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 REFERENCE CYTOCHROME C OXIDASE SUBUNIT I DATABASE CURATED FOR HIERARCHICAL CLASSIFICATION OF ARTHROPOD METABARCODING DATA
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This is a very nice paper, generally well-written, that describes how the authors constructed a database that can be used for taxon identification when using the Zeale primer set in a metabarcoding study. The authors are correct that there are many technical aspects of metabarcoding and other molecular methods using NGS platforms that need to be explored, and this is a contribution toward constructing a better reference database.

1.	I understand that the extensive curation resulted in a more compact database that would result in faster processing times, but it is not entirely clear what is gained by the extraction and trimming and removal of redundancy to create the curated dataset. How much is processing time reduced? How much better is the true positive rate? As COI sequences and whole mitogenomes are being added to public databases at an ever increasing rate, how often will the database need to be recurated? How easy will it be to recurate it? The authors should consider addressing some of these questions in the present paper.
2.	On a different tack, it would be very interesting if the authors could show (or not) that the accuracy of classification of test sequences was related to the taxonomic “density” of training sequences.  For example, is classification of an unknown Lepidopteran more accurate than for an unknown beetle?  What about Hemiptera compared to Orthoptera? Also the comparison can be made at the family level, and could be done more generally if “density” were appropriately quantified. This would be very useful for people to know.
3.	The authors should acknowledge that theirs is an in silico analysis, and suggest ways in which their conclusions could be verified with true unknowns, or with new sequences.
4.	Sensitivity is not defined (at least I could not find a definition). As this is one of the most used words in the results and discussion, it is critical to have it clearly defined. Technically, sensitivity is the true positive rate, and I assumed that it is used this way, and it would be very helpful to state this in the methods. However, in Figure 3C, family level sensitivity is only .2 to .3. If sensitivity is true positive rate, these values seem extremely low. Also, at line 260, the authors suggest a tradeoff between sensitivity and accuracy. However, if the sensitivity is true positive rate, then how does this differ from accuracy? In addition, false positive rate plus true positive rate = 1, so it doesn’t make sense to say there is a trade-off between these. This leaves me wondering what is sensitivity?
5.	A statistical technicality, that would be a great improvement (although perhaps not critical here), would be to use cross-validation to calculate true and false positive rates. By splitting the data set only once (or possibly twice – this is not clear to me), the best estimates of these rates are not obtained.  However, implementing cross-validation on the dataset would not be a simple task.
6.	I understand from the stated methods that all of the Bemisia tabaci sequences were boiled down to one sequence in the final reference database. However, several researchers have suggested that the Bemisia biotypes may be species, so it seems that the curated database should include this variation. Also, other examples with extreme “intra-specific” variation should be similarly addressed.

Minor points easily addressed
Line 266. The statement also applies to different amplicons of the COI barcode, not just different barcode loci.
Lines 275ff. It seems strange to refer to a part of a gene as a locus, and then to refer to genes as regions.  I think it would be better to refer to the region of the COI locus coding for the Zeale amplicon, so that COI and 18S can be referred to as loci.
Line 277-279. The use of test sequences from genera that are not in the training dataset is very nice, but it does not distinguish unrepresented taxa from well-represented taxa. It indicates that classification is more accurate for represented genera than for unrepresented genera. My point 2 above could address the effect (if any) of well-represented taxa.
Fig 1 legend. There is no reference to panel C
It is not clear if the github Zeale file is the curated dataset or the longer sequences between 150 and 157 bp (line 179-181). I was not able to see the file contents.


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: SINGLE-NUCLEOTIDE POLYMORPHISMS OF URACIL-PROCESSING GENES AFFECT THE OCCURRENCE AND THE ONSET OF RECURRENT DEPRESSIVE DISORDER
Review round: 1
Reviewer: 1

Output:
Basic reporting: The English language should be improved by a linguist, because of some errors, i.e.,
43. patients suffers – suffer
57 an exposure –exposure
63 This leads - It is unclear what This refers to
66 for a removal-for removal
79 shifting of balance-shifting of the balance
…
and the like.
Experimental design: No comment
Validity of the findings: The strong side of the work is well documented, in the introduction, the occurrence of the oxidative DNA damage in depressed patients, providing the foundation for the research undertaken by the authors. The genes and their polymorphisms were selected adequately to the presented hypothesis, although the list has not been exhausted.
Additional comments: The weakness of the work is the lack of consideration of the power analysis when designing the study. It is not known whether the number of patients tested is sufficient for correct inference.

It is not clear to the reviewer why the authors divided patients due to the age of onset of the disease before and after the age of 35 - explanation is necessary.

As a researcher, I would suggest to authors to supplement research and analyze the expression of the analyzed genes because the space-time shift and numerous transcriptional and post-translational modifications can significantly alter the final effect of the genes studied.


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: SINGLE-NUCLEOTIDE POLYMORPHISMS OF URACIL-PROCESSING GENES AFFECT THE OCCURRENCE AND THE ONSET OF RECURRENT DEPRESSIVE DISORDER
Review round: 1
Reviewer: 2

Output:
Basic reporting: Not appropriate.
In Discussion section, genomic mechanisms beyond the current study are mentioned, which seem  just  specuration beyond the current findings.
Experimental design: Generally excellent, but small sample size.
The author report statistical power based on the previous studies.
Validity of the findings: Not enough.
The authors show clinical usefulness of the current findings.
Additional comments: This study assessed the associations between SNPs of uracil-processing genes and occurrence or onset of recurrent depressive disorder as well as treatment effectiveness. Although the authors found some significant associations between studied SNPs and depression, they failed to find the influence of those SNPs on effectiveness antidepressant therapy nor the severity of depression before and after the treatment.
(1)	Although study protocol using case-control design is advantage of the current study, the sample size seems to be too small to detect any potential associations between those SNPs and characteristics of depressive disorder (usually 5000 controls and 5000 cases are required for this kind of analysis of susceptibility genes). Many non-significant associations observed in the current study may due to insufficient sample size. The authors should report statistical power of the current study based on the previous findings regarding this issue.
(2)	In addition, the calculated effect size is not so large (odds ratio ranged from 0.5-1.7) as to explain the clinical significance of these SNPs on the disorder. What can clinicians do next step based on the current findings? What is the clinical significance of these findings? Without these answers, the valuable case-control design is spoilt. Relatively large effect size is observed between the combination of three genes and depression (in Table4, T/T-A/A-G/C; adjusted odds ratio =3.4), but this was calculated by only 21 patients and 7 controls, resulting in wide range of confidence interval.
(3)	Most basically, since the authors did not show which genotype is the referent, readers could not understand what the presented odds ratios mean, i.e., how many times the studied SNPs are risky or protective in comparison with WHAT GENOTYPE.
(4)	In my opinion, this kind of study using common SNPs should focus much on treatment effectiveness to clarify the clinical usefulness. However, unfortunately, the authors failed to find any clinical effectiveness related to the studied SNPs, which may be, at least in part, due to the small sample size as mentioned above.


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

Input:
Title: SINGLE-NUCLEOTIDE POLYMORPHISMS OF URACIL-PROCESSING GENES AFFECT THE OCCURRENCE AND THE ONSET OF RECURRENT DEPRESSIVE DISORDER
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment.
Experimental design: no comment.
Validity of the findings: no comment.
Additional comments: This paper investigated the influences of three SNPs localized in genes encoding uracil-processing proteins on occurrence and the onset of depression. Although the onset of depression can be determined only by rs2337395, their findings were very important and interesting for further studies.

It would be interested to see whether rs2337395 showed similar significant influence after adjusted for age in addition to sex in the logistic analyses. Also, it would be nice to see actual median and interquartile data in the figures.


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: SINGLE-NUCLEOTIDE POLYMORPHISMS OF URACIL-PROCESSING GENES AFFECT THE OCCURRENCE AND THE ONSET OF RECURRENT DEPRESSIVE DISORDER
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors took into account all my comments and recommendations, they supplemented the calculations and explanations. I recommend the manuscript 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: SINGLE-NUCLEOTIDE POLYMORPHISMS OF URACIL-PROCESSING GENES AFFECT THE OCCURRENCE AND THE ONSET OF RECURRENT DEPRESSIVE DISORDER
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
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: ANNUAL PLANKTON COMMUNITY METABOLISM IN ESTUARINE AND COASTAL WATERS IN PERTH (WESTERN AUSTRALIA)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The quality of the written English, though adequate, could be improved by breaking some of the more complex sentences into simpler, shorter sentences.
Experimental design: The experimental design is sufficient to address the goals of the study, and has the great strength of regular fortnightly measurements over a year.
Validity of the findings: As the authors note, this is the only study of coastal pelagic metabolism in temperate Australia. The study is well conducted and the methods and conclusions appropriate.
Additional comments: Line 68: Both study sites are within the greater Perth metropolitan area (Perth has a population of over 2 million).
Line 70: The study by McKinnon (2017) includes a number of Australian coastal areas, not just the Great Barrier Reef study of McKinnon (2013). Your point that autotrophic plankton metabolism prevails is still valid - but applies in a number of sites. The main contrast between your study and those included in McKinnon (2017) is that your study is the only one in temperate Australia. You could probably build on on this contrast a little more than you have.
Line 84: you mention bacterial abundance here, but present no data and no analyses of bacterial abundance as a predictor of metabolic processes, other than a comment in the abstract that no correlations were observed.
Line 118: I note the authors used borosilicate bottles, a practice they have criticised elsewhere on the basis of these not being UV transparent.
Lines 213-219: Note other Indian Ocean sites described in McKinnon et al (2017).
Line 222: I suggest you remove the word eutrophic - which these days is a loaded term. Maybe "productive" might be better.
Line 231: Not just GBR, as above.
Line 243: If GPP and CR will be affected in a similar way, what ecosystem effects do you predict?
Figures 4&5: I assume you used Model II regression?


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: ANNUAL PLANKTON COMMUNITY METABOLISM IN ESTUARINE AND COASTAL WATERS IN PERTH (WESTERN AUSTRALIA)
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors clearly reported their findings: their study was outlined well and the results were easy to follow. There are some grammatical issues that I commented on that should be addressed. Additionally, several of the sentences are very comma heavy. While most of the instances are grammatically correct, it gets hard to follow. I would recommend trying to reduce comma use by restructuring some of the sentences.
Their review of the literature was thorough. It may be possible to contextualize what may be happening to the organic matter that is being produced more than what they have done.
The whole piece (article, figures, tables, and data) was well done.
The work was observatory in nature and the authors clearly achieved this goal.
Experimental design: The experimental design was impressive in terms of scope—they made regular measurements for a year and fill existing gaps in the literature (very little plankton metabolism work has been done for coastal waters in that area).
The research was more observatory in nature and they fulfilled this aim well.
The methods were described very well. The only comments I have for this section is to mention at what time their incubations were started/finished and to also give a little more background information about Woodman Point.
Validity of the findings: I think the authors contextualized their findings well. I think it would have been possible to discuss what they think may be happening to the organic matter that is being produced more than what they have done.
The data was robust and their conclusions are well stated.
Additional comments: This work assessed community respiration, net community production, and gross primary production at two locations off the West coast of Australia.
The results the authors present are impressive in terms of scope—they made regular measurements for a year and fill existing gaps in the literature (very little plankton metabolism work has been done for coastal waters in that area).
I think that the journal and oceanographic literature would benefit from this work being published. The biggest benefit would be that future metabolism work in the Southern hemisphere and the Indian Ocean will have now have existing work to contextualize their own research and modelers will have more data to build from.
There are a few minor issues that I think need to be addressed in order to ensure the work is as clear to readers as possible. I have added line by line comments that may help to improve the work (mostly grammatical in nature). Additionally, I think the end of the discussion would be improved by the authors mentioning what they think might be happening to the organic matter that is being locally produced. Are there any estimates about the rate of sedimentation in the area? Do they think the currents are taking it elsewhere where it is being respired? Etc.

Introduction
Line 54: Use the abbreviations GPP and R here (or CR if you choose CR rather than R throughout the paper).
Line 57-59: These two sentences seem related enough that they could be one sentence.
Line 66-70: Linking these sentences to the previous paragraph might help to guide the reader a bit. Something along the line of: While this has important implications, virtually all of the above results are from work in highly populated regions of the Norther hemisphere (i.e. Europe, the USA, and Asia) and plankton metabolism may differ in Southern hemisphere waters.
Line 75: You mentioned the Great Barrier Reef above but did not define GBR to be the abbreviation.
Line 81: I think the word fortnightly might confuse some readers. That is just a personal preference though.
Line 82: I think it is confusing that you refer to community respiration as R earlier in the introduction and as CR here. It seems like you prefer CR so I would stick with that. You also don’t have to redefine the abbreviations for GPP and CR since they were defined above.

Methods
Line 90: Change: “The estuary is permanently…” to “The estuary has been permanently…”
Line 92-93: This seems oddly phrased to me. It might be improved by slightly different punctuation or reordering of the sentence.
Line 97: Change to “purposes, urbanization, dam construction, and other factors…”
Lines 88-103: You spend so much time orienting us to Matilda Bay but so little on Woodman Point. It would be good to orient the reader to Woodman Point a little more (how many kilometers off shore, is there seasonal upwelling, etc.)
Line 105: Again, I would suggest a different word choice for the frequency at which you took your samples.
Line 115: You don’t have to redefine the abbreviations here.
Line 120: What time of day did you start incubations?
Line 128: Delete “of water samples”
Line 134: Italicize the “a” after chlorophyll.

Results:
Line 153: Replace “units” with “PSU”
Line 155-156: This is oddly phrased. I would suggest: “and while the pattern was less clear in Woodman Point, the lowest salinity was also observed in water and early spring.”
Line 158: Write phosphate instead of phosphorus.
Line 160. Delete “in”
Line 168: Shows should be past tense and delete “a”
Line 172: Change “that” to “than”
Line 173: “Displaying” should be past tense.
Lines 175-179: Do you have stats for these statements? P values? R2 values?
Line 182: This interpretation seems better suited for the discussion.

Discussion
Line 190: Change “which” to “but all” and cite both Pearce and Thompson in Line 191.
Line 194-196: I think this sentence should be deleted because you already spoke about Chl a values being in range above.
Line 199: “was” should be “were” or you should delete the word “rates”; also, you shouldn’t capitalize “Respiration”
Line 235-238: There are a lot of commas in this sentence and I can’t follow the train of thought. I noticed that high commas use was an issue throughout the paper. While it is grammatically correct in most instances it makes many of the sentences hard to follow. I think it would be possible to reduce the use of commas by restructuring sentences in many cases.
Line 242: Delete “on”

Figure 1 caption: Change “as blue line and symbols” to “in blue” and change “as red line and symbols” to “in red” and change “, along the study period” to “over time”
Figure 2 and 3 captions: Change “along the study period” to “over time”
Figure 5 caption: Change “shows” to “show”


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: ANNUAL PLANKTON COMMUNITY METABOLISM IN ESTUARINE AND COASTAL WATERS IN PERTH (WESTERN AUSTRALIA)
Review round: 1
Reviewer: 3

Output:
Basic reporting: The authors do a good job setting up the context for this study, including the importance of understanding the role of coastal metabolism in global carbon budgets. Thus, measures of NCP and CR are useful for placing the coastal margins into a broader context. The figures are generally well-drafted, showing temporal patterns in the key results, and relationships between metabolism and key environmental variables (temperature, chlorophyll a). My biggest gripe is that there are numerous grammatical issues, including verb-tense disagreement, missing articles, and wordiness.  The manuscript would be significantly improved with a careful edit to improve grammar and to reduce redundancy. I also think a map showing the location of sampling sites would be helpful to readers unfamiliar with this area.
Experimental design: The authors point out that measurements of plankton metabolism are rare in coastal environments of the southern hemisphere, thus questioning whether generalities drawn from the existing literature studies are sound given that they are predominately drawn from studies in the northern hemisphere. The sampling design is straightforward and clear, repeatedly sampling two sites over an annual cycle and conducting metabolism experiments on collected water. The experimental design of the metabolism experiments is also straight-forward and the methods appear appropriate for dissolved oxygen, chlorophyll, and nutrients. One omission or inconsistency I note was that the authors refer to bacteria samples, but no such data were presented.
Validity of the findings: The main findings from this paper were that the sites studied consistently displayed autotrophic behavior, and that the estuarine site was more metabolically active than the open water site, which is consistent with the expectation that estuaries tend to have more nutrients and organic matter than more open water areas. I think the authors should acknowledge a limitation of their experimental design, given that they only considered processes in surface waters and this limits the scope of the results and interpretation. To address net ecosystem metabolism more holistically, one must grapple with processes occurring throughout the water column and at the sediment water interface, the latter being particularly critical in shallow environments (e.g., Kemp et al. 1992). I encourage the authors to speculate how their interpretations may be tempered by taking into account the likelihood that processes nearer the bottom will become more heterotrophic, due to light limitation. One pattern that I found intriguing was the strong peak in phosphorus in Matilda Bay during summer.  Could the authors speculate as to the reason for this? Perhaps sediment P regeneration?

Kemp, W.M., Sampou, P.A., Garber, J., Tuttle, J., Boynton, W.R., 1992. Seasonal depletion of oxygen from bottom waters of Chesapeake Bay: roles of benthic and planktonic respiration and physical exchange processes. Marine Ecology Progress Series  85, 137-152.
Additional comments: I include here specific instances of grammatical errors that should be addressed, referenced by line number.

L25: Abstract states experiments were conducted from Mar. to Oct. 2014, but text and data suggests Mar 2014-Mar 2015.

L27: Extraneous use of the word ‘the’.  Should read ‘…was net autotrohic…’.

L28: Replace ‘higher than one’ with ‘>1’.

L29 and L35-36: Repetitive statements about negative correlation with salinity.

L36-38: Broad statements about role of import/export of organic matter require a more comprehensive budget that includes contributions throughout the water column and the benthos.

L47: Replace ‘ration’ with ‘ratio’.

L47-48: Omit redundant phrase ‘, or experiences small deviations from this balance’.

L49: Replace ‘inputs’ with more generic term ‘fluxes’, given that inputs AND exports will affect P/R ratio.

L50: Omit ‘in the open ocean’ as this is already stated at the beginning of the sentence.

L51: Replace ‘present’ with ‘have’ (2 instances).

L58: Omit ‘What’. Start sentence with ‘The’. Also omit ‘is’.

L63: Misspelling: ‘fueled’.

L65: Add clause to complete the comparison. Something like: ‘, whereas outer reaches of estuaries tend to be CO2 sinks.

L89: Awkward sentence with two subjects: Matilda Bay and Swan River.

L89 and throughout: ‘Km’ should read ‘km’.

L90: Omit ‘permanently’, given that you go on to describe an alteration in 1987.

L92: Omit ‘rainfall seasonal variations with’

L100-101: Replace ‘abundance of phytoplankton species’ with something like ‘variation in phytoplankton biomass’

L106-107: Too many significant figures on latitude/longitude. Suggest that 4 decimal places are sufficient. Also, consider omitting words ‘latitude’ and ‘longitude’ as it is self-evident from the °S and °E notation.

L111: Omit ‘as well as’.  Reword as: ‘temperature (…), conductivity, and an optode….’

L116: What does ‘micro-Winklers’ mean here?

L118: Volume of bottles?

L131: Omit ‘their’.

L152: Be consistent with significant figures: ‘12’ and ‘25’ should read ’12.0’ and ’25.0’.

L153: One decimal place for salinity is sufficient.

L160: Remove extraneous ‘in’.

L162: What do you mean by ‘significantly’?  Omit or explain with statistics.

L174: Describing statistical relationships between GPP and CR is problematic, because they are not independent (GPP  = NCP + CR).

L180: Provide units for AE.

L197: Regarding the phrase ‘relatively high GPP rates’: relative to what?

L199: Do you mean ‘NCP’ here instead of ‘GPP’?

L199: ‘Respiration’ should read ‘respiration’.

L224: Should read ‘locations’, not ‘location’.

Figs. 1-3: Awkward month abbreviations. I suggest ‘Jan’,’Feb’,’Mar’,’Apr’,’May’,’Jun’,’Jul’,’Aug’,’Sep’,’Oct’,’Nov’,’Dec’.

Figure 6: Misspelled. Should be ‘Arrhenius’.


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: HI-MC: A NOVEL METHOD FOR HIGH-THROUGHPUT MITOCHONDRIAL HAPLOGROUP CLASSIFICATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors should provide a more detailed statistical basis for their haplogroup selection criteria. Why certain SNP combinations are better representatives in the minimalistic tree. Also the authors should provide some statistical analyses of genetic variation within each population, for example between ethnic groups.

In large number of mtDNA haplogroup studies many mtDNAs in a data set can not be assigned to the recognized haplogroups. To identify new basal lineages whole mtDNA sequencing is a must. How does Hi-MC handle this problem which can confound haplogroup assigments.

The authors should elaborate their rank calculation method mathematically. Without the exact details its difficult to assess the exact working of the algorithm. For example how does the algorithm incorporate the phylogenetic weight of each polymorphism in a particular combination of SNPs.
Experimental design: The experimental design is basically the same as Mitchell et al. Hum Genet. 2014. As mentioned above, without the detailed mathematical presentation of the algorithm its difficult to assess the exact working of the algorithm.
Validity of the findings: The conclusions are valid and the current limitations are well documented but the authors need to put some effort in explaining the basis of these limitations. Why are many Asian-specific haplogroups not well captured? What are the features that need to be improved for the next iteration so that the algorithm will perform well in most populations including Asian ancestry?
Additional comments: The authors should include a section detailing specific advantages and disadvantages of the different mitochondrial haplogroup classification methods.

mtDNA sequencing using NGS methods allow detection of mitochondrial DNA heteroplasmy with minor allele frequencies. The authors should include a section on how a selective SNP set can handle mitochondrial DNA heteroplasmy.

Could NuMTs play a bigger confounding role in a selective SNP panel based method given that any NuMT will have a higher mutation accumulation rate than a standard mitochondirail DNA and without the proper sequence context can complicate the results/inferences.


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: HI-MC: A NOVEL METHOD FOR HIGH-THROUGHPUT MITOCHONDRIAL HAPLOGROUP CLASSIFICATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written, and a pleasure to read, with appropriate background and detail of the problem.

The manuscript suggests (line 110) that more information is available at http://www.icompbio.net. However, that website does not include information on this software. I clicked on several links but was not able to find a link to Hi-MC (a direct link to the page should be provided).

The readme file is helpful. However, an example dataset should be provided to enable readers to quickly test the tool before using it on their own data. For example, it was much easier to test drive haplogrep2 than Hi-MC because of the available testdata (https://haplogrep.uibk.ac.at). The release of source code is appreciated (unlike haplogrep2), along with MtoolBox and Phy-mer etc.

Authors are comparing with Haplogrep (Human Mutation 2011), though a newer method (haplogrep2) was released in July 2016, including an updated webserver.
Experimental design: It would be encouraging to see the R packing on CRAN/Bioconductor instead of GitHub. It provides confidence regarding the stability of the code, and enables better version control for reproducibility (especially Bioconductor).
Validity of the findings: As previous reviewers have pointed out; comparisons with other methods are critical to motivate readers to adopt this new tool. Along with Hapmap, 1000g data from phase 1, 3  and Li et al, can be used to benchmark the tool vs haplogrep, haplogrep 2 and Phy-Mer etc

Further, use of a custom Phylotree (a version of figure 1 Mitchell et al) can be tested with haplogrep 2 (standalone version), to compare the two tools using the same reference.

Although results are described well in the text, the accuracy of the findings at different resolutions can be conveyed in a graphical form. For example, figure 1 from Mitchell et. al can be used as a template and nodes can be used to display the number of correctly and incorrectly classified individuals per node (totaling haplogroups below the node). This should be done for Hi-MC and Haplogrep 2, and a supplementary table of the results of these two methods can be used to drive the discussion.
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: HI-MC: A NOVEL METHOD FOR HIGH-THROUGHPUT MITOCHONDRIAL HAPLOGROUP CLASSIFICATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript is clearly written and meets the standard for publication.
Experimental design: Experimental design in the revised version is much more transparent than the original form.
Validity of the findings: The authors have addressed all the major queries comprehensively and this has led to a much improved manuscript.
Additional comments: No additional comments


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

Input:
Title: FORECASTING INFLUENZA EPIDEMICS BY INTEGRATING INTERNET SEARCH QUERIES AND TRADITIONAL SURVEILLANCE DATA WITH THE SUPPORT VECTOR MACHINE REGRESSION MODEL IN LIAONING, FROM 2011 TO 2015
Review round: 1
Reviewer: 1

Output:
Basic reporting: There are a clear manuscript , written in English, this manuscript cover the professional standart of courtesy and expression, the references are sufficient and correct.

Main contruction of the manuscript is aceptable

Main objectives is clear too
Experimental design: Dessign is appropiate, to solve the research question

Rigorous research methods were designed

Authors must be more clear about how internet data were obtained.
Validity of the findings: Data is robust, statistically sound and controlled
Additional comments: Please give more details about who and how internet information was obtained. Additionally time and permisions to use the platform


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: FORECASTING INFLUENZA EPIDEMICS BY INTEGRATING INTERNET SEARCH QUERIES AND TRADITIONAL SURVEILLANCE DATA WITH THE SUPPORT VECTOR MACHINE REGRESSION MODEL IN LIAONING, FROM 2011 TO 2015
Review round: 1
Reviewer: 2

Output:
Basic reporting: Liang et al. Developed and explored the utility of a SVM regression model in the forecasting influenza epidemics by integrating data from internet search queries and data from traditional surveillance. The intention of this work is relevant, because it could improve the strategies for attending expected outbreaks or epidemics.
Authors have found relevant words that have relation with the number of influenza cases in four times: in the same month, Lag one month, lag two months and lag three months, however they don don’t explain why those times were the most relevant. In this sense it should be useful to include in the table 1 the correlation values of search terms in a time in where the number of influenza cases is the lowest. This could show how the search frequency is when using these words "at a basal level", that is, at a time not related to the high frequency of influenza cases, or during national preparations to face seasonal influenza (campaigns or preparations). of prevention).
Figures 1 and 2 does not contain enough legends to understand it, also it does not have titles in the axis and units. I recommend including that missing data to improve the figures and to avoid misinterpretation.
Experimental design: Some important data could improve the work
1.- [Lines 121-138]
There is not clear, why the RMSE, RMSPE and MEPE metrics are adequate to measure the performances of the SVM regression model.
A more detailed explain for the use of this metrics could strength the experimental design. it should be more important to show the epidemiological utility of this metrics instead of the mathematical fundamentation.
2.- [Lines 103-113]
“Official monthly reported number of influenza cases in Liaoning province, China was acquired from China National Scientific Data Center for Public Health (http://www.phsciencedata.cn) from 107 January 2011 to December 2015”
Why did you include those period of time? Why you did not include data from 2016 to 2017?
There are some weakness in the design:
1.- Lines [123-124] “the rest 15 months’ data from October 2014 to December 2015 was performed for model validation”
Why did you only include 15 months for validation? I mean if you nowadays have recent data, why did you only use 15 months for validation? You could strength your SVM regression model if you extend the period of validation from October 2014 to December 2017.
Validity of the findings: Although some tables and figures show relevant results, there are some months in where there is not a good correlation between the ensemble model and the influenza cases (For example, two peaks of cases did not were forecasted, but also there were months that the model forecasted an increased number of cases and the real number was lower). Those findings not necessary imply that the model fail to detect tendencies or even a possible epidemic. If you could extend at least three years the period of validation, there were more available data to know the utility of the proposed model.
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: FORECASTING INFLUENZA EPIDEMICS BY INTEGRATING INTERNET SEARCH QUERIES AND TRADITIONAL SURVEILLANCE DATA WITH THE SUPPORT VECTOR MACHINE REGRESSION MODEL IN LIAONING, FROM 2011 TO 2015
Review round: 1
Reviewer: 3

Output:
Basic reporting: 1. In abstracts, the reported parameters "C=4, ε=0.01, γ=0.04" are out of context. It is unclear what these parameters are referring to.
2. Standard acronym for United States Centers for Disease Control and Prevention is "US-CDC"
3. The model labeled "Past influenza cases" are not clearly stated in the article. My best guess is from line 178 that same SVM model is applied with data of past influenza cases, and it is unclear how many lags are used.
Experimental design: 1. In line 119, the requirement for search terms to have correlation coefficient above 0.4 seems arbitrary. What's the justification for this "0.4"requirement?
2. In line 158, for clarity, the mathematical formula and the parametrization of SVM should be given.
3. In line 161 and Table 3, is cross-validation used to select parameter C? It seems authors are selecting C to minimize overall RMSE, which is prone to overfitting. The same comment applies to parameter γ and ε.
Validity of the findings: 1. What's reason for study period January 2011 to December 2015? Is this due to data limitation?
2. Is there discussion on why search terms can have lagged impact as in Table 2? I found the vaccine terms intuitive and sensible, but found it not as convincing for lag one month search keywords.
Additional comments: The authors try to use Support Vector Machine for real-time nowcast of monthly reported number of influenza cases in Liaoning province, China. In general the article is well written and the results are convincing. However, there is some ambiguity in the methodology section that should be further clarified.


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

Input:
Title: FORECASTING INFLUENZA EPIDEMICS BY INTEGRATING INTERNET SEARCH QUERIES AND TRADITIONAL SURVEILLANCE DATA WITH THE SUPPORT VECTOR MACHINE REGRESSION MODEL IN LIAONING, FROM 2011 TO 2015
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors try to use Support Vector Machine for real-time nowcast of monthly reported number of influenza cases in Liaoning province, China. Although the approach has been previously developed for infectious diseases surveillance in other countries, it is first time being applied to Liaoning province, China. The method is rigorous and findings are convincing, and in general the paper has good quality to join the scholarly literature. PeerJ seems a perfect outlet for this.


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: COMPLEX CHARACTERIZATION OF OAT (AVENA SATIVA L.) LINES OBTAINED BY WIDE CROSSING WITH MAIZE (ZEA MAYS L.)
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: Correct.
Validity of the findings: no comment
Additional comments: Please find below the review of the manuscript: “Complex characterization of oat (Avena sativa L.) lines obtained by wide crossing with maize (Zea mays L.)”. The topic of the manuscript is interesting from practical and theoretical point of view.
High level of homozygosity possessed by DH lines is a feature highly desirable for durability of certain characteristics of new cultivars. The advantage of this technique is the DH lines could be generated in one round of reproduction. Because of this reason the technique allows to shortened time of producing new cultivars. Among couple of method to generate DH lines is wide crossing. For oat this method is most effective to get oat (Avena sativa) haploids (actually polyhaploids since oat is hexaploid) and then DH lines with application of maize pollen. Therefore the manuscript is interesting for plant breeders because is focused on efficiency of getting DH lines. Typically in wide crossing chromosomes from pollen donor are completely eliminated in the early stage of embryogenesis, but in oat one or more maize chromosomes could be retained. Interestingly oat can form stable and fertile hybrids with maize (OMA lines). In the study presented in this manuscript Authors also look at the lines which retained fragments or whole maize chromosomes because it may result in morphological changes and affect the yield of oat, and more generally have impact on fertility.
Although I highly appreciated the topic and the research effort made by Authors I have several minor comments presented bellow.

Detailed comments:

Introduction
Extend literature review to some information concerning mutants of CENH3 centromers, as this method becomes a new tool for haploids production.

Material and methods
Explain the abbreviation NAA and KIN.
Was only roots of haploid plants treated with colchicine for chromosome doubling?
Statistics section is poor. Please, rewrite this.

Results
Information about correlation between observed traits would be interested.

References
Check carefully cited literature e.g. Rines et al. 2009 is listed twice, and some literature is incomplete e.g. Majka et al. 2017, Chaudhary et al. 2013.

Tables
Table 1 needs sum of squares and mean squares for residual.
Table 2 needs LSD or HSD values for observed traits.

Figures.
The Authors use large number of DH lines and gave the encoded name of each one, They also mention cv. Waza used as pollinator, but I found in Figure 1. that Authors used in PCR amplification with Grande 1 primers, maize in line 2 and oat in line 3. Could you please specify in the figure the exact genotype e.g. for maize cv. Waza and in the description of Figure 1, cv. Waza – positive control , and for oat (actually we don’t know what was that, therefore the reader could be lost or not sure what genotype is there so, I suggest in description of line 3 to write cv. Stoper (I assumed that it was this genotype, but it must be clear that there is no oat DH line), and in the description of Figure 1 cv. Stoper – negative control. I also suggest to change the legend above the electrophoresis: “Oat x Maize F1 plants” to “Oat x maize F1DH plants”

In my opinion the manuscript covers an interesting and valuable scientific information about production and characterization of oat doubled haploids and oat x maize hybrids. Therefore I think it meets aims and scopes of the PeerJ journal, and I recommend the manuscript for publication but after minor revision.


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: COMPLEX CHARACTERIZATION OF OAT (AVENA SATIVA L.) LINES OBTAINED BY WIDE CROSSING WITH MAIZE (ZEA MAYS L.)
Review round: 1
Reviewer: 2

Output:
Basic reporting: See General comments
Experimental design: See General comments
Validity of the findings: See General comments
Additional comments: The OMA lines have acted as important materials using not only in the new resource development but also in the fundamental studies such as centromere biology and epigenetic dynamics of imported phenotypes in hybrids. In this study, the authors developed a series of new OMA lines and conducted basic cytogenetic study to characterize the karyotype for those lines. However, disappointed, the story is fairly simple and straightforward. The manuscript was not composed in a professional way and should be rewritten completely.
1\Actually, there are numerus literatures published based on studes using OMA lines. However, only few “old” papers were mentioned by authors. The authors should rewrite the section in Introduction to make an extensive introduction on the utility of the OMA lines.
2\Lines 116, the genotypes should be show as a supplemental table other than as a long-list in the manuscript.
3\ In Methods, the method descriptions should be shortened or deleted if method was conducted as published method and seems no any modifications were made.
4\ Table 2,3,4 looks so redundant and unreadable. They should be rearranged to make them concise.
5\line 271-279 those should be moved to the Method.
6\lines 281 “whole maze chromosome” What is that mean?
7\lines 293 Figures should be shown here to support the description of 45S rDNA.
8\ lines 294 to 301 states that “A total of 12-14 hybridization signals for the maize gDNA probe were detected (Figure 4d)”, which doesn't match what the figure actually shows. Please rectify all the confusing statement in the whole paragraph.
 9\lines 315-316 This paragraph contains only one sentence, it is so strange.
10\ Scale bars for every separate image should be added in Figure 1.
11\ lines 311, the noun progeny can be countable or uncountable. In more general, commonly used, contexts, the plural form will also be progeny.


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: DIFFERING RESPONSES OF RED ABALONE (HALIOTIS RUFESCENS) AND WHITE ABALONE (H. SORENSENI) TO INFECTION WITH PHAGE-ASSOCIATED  CANDIDATUS XENOHALIOTIS CALIFORNIENSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1/. Basic Reporting:
•	The manuscript is written in unambiguous and professional English. The manuscript does not require English language editing services.
•	The manuscript’s introduction provides an overview to the Ca. Xc infection of abalones and the history and severity of the problem, including how changes in water temperature effect abalones. All of these are topics relevant to the study’s findings.
•	The introductory section is sparse on the biology of phages. The review of Friedman et al. (2014), which is referenced within the introduction, does discuss the diversity of phages within oceans and phage lytic versus lysogenic lifecycles. These topics are relevant to the study’s findings.
•	The structure and format of the manuscript is professional and correct.
Experimental design: 2/. Experimental design
•	The authors do note that this study builds upon other work, lines 294-296, where ‘they replicate a thermal induction study undertaken with red abalone prior to the appearance of the phage’. However, the work presented in this study is a self-contained unit of research that advances the scientific community’s understanding of Ca. Xc infection of abalones under a different conditions.
•	While the study is well designed and conclusive in its findings (that there have been recent differences in Ca. Xc pathogenicity of abalones with changes in water temperature), the title of the manuscript is misleading. The study suggests the altered effect/reduction or elimination of Ca. Xc in abalones is caused by phages. At no point during the study are phages confirmed as present. The phenotypic alterations of the Ca. Xc (which are clearly observed) could be due to the past exposure of Ca. Xc strains to phages and not due to continued phage presence (for example, see Leon & Bastias (2015) “Virulence reduction in bacteriophage resistant bacteria”). Thus, the manuscript is more an examination of the current effects of Ca. Xc on red and white abalones (with phage as a potential confounding factor explaining the discrepancies between present and past observed differences).
•	The work presented has been performed to a high technical standard, with statistical analysis performed to underpin the study’s observations.
•	The raw data and R scripts for Figures 2, 4 and 5 allow for the reproduction of Figures within the manuscript. The R script for Figure 3 appears to be missing its start, and the relevant tables/objects cannot be loaded, thus the final image cannot be recreated without additional input. Therefore, the raw data for Figure 3 is also not verified.
•	The study is well designed, even acknowledging some of its limitations (lines 291-292).
Validity of the findings: 3/. Validity of the findings
•	As stated previously, the study is well designed and conclusive that there are current differences in Ca. Xc virulence on abalones relative to previous years. The reduced mortality observed in abalones coincides with the appearance of a phage in Ca. Xc populations.
•	However, no description of Ca. Xc populations before and after the appearance of this phage is presented nor is the phage characterised in silico or in vitro. Thus, any changes in Ca. Xc and phage populations are anecdotal and need to be treated more cautiously.
•	The observed differences in abalone mortality may have been as a consequence of changes in bacterial populations, whereby an emergent lytic phage changed the Ca. Xc population. Alternatively, a new Ca. Xc strain emerged which carried a prophage. Scenarios such as these have not been sufficiently discussed as plausible and the authors claim an uncharacterised phage is responsible for their observations without sufficient evidence.
•	While the study is of merit showing clear differences are observed in abalones with current Ca. Xc populations, there is too much emphasis on the phage being a sole driver of change and not sufficient explanation of future directions. Only the final sentence of the manuscript, lines 337-339, provides a positive outlook and future direction for controlling Ca. Xc decimation of abalone populations.
•	The authors should consider discussing the need for a population examination of Ca. Xc, looking at strain level differences and potential attenuation of virulence between current populations and previous infective bacteria.
•	The manuscript’s discussion also needs to build upon the need for characterising all mobile genetic elements, including phages, and also their encoded functions.
•	Finally, the selective pressure exerted by continued Ca. Xc infection and mortality may have caused population shifts in abalones (perhaps more dramatically in red abalones than white) resulting in resistance. This is mentioned in the text, lines 327-330, where the authors note the introduction of genetic variation in abalones. Again, however, there is no discussion for the need to study abalone populations considering its endangered status and economic importance.
Additional comments: The study is of interest, showing recent changes in the virulence of Ca. Xc and thus increased survival of abalones. As global water temperatures increase, this will become an even more important topic. If presented correctly, this manuscript could be referenced frequently as a keystone upon which is built an example of how changes in oceanic conditions could lead to changes to phage, bacterial, invertebrate and vertebrate populations. However, in my opinion, too much weight is put on phages as the sole driver of the change in Ca. Xc. There needs to be a more cautious approach to explaining that phage may be the reason there has been an improvement in abalone populations. This is until Ca. Xc and phage populations are characterized in more detail. In addition, there are many avenues for future research that should be discussed to give a more complete picture to the severity of the problem faced.


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: DIFFERING RESPONSES OF RED ABALONE (HALIOTIS RUFESCENS) AND WHITE ABALONE (H. SORENSENI) TO INFECTION WITH PHAGE-ASSOCIATED  CANDIDATUS XENOHALIOTIS CALIFORNIENSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is very well written and clear
Experimental design: The were some minor issues with the experimental design, nothing that cannot be accounted for in the interpretation of the results. See notes to the authors.
Validity of the findings: It is difficult to draw strong conclusions about the effects of the phage given your experimental design. This isn't critical, but I do think its best to reframe this manuscript. See notes to the authors.
Additional comments: I was very excited to review this manuscript. Abalone withering syndrome has led to dramatic population declines in California black abalone and contributed to the closure of the multi-species California abalone fishery. All of California’s abalone species appear to have differential resistance to the agent of withering syndrome, the Rickettsiales-like prokaryote Candidatus Xenohaliotis californiensis (Ca. Xc), and if infected with this pathogen, all abalone species also appear to demonstrate differential susceptibility to clinical signs of withering syndrome. Much of this fantastic body of work has been conducted by the authors here. Thus, this system has brought new insights into the ecology of marine diseases and the role of environmental conditions on disease pathology and spread, all within a multiple host community. Recent work has also identified a novel bacteriophage infecting Ca. Xc. There is a rich future ahead for innovative research on the ecology and pathology of marine diseases using this system as a model.

That said, I feel you tried to do too much with this dataset. The single biggest issue is that you cannot draw causal inference about the effects of the bacteriophage given the experimental design. Koch’s postulates apply to the effect of the bacteriophage on Ca. Xc. Given your experimental design, you cannot decipher whether presence of the bacteriophage led to decreased pathology, or increased immunity (and decreased pathology) led to the presence of the bacteriophage. I don’t think your inference is totally off, but I do think that both processes may be occurring. Understanding the relative contributions of 1) the interaction between abalone and Ca. Xc on phage dynamics and 2) the interaction between Ca. Xc and the phage on abalone health will be an exciting area for work in the future. Since we cannot yet culture either Ca. Xc or the phage, or reliably isolate the Ca.Xc from the phage and the phage from the Ca.Xc, this unfortunately has to remain a question for the future.

The second issue, and I don’t think this is huge deal, is the overall “frailty” of white abalone in your study, even in your unexposed control group (please replace the term “naïve” with “control” in your revision). I could be wrong, but I think two things are going on: first, white abalone are very susceptible to Ca. Xc, hence high mortality in both exposed groups. Second, you did not have a control group at ambient (cold) temperature, so I can’t make a strong inference here, but it seems white abalone are more sensitive to temperature independent of exposure to Ca.Xc. This makes sense given that they are presumptively a deeper water species. Given this though, your baseline hazard in your controls differed between the two species. Which is fine, but you should be clear about this in your interpretation of any results. A Cox model stratified by abalone species would apply well here.

I think it will be best for you to reframe this manuscript. Rather than focus on the phage, focus on the clear differences between the species – both in overall frailty and the effect of exposure to Ca.Xc. You can discuss the presence of the phage in response to your treatments, especially since you report the occurrence of the phage in white abalone (which is novel and exciting), but you should be clear about cause and effect. A clear presentation of differences between red and white abalone in WS pathology following exposure to Ca. Xc will be a valuable contribution to science. I am happy to help you reframe and revise this manuscript in any way.

Also, if you have PE or DG samples taken at the time of observed mortality, I think it will be very helpful to have qPCR and histology data from these time points.

Another minor issue is your source of exposure. A head tank full of abalone presumptively infected with Ca.Xc is well documented as a valid source of exposure. I imagine you placed abalone in the head tank of your control group to also control for exposure to everything else beyond Ca.Xc that is associated with abalone feces. The problem with doing this lies in using qPCR of feces to confirm exposure. The qPCR is a sensitive test but it is not definitive. You therefore cannot rule out some exposure to Ca.Xc in your unexposed control group. I don’t think this is a big deal since you didn’t see much Ca.Xc in your control animals over the course of your experiment, but be clear about all possible sources of exposure in your reporting.

And a minor reporting note. When reporting statistical tests such as ANOVA and the Cox model, please report full statistical results in the manuscript text rather than just P-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: DIFFERING RESPONSES OF RED ABALONE (HALIOTIS RUFESCENS) AND WHITE ABALONE (H. SORENSENI) TO INFECTION WITH PHAGE-ASSOCIATED  CANDIDATUS XENOHALIOTIS CALIFORNIENSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: 1/. Basic reporting:
•	Possibly a few typos and commas which will be picked up by PeerJ’s proofing, but overall the manuscript is well written and very easy to follow. Thank you.
•	Sufficient and informative references are provided.
•	Images look well, and with the help of the figures legends, show clearly what is desired.
•	Raw data and R scripts are provided and working correctly to reproduce all images. However, there are a few extra lines of code at the bottom of Figure_2’s script (which are not necessary to produce Figure_2). In order to run this extra few lines of code I needed to install and load extra packages (‘ggplot2’ and ‘survminer’). Just so you know.
•	Overall, the results of the manuscript are ‘self-contained’ and not dependent on additional publications or knowledge to read and understand.
Experimental design: 2/. Experimental design:
•	While the experimental design has its limitations, these limitations are discussed. The overall study design is clearly described to independently reproduce the results observed.
Validity of the findings: 3/. Validity of the findings:
•	The study’s goal is clearly defined with the results and discussion addressing the current and future aims sufficiently. These results are important and novel and will be important for future implementation of best practices into abalone farming.
Additional comments: 4/. General comments:
I am very pleased to have been involved in reviewing such a well prepared and clearly described experiment, looking at the effects of temperature and pathogens against abalones. I had concerns in the previous draft regarding the over-emphasis of the phage’s role in the observed effects. However, the authors have done a very good job in providing additional background information and also cautiously explaining other possibilities for their observed results. With these changes, I will support the publication of this manuscript without additional edits.
Thank you for taking the time to address my concerns, and best of luck with what appears to be many future avenues of research ahead.


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: DIFFERING RESPONSES OF RED ABALONE (HALIOTIS RUFESCENS) AND WHITE ABALONE (H. SORENSENI) TO INFECTION WITH PHAGE-ASSOCIATED  CANDIDATUS XENOHALIOTIS CALIFORNIENSIS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript is clear, well-written, unambiguous, sufficiently cited, professional, and self-contained with relevant results to the hypotheses tested.
Experimental design: The research question is well defined and rigorously investigated.
Validity of the findings: The data are robust and conclusions are well stated.
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: DRY SEASON DIET COMPOSITION OF FOUR-HORNED ANTELOPE TETRACERUS QUADRICORNIS IN TROPICAL DRY DECIDUOUS FORESTS, NEPAL
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment. Nicely written article on a lesser known species
Experimental design: Original research work with well defined research question. Methods described with sufficient details.
Validity of the findings: Fairly good results. Conclusion are well stated, linked to original research questions.
Additional comments: Good work


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

Input:
Title: DRY SEASON DIET COMPOSITION OF FOUR-HORNED ANTELOPE TETRACERUS QUADRICORNIS IN TROPICAL DRY DECIDUOUS FORESTS, NEPAL
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comments
Experimental design: no comments
Validity of the findings: na
Additional comments: 1.	Removed chi/statistical value from abstract make it, simple and understandable.
2.	Introduction section is not well-organized need to with general background, species status, hypothesis, what are you testing for and why? And innovation in your research
3.	Line 49: not clear about Species: animal or what ?? this paragraph not appropriate with starting background, add more about dietary stuff,  line 55 is odd sentence does link above or later.. revised it.
4.	It is not the first study as author claim more advanced study has been already done
Kunwar, A., R. Gaire, K.P. Pokharel, S. Baral & T.B. Thapa (2016). Diet of the Four-horned Antelope Tetracerus quadricornis (De Blainville, 1816) in the Churia Hills of Nepal. Journal of Threatened Taxa 8(5): 8745–8755; http://dx.doi.org/10.11609/jott.1818.8.5.8745-8755
Pokharel, K. P., Yohannes, E., Salvarina, I., & Storch, I. (2015). Isotopic evidence for dietary niche overlap between barking deer and four-horned antelope in Nepal. Journal of Biological Research-Thessaloniki, 22(1), 6.
4.	Line 58 jumping: write about species background then distribution behaviours, diet and what has been done, problems, research gap etc..
5.	Line 115 Key informant interviews what purpose what authors asked, whey, how many.
6.	Line 117; how transect line was developed, how many, why they did survey in transect line,
7.	Line 119 FHA pellets: how experts distinguish it??
8.	Line 116 to 118: who were assistants and who were experts what the role was from authors on field survey???
9.	Line:134  need to put the supplementary file with GPS points pellet presence sites.
10.	Line 142: use the latest reference for this methodology:
Aryal A, SCP Coogan, W Ji, JM Rothman, D Raubenheimer. 2015. Foods, macronutrients and ﬁbre in the diet of blue sheep (Psuedois nayaur) in the Annapurna Conservation Area of Nepal. Ecology and Evolution 5(18): 4006-4017.
Aryal A., D Brunton, W Ji, J Rothman, SCP Coogan, B Adhikari, S Juhnu, D Raubenheimer. 2015. Habitat, diet, macronutrient, and fiber balance of Himalayan marmot (Marmota himalayana) in the Central Himalaya, Nepal. Journal of Mammalogy 96(2): 308-316.
11.	Line 149 to 154 add above reference
12.	Line 160 A total of 133 micro-histological photographs Put this file and photo for as supplementary file for publication. These could be future reference for follow researcher..
13.	In discussion need to discuss micro histological methods, its drawn back and how you address method bias and also discuss with this methods how it can use for herbivore and carnivores discuss it such as
Aryal A, J Hopkins, W Ji, D Raubenheimer, D Brunton. 2012. Distribution and diet of brown bear in the upper Mustang region, Nepal. Ursus 23 (2): 231–236.

Discussion section: discuss how non-invasive genetic analysis can be helpful for future research, conservation measure/effectiveness and impact of climate change etc… on this species for example:
Aryal A, D Brunton, T McCarthy, D Karmachharya, W Ji, R Bencini, D Raubenheimer. 2014. Multipronged strategy including genetic analysis for assessing conservation options for the snow leopard in the central Himalaya. Journal of Mammalogy 95(4):871-881.
Aryal A, UB Shrestha, W Ji, S Ale, T Ingty, T Maraseni, G Cockfield, D Raubenheimer. 2016. Predicting the distributions of predator (snow leopard) and prey (blue sheep) with climate change in the Himalaya. Ecology and Evolution 6(12):4065–4075.
discuss conservation issue and its preys species interaction and conservation measurement such as:
Aryal A,  KP Acharya, UB Shrestha, M Dhakal, D Raubenhiemer, W Wright. 2017. Global lessons from successful rhinoceros conservation in Nepal. Conservation Biology. http://onlinelibrary.wiley.com/doi/10.1111/cobi.12894/full
Aryal A, RP Lamsal, W Ji, D Raubenheimer. 2016. Are there sufficient prey and protected in Nepal to sustain an increasing tiger population? Ethology Ecology and Evolution 28(1): 117-120.
Aryal A, W Ji, UB Shreshta, R Bencini, D Raubenheimer. 2015. Conservation conflict: Factor people into tiger conservation. Nature 522: 287-287.


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: DRY SEASON DIET COMPOSITION OF FOUR-HORNED ANTELOPE TETRACERUS QUADRICORNIS IN TROPICAL DRY DECIDUOUS FORESTS, NEPAL
Review round: 1
Reviewer: 3

Output:
Basic reporting: This manuscript is well organized and generally follows the scientific format; however, to be acceptable for publication it requires substantial revision in regards to the following:

1) The writing itself, while good, does need substantial work to improve the clarity and flow of the paper. Significant polishing of the text is necessary before being acceptable for publication. I provide some suggestions in the General Comments to the Author, but further polishing of the text will be required.

2) The Introduction wanders and does not really get at the purpose of the study and hypotheses/predictions tested by the authors. Much of the Introduction contains “filler” text about the species that is not particularly germane to the current study. In my view, the authors really need to focus on why understanding the winter diet of four-horned antelope is of interest. To do so, they need to really draw on the ungulate diet literature in general, and what is already known about FHA diets specifically. I was surprised that much of the reference on FHA diets was not mentioned earlier in the Introduction (but it was in the Discussion). This literature needs to be the backbone of the a revised Introduction, accompanied by a solid rationale and hypotheses (if applicable, see my comments below). Most importantly, the purpose of the study needs to be made crystal clear.

3) Too much of the text focuses on Banke National Park itself, FHA in Banke National Park, or studies on ungulates in Nepal. In my view, the authors need to focus the paper on diets of FHA while at the same time broaden the scope of the paper to ungulate diets in a global context. That is, I recommend that the authors a) delete much of the text about Banke National Park that has little to do with the current study; b) consider what is known about FHA diets and ecology across their range, not just in the park or Nepal; and c) draw much more heavily on the ungulate diet literature globally, than specific to Nepal.

4)  There are many instances where I thought unnecessary information was provided by the authors that is not of the type that is normally provided in scientific papers (e.g., Lines 117, 123, 134, and others), and this information should be deleted.

5) The captions for Figure 1 and Table 1 need to provide much more detail about what information the figure and table provide. They should be able to stand alone.

6) Please iInclude both the common name and scientific name at first use for all species (e.g., barking deer at Line 70; tiger at Line 99, Hyena hyena at Line 107, and others).

7) Please avoid starting sentences with numbers.
Experimental design: I have difficulty evaluating the experimental design of this study because there really isn’t one there. In essence, this is a descriptive natural history study that doesn’t really aim to test any meaningful hypotheses. That is not a judgement on the value of the work, just to state that it is quite descriptive and not experimental.

As noted above in the Basic Reporting section. The research question is not well developed, and the context to assess whether it is relevant or meaningful, or fulfills an important information gap, is lacking. I want to believe that it is relevant and meaningful, but I need the authors to explicitly develop that argument for the reader; rather than having the reader trying to figure that out for themselves.

In terms of the study methods/techniques used to determine FHA diets, the authors do a good job of following standard protocols for microhistological analyses of ungulate diets from fecal samples. I have few substantive issues with how the work was done and, generally, it is reported to sufficient rigor to permit the study to be replicated. Good work.

Some methodological questions that should be addressed in a revised manuscript include:

1) How easily was it to determine FHA pellets from those of barking deer, or any other sympatric ungulate that also defecates pellets? It is quite important that the paper address the reliability in distinguishing between the pellets between FHA and sympatric species with fecal pellets that are similar.

2) If fresh pellets (within 7 days – Line 133) are important, then the authors need to address how they could ascertain this in the field, taking note that in arid environments pellets may dessicate at different rates in different habitats (see: Jung and Kukka. 2016. Wildlife Biology 22: 160-166; Hibert et al. 2010. European Journal of Wildlife Research 57: 495-503).

3) The authors need to describe in detail the sampling protocol for obtaining reference collections of available plants that FHA may use as forage.
Validity of the findings: The data from this study are robust and statistically sound – I have few substantive issues with the methodology employed.

A major issue that is only partially addressed in the manuscript is that the data come from a single year, at a single study site, during a single season. This imposes some major limitations on what can be inferred about the diet of FHA, and the authors need to tackle this limitation in the Discussion. For instance, how representative is this study area of the vegetation communities found across the range of FHA? Was the climate and weather typical the winter of the study, or might the availability of some of the forage resources vary from year to year, resulting in differences in use by FHA?

As noted above in the Experimental Design section, this is a descriptive study so the ability of the authors to link conclusions to supporting a priori hypotheses are limited.

Finally, a minor point, but the authors should discuss the limitations of microhistological anaylses. For example, some forage classes, such as forbs, are chronically underrepresented in microhistolocical analyses, which will bias the results.
Additional comments: Overall, I’d like to state that I enjoyed reading this manuscript and believe that it strives to fill an important gap in our knowledge of the ecological requirements of FHA. Thank you for doing this study.

I believe that through a critical and substantive edit to focus the manuscript on the question at hand – while more broadly drawing from the global literature – this study would be most appropriate as a Note or Short Communication in a mammalogy or zoology journal, such as Mammal Research, Mammal Study, Mammalia, or Mammalian Biology. The data is certainly valuable, but is limited in it’s spatial and temporal scope, which restricts making broader inferences about FHA diet.

I really hope the authors expend the effort to substantially rework this manuscript and publish it in an appropriate venue. The data are of interest and value, and the authors have done a lot of work in the field and lab to collect these data, which can benefit our understanding of FHA ecology.

Below are suggestions aimed at helping the authors improve their manuscript.

Introduction

Line 51: Replace “large ungulate herbivores” with “ungulates”

Line 52: Delete “such as alpine meadows, savanna grasslands, and dry forests of tropical regions”

Line 54: Replace “dry” with “the arid”

Line 55: Replace “have” with “has” and “on” with “for”

Line 56: Delete: the last part of this sentence, beginning at “, and thus studies on their…”

Line 58: Replace “one such solitary medium sized ungulate species, which patchily occurs” with “a medium-sized, solitary ungulate that is patichly distributed”

Line 60: Replace “animals of this species” with “FHA”

Line 62: Replace “decline” with “declined”

Lines 63-67: I think this long sentence about where they occur in Nepal is not relevant and should be deleted.

Line 68: So, if it is already known to be a browser based on other studies, I am wondering what, specifically, new information this study adds. The Introduction needs to explicitly layout the rationale and value of the present study, within the context of what is already known about the diet of FHA.

Methods

Line 96: This sentence should be in the Acknowledgements, not the Methods.

Lines 104-110: These lines aren’t needed and can be deleted. The paper is about FHA, not the park.

Line 115: I like that local knowledge was used to guide the field work. Well done.

Line 117: What defined the “expert”? Please explain.

Line 117: the number of field assistants is not important in the reporting of the work and should be deleted.

Line 119: Please describe or define, or provide a reference for “purposive sampling”, or delete this sentence.

Line 123: Delete the last part of this sentence, beginning with “and labeled in …”

Line 125: Rework this sentence using wording such as: “FHA pellets are usually elongated; however, in some cases, they may be cylindrical with a point on one end (Pokharel 2000).”

Lines 129-131: Delete the text here, beginning at “at the office of…” and ending at “pellets during field survey.” Unnecesary detail.

Line 131: This sentence, beginning with “ Total 53 pellets group…” belongs in the Results, not the Methods.

Line 134: Delete the last part of this sentence, beginning at “were collected in zip lock bags…” Unnecessary detail.

Line 135: Reword to “We randomly subsampled 25% of each pellet group for further analyses.”

Line 136: For how long were the samples air-dried?

Line 137: More importantly than where the collected plant materials stored, the authors need to describe in detail the sampling protocol for obtaining reference collections of available plants that FHA may use as forage.

Lines 143-145: Replace “of plant eating species in Nepal” with “ungulates”, and reduce the number of cited papers. I suggest that the focus be on cited works not only from Nepal but include the modern use of microhistological studies of ungulates from other parts of the world, in general (e.g., Jung et al. 2015. Journal of Wildlife Management 79:1277-1285; Jung. 2015. Mammal Research 60:385-391; Wangchuk et al. 2016. Journal of Natural History 50: 759-770; Cain et al. 2017. Wildlife Biology; ., or many, many others).

Line 149: Replace “through” with “using an”

Line 151: Replace “given by” with “of”

Line 170: What are “climbers”? Are these vines? Please define.

Line 175: Replace “eats” with “ate”

Line 178: Why was a P value of 0.01 used instead of the more widely used P > 0.05? I would think P > 0.05 would be sufficient.

Line 184: Replace “thirty” with “30”. Use numbers of it is ≥10.

Line 176: This is a fairly weak hypothesis. I suggest rephrasing to something along the lines of you tested for selection.

Results

Line 189: Here and elsewhere, please replace “<<” with “<”

Line 198: Here and elsewhere, please avoid beginning a sentence with a number.

Line 203: Add “the” after “species in”

Discussion

Line 220: These studies should be highligted in the Introduction as well, to provide context for the current study.

Lines 223-238: Same comment as for Line 220. These studies should be also discussed in the Introduction, to provide context for what is already known about the diet of this species.

Line 247: Replace “the tamed” with “captive”

Line 256: The statement that the study obtained a “reasonable optimum sample size” requires justification, or should be deleted. I would argue that 53 pellet groups is not a large sample from a statistical perspective; however, I appreciate the significant field effort that went into obtaining these samples, not to mention the amount of lab work to process this many samples. Good work.


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

Input:
Title: MULCH AND GROUNDCOVER EFFECTS ON SOIL TEMPERATURE AND MOISTURE, SURFACE REFLECTANCE, GRAPEVINE WATER POTENTIAL, AND VINEYARD WEED MANAGEMENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: Objectives well stated. Manuscript is well organized and very well written.
Experimental design: The design appears appropriate, although a strip-plot field design might have been more efficient. I do have some concerns about potential interaction among the main effects. These concerns are expressed in the "General Comments" section.
Validity of the findings: No comment.
Additional comments: This is a well organized and well written manuscript and should provide Midwestern winegrape growers with additional options for vineyard floor management. I have a few minor editorial suggestions and a few more substantive comments, as follows:

I’m unclear on the actual statistical field plot design given the nature of how data are presented in the tables. Authors state that a “randomized factorial design” with 5 intra- and 3-inter-row treatments were used. If a true factorial experiment was established, this would entail 5 x 3 (15) treatments, replicated 4 times = 60 field plots. I would then anticipate that statistical interpretations would include main effects (intra- and inter-row floor treatments), as well as their potential interactions. I failed to find mention of the potential inter- X intra-row interaction in the results or in the tabular data presented.  The main effects are presented separately, so I must assume that there were no significant treatment interactions. This should be reported for each dataset.

Some of the methodology is unclear. For example, in the discussion of soil water content, we’re informed that each recorded value was an average of three measurements (Line 163). Is that three measures per treatment replicate (3 X 4 reps)?  Similarly, how many leaves were sampled for mid-day stem water potential?

Authors mention at lines 246-247 that the lack of treatment effects on reflected PAR was unexpected “because there were obvious visual differences among the treatments.” This is also mentioned in the abstract, yet we’re not told how those differences were visually identified. What is the value of the subjective comments?

The ecophysiological measures that were taken were helpful in explaining potential vine responses, but the obvious potential responses of vine size (cane pruning weight), shoot vigor, components of yield, and fruit chemistry are all lacking. Presumably those responses are discussed in a companion paper, but it would be more satisfying to see the vine responses in this same paper with the data presented here.

Some very minor issues:  the work of Giese et al. of 2014 (lines 338-340) was conducted in the Yadkin Valley of NC, not in Virginia.  The soil temperature data in Table 2 should have a footnote defining the depth at which the soil temperature was measured. Also – the similarity of the standard errors reported here is suspicious. Line 40:  “none of the treatments affected mid-day vine water potential”. How do you know that all treatments didn’t affect mid-day vine water potential the same way? In reality, Table 5 is probably not needed – the results could be discussed in the narrative.


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: MULCH AND GROUNDCOVER EFFECTS ON SOIL TEMPERATURE AND MOISTURE, SURFACE REFLECTANCE, GRAPEVINE WATER POTENTIAL, AND VINEYARD WEED MANAGEMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: Mulch and groundcover effects on soil temperature and moisture, surface reflectance, grapevine water potential, and vineyard weed management (#22845)

Line 50-52: How does maintaining permanent sod cover between vineyard rows… contribute to the sustainability of vineyard agroecosystems?
Line 60-62: REF?
Line 72-73: RE-word/DELETE: Excess vine vigor also creates a lack of vine balance requiring
requires high labor inputs.
Line 75: REF?  especially regarding time requirements to prune and position shoots
Line 77: the phrase: “vine balance” is open to wide interpretation. In this sentence, the phrase                           “restore vine balance” might be replaced with the phrase: “reduce excessive vine vigor”
Line 88: REF?
Line 95: REF?
Line 108: own-rooted Marquette vines?
Line 115-121: it is not clear to me if the 5 under-trellis treatments had a single and consistent
inter-row treatment or if each under-trellis treatment was combined with each of the 3 inter-row treatments. Or…were each of the 3 inter-row treatments maintained with a consistent under-trellis treatment?
Line 122-137: What is the width of glyphosate treated strip and the width of the intra-row ground cover treatments?
Line 190-196: Could calculated GDDs be added in order to allow comparison with other regions?
Line 211: DELETE: “both”
Lines 231-241: At what soil temperature can one expect to see impacts on vine growth? How do these temperatures compare with your reported soil temperatures?
Line 239: DELETE “this” and replace with “our”
Line 245:  A single date measurement of PAR likely did not provide an adequate depiction of field conditions or treatment effect
Lines 253: and thus alters the spectral quality of the incident light on the underlying surface is altered
Line 255: DELETE “since” which indicates a time past…and replace with “because”
Line 269: why wasn’t a gravimetric measurement of soil water provided? It could have been used
as a benchmark and as calibration reference for possible interpretation of the soil water
measurements collected with the TDR probe after the fact
Line 304: this is a confusing sentence…is drip irrigation necessarily associated with less soil water content
compared to sprinkler irrigation? If this was the case in the cited research, then state that fact.
Line 320-321: DELETE: Table 5, no reason to include a table that does not contain differences or unusually high or low vine water status.
Line 332-333: appropriate discussion statement…any reference to support the likelihood of deeper grapevine roots?
Line 338: DELETE: “Virginia” and replace with “North Carolina”, the referenced study was conducted in North Carolina
Line 341: What “other” ways may groundcovers compete with grapevines?
Line 355: Again…I suggest to defer from the use of “improve vine balance” as an effect or outcome…”reducing vine vigor” is more exact or accurate

CONCLUSION:
** Although data was collected on groundcover treatment impact on light interception by the vine canopy (PAR), soil moisture, vine water potential and soil temperature, these parameters were not correlated to vine growth or yield. Groundcover biomass or weed % may have correlated to vine canopy density or pruning weights. Why was vine nitrogen status not measured?**

Line 362-364: This is a broad statement that is not supported by your research…you show no pruning weight or yield data that would support it. How can you be sure that the glyphosate intra-row strip is “unnecessary”, if this yield and pruning weight data…is not shown or presented? Most growers would be want to know the effect of a vineyard practice on yield.
Line 363-365: the reduction of vineyard labor was not directly supported/substantiated by your
results…did you measure it? Was “vine balance” measured? Overall, I recommend refraining from the use of the terms “vine balance”
Line 367-369: DELETE: Cool- season grasses are the most practical inter-row groundcovers because they resume growth early in the spring, which facilitates vineyard management tasks by providing a firm footing for tractor and foot traffic. This was not a measured finding of your research.
Experimental design: no comment
Validity of the findings: Mulch and groundcover effects on soil temperature and moisture, surface reflectance, grapevine water potential, and vineyard weed management (#22845)

Line 50-52: How does maintaining permanent sod cover between vineyard rows… contribute to the sustainability of vineyard agroecosystems?
Line 60-62: REF?
Line 72-73: RE-word/DELETE: Excess vine vigor also creates a lack of vine balance requiring
requires high labor inputs.
Line 75: REF?  especially regarding time requirements to prune and position shoots
Line 77: the phrase: “vine balance” is open to wide interpretation. In this sentence, the phrase                           “restore vine balance” might be replaced with the phrase: “reduce excessive vine vigor”
Line 88: REF?
Line 95: REF?
Line 108: own-rooted Marquette vines?
Line 115-121: it is not clear to me if the 5 under-trellis treatments had a single and consistent
inter-row treatment or if each under-trellis treatment was combined with each of the 3 inter-row treatments. Or…were each of the 3 inter-row treatments maintained with a consistent under-trellis treatment?
Line 122-137: What is the width of glyphosate treated strip and the width of the intra-row ground cover treatments?
Line 190-196: Could calculated GDDs be added in order to allow comparison with other regions?
Line 211: DELETE: “both”
Lines 231-241: At what soil temperature can one expect to see impacts on vine growth? How do these temperatures compare with your reported soil temperatures?
Line 239: DELETE “this” and replace with “our”
Line 245:  A single date measurement of PAR likely did not provide an adequate depiction of field conditions or treatment effect
Lines 253: and thus alters the spectral quality of the incident light on the underlying surface is altered
Line 255: DELETE “since” which indicates a time past…and replace with “because”
Line 269: why wasn’t a gravimetric measurement of soil water provided? It could have been used
as a benchmark and as calibration reference for possible interpretation of the soil water
measurements collected with the TDR probe after the fact
Line 304: this is a confusing sentence…is drip irrigation necessarily associated with less soil water content
compared to sprinkler irrigation? If this was the case in the cited research, then state that fact.
Line 320-321: DELETE: Table 5, no reason to include a table that does not contain differences or unusually high or low vine water status.
Line 332-333: appropriate discussion statement…any reference to support the likelihood of deeper grapevine roots?
Line 338: DELETE: “Virginia” and replace with “North Carolina”, the referenced study was conducted in North Carolina
Line 341: What “other” ways may groundcovers compete with grapevines?
Line 355: Again…I suggest to defer from the use of “improve vine balance” as an effect or outcome…”reducing vine vigor” is more exact or accurate

CONCLUSION:
** Although data was collected on groundcover treatment impact on light interception by the vine canopy (PAR), soil moisture, vine water potential and soil temperature, these parameters were not correlated to vine growth or yield. Groundcover biomass or weed % may have correlated to vine canopy density or pruning weights. Why was vine nitrogen status not measured?**

Line 362-364: This is a broad statement that is not supported by your research…you show no pruning weight or yield data that would support it. How can you be sure that the glyphosate intra-row strip is “unnecessary”, if this yield and pruning weight data…is not shown or presented? Most growers would be want to know the effect of a vineyard practice on yield.
Line 363-365: the reduction of vineyard labor was not directly supported/substantiated by your
results…did you measure it? Was “vine balance” measured? Overall, I recommend refraining from the use of the terms “vine balance”
Line 367-369: DELETE: Cool- season grasses are the most practical inter-row groundcovers because they resume growth early in the spring, which facilitates vineyard management tasks by providing a firm footing for tractor and foot traffic. This was not a measured finding of your research.
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: MULCH AND GROUNDCOVER EFFECTS ON SOIL TEMPERATURE AND MOISTURE, SURFACE REFLECTANCE, GRAPEVINE WATER POTENTIAL, AND VINEYARD WEED MANAGEMENT
Review round: 2
Reviewer: 1

Output:
Basic reporting: no further comments
Experimental design: no further comments
Validity of the findings: no further comments
Additional comments: no further 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: IT’S A MATTER OF DESIGN—HOW PITFALL TRAP DESIGN AFFECTS TRAP SAMPLES AND POSSIBLE PREDICTIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Thank your for this very interesting study on different pitfall trap designs and how these affect invertebrate samples. I really enjoyed reading as the article is concise, straight-forward and well written. The introduction is very good and all relevant references are cited. The question addressed in this study are very important and will improve our knowledge regarding the applicability of pitfall traps. The idea to test the performance of traps with barriers and to compare them to other designs is timely and very smart. I have some remarks (see below) that should be addressed before final acceptance.
Experimental design: The design is well-conceived and appropriate to answer the research questions. The methods are described with sufficient details but regarding the statistics I have three questions:
1. Why did you transform the carabid data to proportion data instead of using count data for NMDS? Please explain. I am concerned that this might obliterate differences in species composition. I was thinking about this because you found twice as much species in traps with barriers than in the other designs and I think that this should lead to a higher dissimilarity in species composition.
2. The fit was tested ... Which fit? What do you mean? Did you test if trap design affected the species composition by using the PERMANOVA? If yes and if test results were significant please be more careful in stating that differences in assemblage composition were rather low (see discussion).
3. I know that this means a lot of additional work but I would like to recommend to run analyses at least on spider species data. Maybe you could manage the identifications of spiders as well?
Validity of the findings: Data is robust - although I would be happy to see data on spider species as well. However, all conclusions are well stated, but two questions remain:
1. You recommend the use of pitfall traps with barriers but you should keep in mind that vandalism is a common problem in pitfall trap studies (especially in cities). Pitfall traps are better visible with barriers so I would expect more destruction.
2. Pitfall traps with barriers yielded significant higher species numbers. But at the same time carabid assemblages are rather similar among all pitfall trap designs. Please check the validity of the NMDS again and re-run the analysis with count data. If there are still no differences in species composition you should add a few sentences to your discussion. In particular, if there are no differences in species composition it may be not necessary to kill more individuals with barrier traps. But however, this clearly depends on the reserach questions. If one is interested in species inventories, using traps with barriers can be reasonable. In this context, it would be very interesting to analyse if the number of species of conservation concern (RL species) is also higher in barrier traps.
Additional comments: Thanks again for giving me the opportunity to read and review this very interesting study.