as though they may not be significantly different.

figure 1 you don't have a variable body mass effect.  Proper description would be:

Regression scatterplot of the inverse of the average mismatches of
imperfect SSRs on the log of body mass.

figure 2 you aren't regressing onto mismatches nor body mass effect... Usually, the description of a regression is the opposite of the way you are presenting it. What you have plotted would be described as:

Regression scatterplot of the inverse of the average mismatches of
imperfect SSRs in five classes on the log of body mass.
Experimental design: Problems with the ability to replicate are described above with lack of tree source.
Validity of the findings: Seems sound without the phylogeny some items cannot be evaluated.
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: A GENOME-WIDE INVESTIGATION OF MICROSATELLITE MISMATCHES AND THE ASSOCIATION WITH BODY MASS AMONG BIRD SPECIES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript submitted by Fan and Guo aims to test the link between mismatches in microsatellites and body and 48 of the birds species for which the genome is available.

The manuscript is well written and easy to understand for a non native English speaker (which I am). Yet, I think that some part of the manuscript are a bit difficult to understand (lines 154, 171, 183) and  could be improved by a native English speaker. The world 'Moreover' is probably repeated too often (lines 136-144).

The overall structure of the manuscript is standard for scientific articles.

To help the understanding of the manuscript, I think that some of the table added in Supplementary Material (e.g. Table S2) could be added in the main text.
Experimental design: The theoretical background is well presented and the underlying question well presented. The results are interesting and suggest that small birds have a higher number of mismatches in microsatellites than larger birds.

Why did the authors not use sequences from genomes that have been published since 2014 as their approach (SciRoKo) could have allowed to do it 'fairly easily' ?

This is especially pertaining as some these newly published genomes have higher coverage than some of the 48 genomes published in 2014.

Body mass is a fairly simple trait to find but I wonder why it was the only one life history trait that was analysed. Other traits could be have been easily tested using the same hypothesis and/or controlled for (clutch size, longevity)
Validity of the findings: The statistical analyses seem to have been well performed, although i think that other easy to gather life history traits could have been added (clutch size, longevity) and controlled for in the analyses. Given the limited number of species analyses, this could be easily gathered in a short period of time and will strengthen the results.
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: A GENOME-WIDE INVESTIGATION OF MICROSATELLITE MISMATCHES AND THE ASSOCIATION WITH BODY MASS AMONG BIRD SPECIES
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have made significant changes to the manuscript and addressed my concerns.  I feel that the revised manuscript is acceptable.
Experimental design: The authors have expanded to include more data and dealt with the minor statistical issues I had suggested.
Validity of the findings: Supplemental data is now available (i.e. the phylogeny) that will make their research reproducible by other labs and I see no issues with the applied approaches.
Additional comments: I appreciate your efforts to address the issues that I noted in the paper. I feel that the revised manuscript will be accessible to a wider audience.


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: DIFFICULTIES WHEN USING VIDEO PLAYBACK TO INVESTIGATE SOCIAL COGNITION IN CALIFORNIA SCRUB-JAYS (APHELOCOMA CALIFORNICA)
Review round: 1
Reviewer: 1

Output:
Basic reporting: This study investigates whether scrub-jays change their caching behaviour in response to video playback of a conspecific. In contrast to previous studies with live observers, video playback of an observer did not influence scrub-jays’ cache protection strategies. This suggests that video playback might not be an appropriate method to simulate conspecifics in this context.

The paper is generally very well written and easy to read. Research questions and predictions have been stated clearly in the introduction, and relevant literature is cited. Results have been reported clearly and the discussion is logical. Figures are relevant and easy to interpret, although the pictures of the video clips (Figure 1c) could be bigger. The raw data has been supplied and it is sufficiently described.
Experimental design: Research question is well defined and relevant: video playback could be a useful tool to manipulate social stimuli in behavioural experiments, but we don’t know if corvids perceive conspecifics in the video same way that they perceive live conspecifics.

For most part, the methods have been described with enough detail (see detailed comments below for few clarifications).

Experiment has appropriate controls. Including fourth treatment with live conspecific would have made the results stronger, as it would have been possible to compare birds’ response to live observer to their response to video playback. However, I don’t think that this is a big issue, as many previous studies (with similar methods) have shown that birds change their caching strategies when observed by live conspecifics.

Another weakness of the study is a small sample size. I understand the difficulty of getting a big sample size in these kinds of experiments, but as there seem to be a lot of variation among individuals (Figures 2 and 3), it is difficult to make conclusions based on the number of individuals tested.

Detailed comments

The sample size in the first experiment is unclear. First it is stated that 10 individuals were tested (line 117). Then it is said that two birds died (lines 122-124), which resulted the sample of 6 scrub jays (shouldn't this be 8?). However, in the results (lines 200-201) the final sample size is stated to be 9. Could you please clarify this?

In both experiments individuals completed three test trials. How much time there was between the trials?

Lines 125-135: Did the videos have sound?
Lines 139-140: Three different birds were filmed for video playback. Were these individuals familiar to the birds that were tested? Were they females or males?
Lines 254-255: Did you use the same birds as in the Experiment 1, or did individuals see a different observer in the second experiment?
Validity of the findings: The study did not find evidence that scrub-jays changed their caching behaviour in response to videos of a conspecific. As authors mention in the discussion, these null results are difficult to interpret, and could be the result of many factors, such as the looped material used in the videos. In addition, small sample size and high individual variation make it difficult to interpret the results.

I don’t think that the study provides clear evidence that video playback could not be a useful tool in these kinds of experiments, as its efficacy could depend on the content and presentation of the video. However, authors have discussed these issues and have not overstated their findings. Overall, the study provides relevant information on the challenges to use video playback in this context.
Additional comments: Were there any differences in the total number of caches (in-view + out-of-view caches) among video treatments? I would suggest including this test in the results. Also, did you test if trial order had an effect on the results?

In the discussion, authors mention that one explanation for the results could be the lack of interaction between an observer and a cacher, and I agree that this could be important. Did you see any of the cachers trying to interact with observers (vocalize, for example)? Also, did you look at any other behaviours during video playback, besides caching? For example, did birds pay more attention (e.g. spent more time looking at the screen) to video playback of an observer, compared to the controls?

When reporting the results of the experiment 1, please provide both minimum and maximum number of caches for each treatment (now range seems to include only maximum values?). In the results of experiment 2, medians and range for each treatment have been reported twice (lines 280-282 and 286-288), which is unnecessary.

Minor things
- I think that the statistics should be in brackets (e.g. lines 206-207, 210, 211 and so on).
- The subheading in the first experiment is “Results and Discussion” and in the second experiment only “Results”. Please change one of them, so that they are consistent.
- Line 30: change allows to allow
- Line 41: change investigating to investigation
- Line 57: I would suggest citing here also a more recent video playback experiment: Guillette, L. M., & Healy, S. D. (2017). The roles of vocal and visual interactions in social learning zebra finches: A video playback experiment. Behavioural processes, 139, 43-49.
- Line 280: change re-cache to re-cached
- Figure 2. Change y-axis title “Number of cached” to “Number of caches”
- Some of the references are missing DOI.


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: DIFFICULTIES WHEN USING VIDEO PLAYBACK TO INVESTIGATE SOCIAL COGNITION IN CALIFORNIA SCRUB-JAYS (APHELOCOMA CALIFORNICA)
Review round: 1
Reviewer: 2

Output:
Basic reporting: The current manuscript examines the use of video playback in California scrub jay caching behaviour. The main objective is to test is video playback produces the same results as in previous work. To do this, the authors set out to replicate previous findings—that: 1) California scrub jays, in the presence of a conspecific, preferentially cache in ‘out-of-view’ locations; and, 2) demonstrate a higher propensity to re-cache—under a video playback context in two experiments. In both Experiment 1 and 2 birds were tested under three treatments: 1) observer: video playback of a cage with a conspecific; 2) empty cage: video playback of a cage with no conspecific; and, 3) rope: video of a cage with a rope attached to the ceiling. Experiment 1 examined the relative difference in the number of caches made by birds behind an opaque and a transparent barrier across treatments. Experiment 2 examined the proportion of re-caches made by birds across treatments. Analyses showed that neither cache ratio transparent:opaque barrier did not change significantly across condition (Exp 1) nor re-cache propensity (Exp 2).

General comments:

There needs to be more information included to make this paper interesting to a wider audience. Can you include information about what other corvid cachers do? There has been work on other caching species in relation to social conditions e.g. Clary & Kelly 2011 Anim. Cog. There has also been some recent work on comparing results from live and video demonstrators in a social learning task in the zebra finch e.g. Guillette et al. 2017 Behav. Process. and in using video playback in foraging in  great tits Hamalainen et al. 2017 PeerJ.  There is an overall light touch with the introduction and many relevant papers are not included. Please expand the intro and discussion.

I am not sure if this paper should be published with the conclusion that 'videos may not be an appropriate tool to manipulate social stimuli in the context of cache protection strategies (abstract)' because of the null results with a low N and, moreover, because unaltered video playback was not used.
Experimental design: Unclear if the rope in test condition 3 was indeed moving? Please clarify.

L129-130 Is this height within the normal range for jays at this distance? Please clarify.

L135 was the sound in the video on? who was the demonstrators? Male? Female? Familiar? Dominant? Please add this information.

L173 how many trials per day?

L303 I would not rule out this method, as you should try unaltered playback and a larger sample size.
Validity of the findings: If the same birds were used in both experiments wouldn’t they have learned from the first experiments that their caches are never pilfered which could lead to low to no re-caching in the second experiment? Hasn’t previous work found that birds need experience being pilfered to learn to re-cache?

Unclear why in Experiment 1 only the difference in cache number between the two sites of interest was analysed – why not also look at the difference in the number of caches across test conditions? Condition might, for example, affect caching propensity, even if it does not affect ‘preference’ in cache location. Can the authors please include this information?

It is unclear what the sample size was (see specific comments for line 124, below) but if it was 6, then that may be too few, especially for null results. Can the authors please not only clarify how many subjects were run per experiment (and how many were used in the analyses), but also include a power analysis from the published work of the effect size for the study that they are currently replicating? How many individual were included in the original study?
Additional comments: The methods section requires restructuring to present details in a more concise/non-repetitive manner. Please include a general Subject, Housing and Husbandry section, followed by an apparatus section to detail the testing set-up. Then introduce each experiment, and when doing so, please limit procedural details to the experimental procedure section i.e., remove large paragraphs under Experiment 1 and 2 headers.

L30 – some words missing e.g. ‘for a’ contrast ‘between’

L31 insert ‘using video clips’

L42 Please remove ‘sophisticated’ here and elsewhere, as this (and other similar/frequently used terms e.g., ‘complex’) was not measured.
L45 Please consider adding a full stop after ‘detail’.

L5-60 this info is from a PhD thesis, I’m not sure about the journals policy of citing as such. Maybe ‘Pers Comm’ is more appropriate? Same for line 325.

L63-4 I’m not following the reasoning here that the bird may not interpret the video as a social stimulus. Please clarify/expand.

L76-80 Please consider moving these examples into the previous paragraph, making L81-89 the final paragraph describing the current study’s aims.

L82 – who is ‘they’ referring to? The observer? The focal animal? Please clarify.

L91-115 More or less states the same information detailed in the Procedure section L149-175 below. Please streamline such that this information is presented in a concise and non-repetitive form.

L95-97 These data are already detailed in the introduction, please remove.

L107-109 Same comment as above.

L109-111 These predictions are stated previously in L99-102 and are therefore repetitive, please remove.

L124 Sample size of six? But 10 birds – 2 lost = 8. And similarly, in L201 and Figure 1 n = 9. Please clarify.

L202-205 Please consider putting this information in a Table. Same suggestion for 280-282

L196-197 Unclear how the Bayesian analysis (BF) would ‘suggest’ support i.e., one either accepts or rejects the null. Please clarify and/or remove this term.

L215 ‘some evidence’ – but this number is <0.333, as is the BF value for Empty Cage versus Observer i.e., both tests support the null hypothesis, but when worded as such the reader is lead to believe there is other evidence to the contrary (when there isn’t). Please reword.

L228-241 Please see comment for L91-115

L234 are these the same birds as in the previous experiment. If so, hadn’t they learned that their caches will not have been pilfered from Exp 1.?

L 286 how many seeds were eaten throughout all experiments? Would this be useful information?


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: DIFFICULTIES WHEN USING VIDEO PLAYBACK TO INVESTIGATE SOCIAL COGNITION IN CALIFORNIA SCRUB-JAYS (APHELOCOMA CALIFORNICA)
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript is now much improved. Especially introduction and discussion are more comprehensive and authors have described the methods in more detail.
Experimental design: The experimental procedure and the conditions of video playback are now much clearer.

I have only one comment regarding the pre-test trials before the experiment (lines 166-174). Did I understand right that during these trials birds saw the same video of an empty cage that they saw later during the actual experiment (empty cage condition)? If so, birds were already familiar with this video, whereas two other conditions (rope and observer) were novel. Do you think that this could have influenced birds’ behaviour? It seems that in Experiment 1, the total number of caches was highest in empty cage condition (although this is not significant), and I am wondering if this could be explained by the fact that birds were already familiar with that stimulus?
Validity of the findings: No comment
Additional comments: The authors have responded well to my and other reviewer’s comments and done a good job revising the manuscript. I have only few minor comments:

Please check that all the papers that you are citing are included in the reference list. At least Silwa and Freiwald, 2017; Bugnyar, 2011; Bugnyar & Heinrich, 2005; and Guillette & Healy, 2017 are missing from the references. Also, Guillette is misspelled (line 60, 333 and 345).

Line 278: I believe that you are referring here to Table 2.

Line 342: misspelling birds


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

Input:
Title: THE IMPACT OF DIFFERENT AGROECOLOGICAL CONDITIONS ON THE NUTRITIONAL COMPOSITION OF QUINOA SEEDS
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: It is correct and well designed to achieve the proposed objectives that are clear. The methods are well explained.
Validity of the findings: The data are robust and correctly analyzed. The conclusions are well stated and provides an answer to the original research question.
Additional comments: The main objective of the present article is to evaluate the influence of the variety and the agroecological conditions on the nutritional properties of quinoa seeds. Three varieties were cultivated in three different countries and the analysis of minerals, phytic acid, saponins, protein, amino acids, fiber, and antioxidant capacity was carried out. The study is very interesting, exhaustive and complete. Also, it is very timely since quinoa production is currently raising worldwide and new studies showing the impact of the environmental and agronomic conditions on the nutritional value of this pseudocereal are required. However, there are some aspects that should be checked and addressed to have an article suitable to be published in the journal. These points are the followings:

1. Materials and Methods:
1.1. Section on “Plant material, experimental design and locations”: the authors should indicate the maximum and minimum temperatures registered in Arequipa region during the study period as they have been indicated for other two regions (line 98). Similarly, the authors should expressed the information provided about the soil type of three different countries in a similar way (units of minerals, pH,…) (lines 99-104).
1.2. The authors should check the results. When decimals are indicated, the comma should be substituted by a period. As an example, in line 99, “4,8” should be substituted by “4.8”.
1.3. The authors should follow the authors’ guidelines to express the units since they use different systems.
1.4. The authors should define the minerals the first time they are cited, and then, they should use the corresponding abbreviation.
1.5. Line 116: The authors should provide the information of Perkin-Elmer.
1.6. Line 127: The authors should indicate the equipment used to measure the absorbance with information of the company that supplied it.
1.7. Line 131: The authors use 6.25 as conversion factor for the Kjeldahl method. Is not a more suitable conversion factor defined for this plant?
1.8. Line 148: Define ACN the first time it is cited.
1.9. Line 157 and 158: Define FRAP and TPTZ (in this case, the full name should be written before the abbreviation).
1.10. Line 163: The authors indicate that the units were expressed as mmmol TE g-1 tomato pulp. I suppose that this is an error and quinoa seed is the correct word.
1.11. Line 168: Provide information of Calbiochem.
1.12. How were the saponins extracted to be quantified?

2. Results:
2.1. Lines 204-207: The sentence should be rewritten for a better understanding.
2.2. Lines 233 and following: The authors should use only the full name or the three-letter code to name the amino acids but not both of them.
2.3. Line 256: The authors should indicate the units used to express the antioxidant capacity (0.75 to 0.15).

3. Discussion:
3.1. Line 284: “2,6” should be substituted by “2.6”.
3.2. Lines 297-302: How can the authors explain the differences found between their results and those results published in the literature? A possible explanation should be included.

4. References: The format should be carefully checked. In addition, the latin names should be written in italics.

5. Table 1:
5.1. Why only one variety (Salcedo) was cultivated in Peru? Was there any problem with the other two varieties?
5.2. Where are the two asterisks in Table 1?

6. Figure 2: As the SD were so big, it is difficult to see the differences in the phytic acid content among varieties but the authors indicate that there were no differences.

7. Figure 4: The figure is a little bit confused because many small figures have been included. Probably, it would be better if only 2 or 3 representative figures are included. In the case that the authors want to show the results of all amino acids, a table would be the best and the clearest manner to show them.

8. As figures 6 and 7 are explain together at the same section, they should be joined in one figure 6A and 6B.


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

Input:
Title: THE IMPACT OF DIFFERENT AGROECOLOGICAL CONDITIONS ON THE NUTRITIONAL COMPOSITION OF QUINOA SEEDS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is written in a clear language. Enough references are included and the manuscript provide a clear general and direct background.

The structure of the manuscript is suitable. Figures (from 1-7), Tables (Table 1) and Supplementary tables (Supp. Table 1) are relevant and in general appropriately described and labeled. However, minor corrections must be done.

For example:
1.- In Table 1 (**) indicate that plants did not yield seeds. Data for varieties  Regalona and Titicaca must be included (even if they are filled only with two asterisks (**).
2.- Figure 1 (figure 1a) must be edited because images are overlapped, consequently labels and asterisks for Na can’t be seen.
3.- Figure 4 must be edited. In the first amino acid mini-graphic (Alanine)   there are 8 labels instead of 7.
4.- In supplemental material some raw data is written in Spanish, and units (like ppm or mg/kg) are missing in some of them.

A few typos must also be corrected throughout the manuscript:
Line 169: must be in English
Line 180: consider total yield
Line 188: dehiscense
Line 234: histidine (His) “is duplicated”
Line 237:  arginine (Arg)
Line 239: aspartic acid (Asp)
Line 240: Arginine (Arg) and
Line 266:  obtained from Spain (Figure 7).
Line 305: when plants are subjected to
Lie 357: point of view.
Line 373: D. Cusack,
Line 407:  Świeca,    Sulkowski,   Czyż
Line 446: FRAP assay,
Line 517: acid concentration,

Methods are described with necessary information to be reproduced.
Minor corrections must be done. For Example:
1.- lines 99-104, don´t use indistinctly ppm, mg/kg mg.kg-1. Choose one.
2.- In all material and methods section use L as a symbol for litter (e.g. µL, mL, L) don’t use uppercase and lowercase letter interchangeably.
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: GENDER DISPARITIES IN THE ASSOCIATION BETWEEN SOCIO-DEMOGRAPHICS AND NON-COMMUNICABLE DISEASE RISK FACTORS AMONG ADULTS WITH DISABILITIES IN SHANGHAI, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors present a well-written study that may reveal gaps in care and preventive measures for chronic illnesses in disabled people in Shanghai, China. The strengths of the work presented includes its applicability to populations similar to that of Shanghai and the authors addressed their objectives in the analysis and discussion. Additionally, the authors presented conclusions according to the objectives and data. However, the study has several weaknesses in the Methodology that the authors should revise before re-submitting as this work does fall within the aims and scope of the journal. In particular, please find below major and minor comments and suggestions according to the section of the manuscript, thank you. Further, please find additional comments in the manuscript marked with either comments or the Track Changes tool in Word.
Experimental design: Major comments
Methods
Data source
1.	In the first paragraph - regarding the health checks and health examination records by the Shanghai Disabled Persons' Rehabilitation Comprehensive Information Platform, could the authors please provide additional information about who performed the disability diagnosis and confirmation back in 2014? For example, professional psychiatrists?

Dependent variables
1.	In the first paragraph – concerning the criteria for defining cut offs – would the authors consider using Chinese national guidelines or WHO guidelines to define cutoffs for high blood glucose, cholesterol, and triglycerides?

Covariates
1.	If the SHDPRCIP has collected comprehensive information from participants, then it would be crucial to include (or explain data unavailability) several additional other covariates: those taking medications for their conditions and physical activity level (decreased physical activity is associated with diabetes and cardiovascular disease (1, 2)).
2.	In the second paragraph of this section the authors describe the classification of disability severity. In order to reduce any bias in the classification of the disabilities into levels, which authors (Y.Z., G.C., etc.) performed the ratings? Were the ratings performed independently and disagreements resolved through consensus discussion?
3.	How did the authors handle the data of individuals with comorbid disabilities? As these data already existed from the Shanghai Disabled Persons' Rehabilitation Comprehensive Information Platform (SHDPRCIP) collected back in 2014 and your dataset only includes one disability per individual, could the authors please note that either the SHDPRCIP did not collect information on more than one disability or for some other reason only one disability per individual is accounted for? It would be extremely misleading to readers and lead to bias in the interpretation of the association between sociodemographic factors and NCDs in the adults in this study if individuals with more than one disability are excluded from the current study's models. Please state clearly why comormid conditions were not collected or why you excluded them from your models. This important aspect is missing from the current report.
Validity of the findings: Results
1.	Major comments regarding covariates used in the analysis are in section 2.
2.	Table 1 – please define hukou in the table or restrict usage of the word to the main text.

Discussion
Limitations
1.	In the first paragraph, fourth sentence - the authors mention that they did not control for 'health insurance', but health insurance coverage still does not mean that a person can access care or use healthcare resources. Could the authors please briefly mention this distinction in this section?

Minor comments
Please change 'lipid' to 'lipids' throughout the manuscript.
In the Introduction section, second paragraph, line 64 – please delete 'the' before the word society, line 65 – please delete 'the' before the word spreading.
In line 93 – please change 'the' to 'a' population with disabilities…
In line 117 – please describe your instituion as 'the Fudan University School of Public Health.'
Line 121 – please provide a reference
Line 128 – please delete 'and'. The word 'or' is sufficient enough.

Results

1.	Table 3 – please change footnotes in the table to *p < 0.05 with logistic regression; **p < 0.01 with logistic regression, for example. Please delete the word 'means' before the p value.

References
1.	Sahlin KB, Lexell J. Impact of Organized Sports on Activity, Participation, and Quality of Life in People With Neurologic Disabilities. PM & R : the journal of injury, function, and rehabilitation. 2015;7(10):1081-8. Epub 2015/04/02.
2.	Carroll DD, Courtney-Long EA, Stevens AC, Sloan ML, Lullo C, Visser SN, et al. Vital signs: disability and physical activity--United States, 2009-2012. MMWR Morbidity and mortality weekly report. 2014;63(18):407-13. Epub 2014/05/09.
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: GENDER DISPARITIES IN THE ASSOCIATION BETWEEN SOCIO-DEMOGRAPHICS AND NON-COMMUNICABLE DISEASE RISK FACTORS AMONG ADULTS WITH DISABILITIES IN SHANGHAI, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Thank you for inviting me to review this interesting manuscript. The reporting in the manuscript is in line with the PeerJ requirements. The abstract is structured and includes appropriate subheadings as well as the manuscript itself. The literature is appropriately referenced and the background provides sufficient context. The manuscript includes labelled figures and tables. My suggestion would be to use clearer language in some places. For example, it is unclear why past tense is used in 2nd and 3rd sentence of the manuscript. The sentence, row 54-56 is unnecessarily long and vague etc. "Pertinently" in line 75 may not be the most suitable descriptor. I would also like to suggest clearer presentation of results across the manuscript, including the abstract. There is a lot of information and in order to reinforce the message, I would like to suggest greater consistency and clarity in reporting of findings. E.g. "women had a significantly larger negative urban hukoku effect on high blood pressure" is unclear. Does that mean that urban residence was more or less likely associated with high blood pressure in women?
Experimental design: The objectives of the study are clearly defined and meaningful. I would suggest clearly referencing similar and pertinent research, e.g. on disability prevalence or NCD risk factors prevalence in China as well as any similar studies from other settings. While I do not have statistical background and am unfamiliar with marginal effect approach to presentation of data, the analyses seem relevant and appropriate and described with sufficient detail.
Validity of the findings: It is important to present the study findings in the light of existing evidence. Presented data seems robust, statistically sound and controlled. Conclusions are clear and relate to the study aims.
Additional comments: This is an interesting manuscript which provides important insight into the areas and population groups which should be targeted with future public health policies. I would like to suggested greater clarity in presentation of findings both in abstract as well as other parts of the paper. There is a need for some editing throughout the manuscript.


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

Input:
Title: GENDER DISPARITIES IN THE ASSOCIATION BETWEEN SOCIO-DEMOGRAPHICS AND NON-COMMUNICABLE DISEASE RISK FACTORS AMONG ADULTS WITH DISABILITIES IN SHANGHAI, CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Thank you for addressing my comments and suggestions as well as those from Reviewer #2. The current manuscript reflects changes that have improved the reporting of your data sources and analyses. Before re-submission, however, please note some additional minor suggestions for revision below.

Abstract
p. 1, line 35 - Women with…percentage 'points' please add an 's' to the word 'point.'
Experimental design: Minor comments

Materials and Methods
Data Source
p. 3, line 117 – please delete 'ed' from the word 'exerted.'
p. 3, line 124 – As the authors already mentioned blood glucose in line 123, please delete ' blood glucose' after the word 'high.'

Conceptual Model and Covariates
p.3, line 143 – please add 'the' before Classification and Grading Criteria of Disability.
p. 3, line 146 – please add 'the' before SHDPRCIP.

Statistical Analysis
p. 4, line 171-172 – could you please revise the last sentence to '… was considered at p < 0.05' instead of 'taken as' and without the word 'value.'
Validity of the findings: Minor comments

Results
p.4, line 197 – The authors' findings are meaningful, so please change the word 'insignificant (unimportant)' to non-significant (lacking statistical significance).'
p. 4, line 199 – please surround the word 'respectively' with commas: …women, respectively, …
p. 4, line 200 – please add 'A' at the beginning of the sentence and the word 'that' before 'women's ME…'
p. 5, line 225 – please add 'the' before 'mental' in this sentence.
p. 5, line 232 – please change 'insignificant' to 'non-significant.'
Discussion

Limitations
p. 6, lines 294 – 297 – thank you for adding additional information to the Limitations, however, please re-word the following sentence for clarity (for example): 'Second, this study did not control for many societal factors, such as the cause of disability, years of disability, employment status, health insurance coverage, use of healthcare resources, individual income, and some behavioral factors, including medication use for their conditions and physical activity level [39-40].' Please delete the text and sentence after '…physical activity level [39-40]' so that the next sentence after the one above is: 'It is critical for future studies to consider more covariates to determine a more complete picture of gender differences.'
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: ASSESSING UNIVERSALITY OF DNA BARCODING IN GEOGRAPHICALLY ISOLATED SELECTED DESERT MEDICINAL SPECIES OF FABACEAE AND POACEAE
Review round: 1
Reviewer: 1

Output:
Basic reporting: Line 121 “For each specie”, spelling error
Experimental design: 1.	Why should this work choose ITS2, matK and rbcLa? Have you ever tried the trnH-psbA region, which is regarded as a supplementary barcode to ITS2 for the identification of medicinal plants?
2.	Have you ever tried the multi-locus barcodes in the scope of your study？Whether the identification efficacy would be better.
3.	Table 1 and Table 2 should be displayed in the supplementary files or not described in the table way (e.g. direct explanation) in Materials and Methods part.
Validity of the findings: Research has been performed to use DNA barcoding for the identification of medicinal species of Fabaceae, and the result showed that ITS2 is an ideal region. What is the innovation and significance of your work?

Gao T, Yao H, Song J, Liu C, Zhu Y, Ma X, Pang X, Xu H, Chen S. 2010. Identification of
medicinal plants in the family Fabaceae using a potential DNA barcode ITS2. Journal of
Ethnopharmacology 130:116-121.
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: ASSESSING UNIVERSALITY OF DNA BARCODING IN GEOGRAPHICALLY ISOLATED SELECTED DESERT MEDICINAL SPECIES OF FABACEAE AND POACEAE
Review round: 1
Reviewer: 2

Output:
Basic reporting: So far, many researches are focused on finding universal plant DNA barcoding, and these DNA barcoding works very well only above the genus taxonomy. Therefore, they don’t focus on species identification in the case of very closely related taxa. This aspect of barcoding is extremely challenging and at the same time difficult to reconcile with barcode universality. This manuscript is focus on “DNA barcoding of selected desert medicinal species of Fabaceae and Poaceae” with a very good purpose.
Experimental design: However, very few samples were tested here to represent on different species. The samples here are representatives of different genera of Fabaceae and Poaceae.
There is not a sufficient number of individuals tested.
Validity of the findings: The manuscript title may be changed according to the plant material.
Please cite some recent references specifically working on species identification using DNA barcodes, like Wu et al., PloS one 12: e0182693.

A combination of ITS, matK, and rbcL should be tested in different genera of Fabaceae and Poaceae.
The indels need to be evaluated through different material.
The conclusion of the paper was “ITS2 and matK both are the suitable barcode markers for medicinal species of Fabaceae and Poaceae”. However, according to the results of BLASTn analysis, the species-level identification rates were low in all three regions. And as mentioned in Line 250-251, “Performance of matK and rbcLa was relatively weak at species resolution ability similar to the study of Saadullah et al. (2016) on the DNA barcoding of Poaceae.”, matK sequence didn’t work well in many species in Poaceae. The conclusion ‘matK was a suitable barcode marker for medicinal species of Fabaceae and Poaceae’ from the references was not true.
For the name of sequences, such as rbcL and matK, the last capital letter is not italic.
Line 283, 302 and 415: Reference with more than six author names, followed by “et al.”
Line 285, 301, 309, 409 and 416: The reference format of “PLoS ONE” was not consistent. Some are “PLoS ONE” and others are “PLoS One”.
Line 311: Italic.
Line 349: Italic.
Line 367: Italic.
Line 391: Italic.
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: ASSESSING UNIVERSALITY OF DNA BARCODING IN GEOGRAPHICALLY ISOLATED SELECTED DESERT MEDICINAL SPECIES OF FABACEAE AND POACEAE
Review round: 1
Reviewer: 3

Output:
Basic reporting: Tahir et al. tested the efficiency of three DNA barcodes (ITS2, matK and rbcLa) for identification of frequently consumed medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan using standard barcode gears. The paper was clearly written and well understood. The introduction part clearly showed the purpose of the paper, and cited important relevant literature. The structure of the paper complies with the journal standards, and raw fasta data was provided and solid. However, the tables and figures are not high quality according to criteria of standard publishing of this kind of work. Firstly, a three-line-table should be used; Secondly, all figures are low resolution and hardly readable; Last, bootstrap value of both ML and NJ method should be labelled, but not in %。
Experimental design: The research is in the scope of PeerJ, and the authors tried to evaluate the efficiency of three barcode markers in identifying medical plant of Fabaceae and Poaceae using a standard method. The questions and methods they undertook were well defined and described. However, I think the paper has severe drawbacks concerning selection of study species. Normally, we need to evaluate the utility of barcodes for discrimination of medical plants from its closest relatives and morphologically similar adulterants. Current research only sampled medicinal plants but not their closest relatives or adulterants.
Validity of the findings: The data were robust and statistically sound, and the conclusions were well stated. The work will add evidence for DNA barcoding as an effective tool for identification of medical plants.
Additional comments: The authors used three DNA barcodes (ITS2, matK and rbcLa) to identify ten medicinal species of Fabaceae and Poaceae in the desert of Cholistan using a standard barcode protocol. Although the paper was well written and structured, the methods were appropriate and results are solid, it is less meaningful concerning selection of study species, as no studied species’ closest relatives or adulterants are included in the analysis. Other concerns are listed below:
1)	In comparing the inter and intra-species K2P distance, the authors should do it separately in Fabaceae and Poaceae, because if you choose species of two families to compare, the inter-species genetic distance should of course be larger.
2)	Table 1 and Table 2 could be combined.
3)	The NJ tree and ML tree could be combined.
4)	The authors should state more clearly in the methods part why to choose these species to investigate. Are they all medicinal plants? Or, some of them are not medicinal plant and just be close relatives of studied medicinal plant. For example, the author only wrote in Introduction that Acacia nilotica is a medicinal plant, and how about A. jacquemontii and A. modesta?
5)	A combination of all three markers should be assessed also by the standard barcode procedure, as normally more markers would do a better job in identifying species.
6)	Some literature needs editing. For example, all genus names are not italic. I strongly recommend the authors check them throughout the paper.


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

Input:
Title: ASSESSING UNIVERSALITY OF DNA BARCODING IN GEOGRAPHICALLY ISOLATED SELECTED DESERT MEDICINAL SPECIES OF FABACEAE AND POACEAE
Review round: 2
Reviewer: 1

Output:
Basic reporting: This manuscript is interested in selected desert medicinal species and to validate the potential barcodes for these medicinal species.
Experimental design: Combination of multi locus barcode has been analyzed.
Validity of the findings: The validated barcodes will be used for species discrimnation of these medicinal spcies.
Additional comments: This manuscript is significant improved after carefully revising by authors.


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: ECOSYSTEM FUNCTIONAL RESPONSE ACROSS PRECIPITATION EXTREMES IN A SAGEBRUSH STEPPE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The basic reporting is quite good. The manuscript is well-written and easy to follow. The statistics and pre-treatment analyses were, despite being complicated, easy to understand. No comments or concerns here.
Experimental design: The study was well executed. I particularly like the use of the Sala experimental design of automated drought+irrigation treatments. I think this is a powerful design that enables the authors to speak more thoroughly about the role of water limitation in this system (as opposed to a drought-only experiment). The author also did an extraordinary amount of work on the statistal analyses and to resolve issues (VWC measurements/ANPP calculations) in a quantitatively rigorous manner.
Validity of the findings: Their results indicate that the sagebrush steppe is actually quite robust to interannual variability in precipitation. This comes as a surprise, as the literature suggests that arid and semi-arid ecosystems (into which the sagebrush steppe easily fits) are quite sensitive to changes in precipitation. Huxman et al. (2004) and Knapp et al. (2015) both showed that drought impacts semi-arid sites more intensely than mesic sites, and Wilcox et al. (2017, in GCB) showed that most systems are more sensitive to irrigation than drought, and this is especially true for semi-arid sites. So far as I can tell, this study doesn't fit neatly into either line of thought (since it was relativel insensitive to drought, and irrigation effects were actually weaker than drought - see Wilcox et al.). It would be beneficial for the authors to put their study into this larger context and perhaps discuss why they think their site doesn't conform to these broader patterns (i.e. shrub-dominated, etc.).

I also have a couple of concerns that potentially influence the results that the authors need to address prior to publication.

1. I appreciate the authors effort in validating and calibrating their NDVI measurements to ANPP, but I am quite concerned about the accuracy of these calibrations. The R2 is quite low for those calibration regressions (0.2 - 0.7), so I wonder how accurately biomass in each plot was represented by these ANPP measures. This is actually quite a large source of error, and I wonder if it isn't responsible for the lack of significance and weak responses observed here. I have two thoughts: would it be better to use raw NDVI measures rather than ANPP conversions? could the authors imbed the ANPP-NDVI calibration into their regressions (see Kiona Ogle's papers on multiple datasets in Bayesian analyses)? This would allow full uncertainty around the estimated ANPP based on NDVI to propogate into the VWC analyses.

2. I didn't see mention of the priors on B, but I might've missed it. See Lemoine et al. (2016) - Ecology for a discussion of this issue. (very minor issue, I doubt the priors make too much difference here).

3. My biggest concern is that the statistical tests don't seem to test the HRF because they treat year/time as a "nuisance" variable that adds noise to the observations. But the HRF is explicitly about time and how the response of ecosystem function changes over time. So incoporating time as an explicit part of the analysis would be necessary. The easiest way would be to regress ANPP against VWC and allow the slope to vary by year to see if the slopes follow the pattern dictated by HRF (or could use a hierarchical gaussian process/LOWESS model or other non-parametric model to allow for non-lienarity along the VWC gradient - drought - control - irrigation). Perhaps another approach would be to calculate a 'sensitivity' for each replicate (or treatment) within a Bayesian model, then look at how sensitivity to drought/irrigation changes through time (in the same model, i.e. plot-level sensitivity nested within year, with fixed effects to contrast sensitivity to drought/irrigation, a la Wilcox et al. 2017). That is an explicit test of HRF, where the sensitivites could show any number of temporl patterns outlined by Smith.
Additional comments: No additional comments