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

Input:
Title: NITROUS OXIDE, METHANE EMISSIONS AND GRAIN YIELD IN RAINFED WHEAT GROWN UNDER NITROGEN ENRICHED BIOCHAR AND STRAW IN A SEMIARID ENVIRONMENT
Review round: 2
Reviewer: 1

Output:
Basic reporting: Most of my comments were addressed by authors
Experimental design: Most of my comments were addressed by authors
Validity of the findings: Most of my comments were addressed by authors
Additional comments: Most of my comments were addressed by authors


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

Input:
Title: NITROUS OXIDE, METHANE EMISSIONS AND GRAIN YIELD IN RAINFED WHEAT GROWN UNDER NITROGEN ENRICHED BIOCHAR AND STRAW IN A SEMIARID ENVIRONMENT
Review round: 2
Reviewer: 2

Output:
Basic reporting: The study is interesting that how to reduce the use of fertilizer and keep environment safe from GHG emission with out compromising crop yield, but the article need significant improvement as GHG emission in semi arid region of china has been explored by many researcher, therefore i suggest to the author that please improve your introduction and discussion section by adding recent and relevant references. Please revised your article to avoid English grammar mistakes.
Experimental design: Correct
Validity of the findings: The presentation of the results are good but the conclusion is poorly written.
Additional comments: Line 40-41: Please rephrase to avoid grammatical mistakes.
Line 60-61: Please add a reference
Please add recent references in the introduction section
Soil sampling, measurements and analyses: Please write in detail

Discussion: In semi-arid region and Loess Plateau, many researchers have done alot of work on GHG emission (organic farming). I suggest to re-write this section with proper and recent citations and please avoid English grammar mistakes. The current form of discussion is not acceptable,

Conclusion: It looks like a summary, please come to the point, Please write about your main significant results and your recommendations, and missing gap for future.

;


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: PREVALENCE OF ABNORMAL URINARY CADMIUM AND RISK OF ALBUMINURIA AS A PRIMARY BIOINDICATOR FOR KIDNEY PROBLEMS AMONG A HEALTHY POPULATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: Authors should measure the sensitivity of the analysis.
Additional comments: This study aimed to determine urine cadmium levels and their link to albuminuria as an early sign of renal disease in the Kepong community.  In general, this plan is an interesting and well-written manuscript. Therefore, I recommend the publication after minor revisions as the following:
1- Please, update the prevalence of chronic kidney disease.
2- Please, refer to B40, M40, and T20 categories.
3- Is the range of age in this study similar to Adnan et. al., (2012)?
4- Could authors add sections for inclusions and exclusions criteria for this study.
5- Authors should measure the sensitivity of the analysis.
6- Authors should discuss is there any relationship between albuminuria and metabolic diseases in this study.
7- Please mention age as having a substantial influence on nephrotoxicity in the discussion section.
Reference: El-Arabey AA. Sex and age differences related to renal OCT2 gene expression in cisplatin-induced nephrotoxicity. Iran J Kidney Dis. 2015 Jul;9(4):335-6.


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: PREVALENCE OF ABNORMAL URINARY CADMIUM AND RISK OF ALBUMINURIA AS A PRIMARY BIOINDICATOR FOR KIDNEY PROBLEMS AMONG A HEALTHY POPULATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: -
Experimental design: -
Validity of the findings: -
Additional comments: This is an interesting study. I have no significant objections. Some parts of the manuscript were repeated unnecessarily. Please consider deleting them, particularly in the Abstract. The part concerning cadmium must be much more strongly written (line 60, 61); I suggest the authors to carefully consider the papers of Stojsavljević et al., Jagodić et al.


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: PREVALENCE OF ABNORMAL URINARY CADMIUM AND RISK OF ALBUMINURIA AS A PRIMARY BIOINDICATOR FOR KIDNEY PROBLEMS AMONG A HEALTHY POPULATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have successfully addressed all issues
Experimental design: The authors have successfully addressed all issues
Validity of the findings: The authors have successfully addressed all issues
Additional comments: The authors have successfully addressed all issues


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: PREVALENCE OF ABNORMAL URINARY CADMIUM AND RISK OF ALBUMINURIA AS A PRIMARY BIOINDICATOR FOR KIDNEY PROBLEMS AMONG A HEALTHY POPULATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: -
Experimental design: -
Validity of the findings: -
Additional comments: No remarks.


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

Input:
Title: THE RELATIONSHIP BETWEEN CHARACTERISTICS OF ROOT MORPHOLOGY AND GRAIN FILLING IN WHEAT UNDER DROUGHT STRESS
Review round: 1
Reviewer: 1

Output:
Basic reporting: In Table 2, the p value of asterisks was missed.
Experimental design: In the "M&M' section, the author performed the significance analysis by using LSD method, Line144-145. As well known, LSD method is always used to detect the difference between CKand its treatment. For example, you have 4 groups, CK, treatment 1, treatment 2, treatment 3. LSD could detect the difference between CK and treatment 1,CK and treatment 2, CK and treatment 3, but not well used to tell wether treatment 1,2,3 have significant difference. We suggest the author use "Duncan method" or other methods.
Also, the author should give the p value they use (0.05 or 0.01 or other value) while calculating the Pearson correlation coefficient Line145.
Validity of the findings: no comment.
Additional comments: This article analyzed the relationship ship between root morphology and grain filling under drought stress in wheat. the experiment design is reasonable.  The results can provide theoretical basis for root architecture optimization, watersaving and high-yield cultivation and quality improvement in wheat. And can be accepted after minor revise.


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

Input:
Title: THE RELATIONSHIP BETWEEN CHARACTERISTICS OF ROOT MORPHOLOGY AND GRAIN FILLING IN WHEAT UNDER DROUGHT STRESS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript described the morphological and structural characteristics of root morphology of root growth and caryopsis enrichment, along with their relationships, in wheat under drought stress. The data are enough to lead their conclusion and the results can provide insights into root architecture optimization and quality improvement in wheat.
Experimental design: well
Validity of the findings: no commet
Additional comments: This manuscript described the morphological and structural characteristics of root morphology of root growth and caryopsis enrichment, along with their relationships, in wheat under drought stress. The data are enough to lead their conclusion and the results can provide insights into root architecture optimization and quality improvement in wheat. Revision is required before acceptance for publication and the questions are listed as below.
1. The abstract need to be more informative. The cultivars of wheat used for the experiment and the specific value of changes in wheat traits under drought stress should be mentioned in abstract.
2. In this study, Yangmai 13 and Yannong 19 were used as materials. Please explain why select these two cultivars and describe these two cultivars in more details.
3. In this study, the control condition and drought stress were set at two different water potential (-20 and -60 kPa). Why use this treatment and is there any references supporting this?
4. Line 113, 116, 124, the font of ℃ seems to be different with the style of the whole manuscript. Please check it.
5. Line 140-141, please explain the term “relative areas of amyloplast and protein body” that was mentioned in materials and methods section in more details.
6. The botanical names in references section should be standard. Please check it.
7. In Table 2, the p-values should be given alongside the correlation coefficient to indicate significance.
8. In Figure 1, the scale bar of (A) is 8 mm in figure legend while is 8 cm in the figure. Which one is correct? Please confirm it.


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

Input:
Title: THE RELATIONSHIP BETWEEN CHARACTERISTICS OF ROOT MORPHOLOGY AND GRAIN FILLING IN WHEAT UNDER DROUGHT STRESS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This article analyzed the relationship ship between root morphology and grain filling under drought stress in wheat. the experiment design is reasonable. The results can provide theoretical basis for root architecture optimization, watersaving and high-yield cultivation and quality improvement in wheat. And can be accepted.


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

Input:
Title: THE RELATIONSHIP BETWEEN CHARACTERISTICS OF ROOT MORPHOLOGY AND GRAIN FILLING IN WHEAT UNDER DROUGHT STRESS
Review round: 2
Reviewer: 2

Output:
Basic reporting: good
Experimental design: good
Validity of the findings: good
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: PHYLOGENETIC RELATIONSHIPS, ORIGIN AND HISTORICAL BIOGEOGRAPHY OF THE GENUS SPRATTUS (CLUPEIFORMES: CLUPEIDAE)
Review round: 1
Reviewer: 1

Output:
Basic reporting: Letter to Authors
peerj-53259-v0
Phylogenetic relationships, origin and historical biogeography of the genus Sprattus (Clupeiformes: Clupeidae)
Cristian Canales, Peter A Ritchie, Sebastian Hernandez, Victoria Herrera, Sandra V Ferrada Fuentes, Fernanda Oyarzun, Cristian E Hernandez, Gloria Arratia, Ricardo Galleguillos

201018

Dear authors,
This may be a potentially interesting MS dealing with sprat phylogeny and historical biogeography. It is goo to publish in the journal you are submitting to, if adequately written. The major concerns that I have are incomplete taxon sampling, choice of outgroups and interpretation of your results regarding character state reconstruction. Absence of S. novaehollanidae and Ramnogaster from your analysis enables only limited extent of discussion. Too few outgroups needs reanalysis adding some more outgroups. Basal character states seem near fifty-fifty for opposite hypotheses.
This MS has some other minor issues in its writing style and story flow.
Introduction and discussion sections are full of simple reference lists (A stated this, B analyzed that, C argued it, or alike). Exact numerics, species names, localities and time periods in the references do not matter. Use noun phrases to make abstract contents of those references. Abstracting contents of references will understate those  of the citing literature and emphasize your current research. I indicated a couple of examples.
See below for detail.
Experimental design: Absence of S. novaehollanidae and Ramnogaster from your analysis enables only limited extent of discussion. Too few outgroups needs reanalysis adding some more outgroups.
Validity of the findings: Basal character states seem near fifty-fifty for opposite hypotheses.
Additional comments: L55 introduction
I am sorry this MS is not interesting. Beginning with your material fish is good for kinky Sprattus geeks. You are submitting to an international multidisciplinary journal. Consider beginning with general statements to draw wider readership. Introduction section also has a function to show a placement of your specific research in a general and wider research field either of marine biology, ichthyology, evolutionary biology or historical biogeography, etc.
An example of a placement of your research may be as follows.
{evolutionary biology of marine organisms,
\t {adaptation to changing environments,
\t \t {evolutionary history of bipolar distribution,
\t \t \t {Sprattus historical biogeography # you are here
\t \t \t }
\t \t }
\t }
};
Make a brief critical review (may be less than 100 words) of the matters at nesting level-1 to 3. Sprattus specific matters will then follow. What research fields would come up to the outer envelopes depends on your choice and insights. You may insert a brief review of recent development of methodology.
Adding a general statements will bloat the text, and you need to make compact the rest of your statements in this section. You may safely reduce detailed but tedious taxonomical review of Splattus over L59-73. You have a figure showing global distribution patterns of Sprattus and relatives, and then you may omit detailed description of their distribution in the text.

L75,76,282,296,299
Sprattus genus -> genus Sprattus
Clupea genus-> genus Clupea

L144
NC009593 -> AP009234
NC entries are of re-annotation of its original annotated sequences. See COMMENT field of the entries. Respect the original.
NC16669 ?
NC16673 ?

L147
20 ng/uL of genomic DNA ?
It is impossible to set up this reaction cocktail unless you added all reagents in powder. See L137.

L156
Clupea pallasi .. were used as outgroup
To stabilize outgroup rooting, more OTUs are necessary. When outgroups are too few, ingroup risks (your case) or misrooting risks (currently unclear) will occur. See L243.

L157
NC009578 (NC_009578 ?) -> AP009134
NC016710 -> ...
NC entries are of re-annotation by NCBI curators from the original. Respect the original. See COMMENT field of the entry.

L161,162
NC -> ...

L259
likely inhabited the North Hemisphere ?
Fig.4A tells it is near neutral.

L269
Fig.4B tells it is near neutral.

L264-273
Delete this simple repetition of your results.

L276
which, challenges -> {which challenges (delete a comma), challenging}

L278
differentiate -> differentiated

L283
however, -> but
only included -> included only

L288
A recent study, that included nuclear loci and a total evidence analyses, -> A recent study based on combined nuclear and mitochondrial loci (delete commas)

L289
Ramnogaster genus -> genus Ramnogaster

L291
although the authors incorporated four genes (two nuclear, Rag1 and Rag2 and two mtDNA, 16S and CytB), (not essential) -> delete
Taxon sampling is essential here.

L293-294
from some of .. and CytB) (not essential) -> delete

L296
confirm -> confirming
previous -> previous hypothesis
not a monophyletic group, but it is paraphyletic -> not [a] monophyletic but a paraphyletic group

L304
, in addition to the pterotic bullae, (redundant) -> delete
This insertion disturbs readers' short-term memory, because the topic of this sentence is not the pterotic bullae.

L305-308
For instance, .. in the genus Clupea (Whitehead, 1985).
Do not make a simple reference list. Use noun phrases to make abstract contents of those references. Abstracting contents of references will emphasize your results. Hint: .. have been used to differentiate the genera Sprattus from Clupea {with, such as} fewer pelvic rays (Whitehead et al., 1985) and anteriorly placed pelvic fin (Whitehead 1985). (Whether six or seven does not matter. Dorsal fin does not matter.)
Please note that this is merely an example. Your introduction and discussion sections are full of simpel reference lists. Make all of them abstract to put your results and arguments forward.

L317
had shared or similar haplotypes -> shared or had similar haplotypes

L318-322
should also be ruled out because ..
This is true only if the divergence in reproductive ecology occurred at an initial stage, older than 16.4 MYA, of speciation between the sprat and herring. As a graduallist, I do not agree with you. The ecological divergence has progressively occurred since 17.6 MYA until 2.0 or 1.5 MYA. Interspecific hybridization was substantiated with current striking ecological differences (Saitoh et al 2010, Kitagawa et al 2011, etc). These studies implicitly tell ecological similarity in old times. Adding brief statements of some reservation is necessary, but do not make it long. Comparison of nuclear sequences is necessary to test if tree topology conflict appear, as in L331-334.

L318
strategies, pelagic -> strategies: pelagic (put a colon)

L336-341
This paragraph tells a different topic and may be in an independent sub-section. You should mention about some reservations under the current analysis without S. novaehollandiae and Ramnogaster.

L349
2.66 - 6.75 MYBP -> 2.66 - 6.75 MYBP with a standard nucleotide substitution rate in fish

L350-352
The molecular dating .. for fish species, (simple reference list) -> delete

L352-353
whereas .. relevant to the two genera. (redundant) -> delete

L361-366
For example, .. 5 - 10 MYBP (Grant and Bowen, 1998; Grant et al., 2005). (simple reference list) -> delete (already abstracted in the previous sentence)

L369-372
Matters in parentheses are of simple reference list. Delete.

L390
likely originated in the Northern Hemisphere .. in the Atlantic Ocean
Fig.4 does not tell that. See my comments on L259,260.

L404
dispersalist and vicariant -> {dispersalist and vicariographer, dispersal and vicariance}

L423
during the cooler Miocene period ?
Miocene period was generally warmer (Herold et al 2012) and the major oceanic cooling down occurred in the Messinian period (Holbourn et al 2018).

L434 references
Check the reference list carefully again from the beginning. Reference lists are frequently den of errors. You might add, omit or swap citation in the main text on the way internal revision. Some might slipped off from the list, or some others might held over the list. It is the authors' responsibility that all references are properly cited.

L449,452,471,535,547,560,
Make sure if paper titles are in lower case.

L527
See L461.

Following items may helpful for further discussions.

Herold N, Huber M, Muller RD, Seton M. 2012. Modeling the Miocene climatic optimum: Ocean circulation, Paleoceanography 27:PA1209.

Holbourn AE, Kuhnt W, Clemens SC, Kochhann KGD, Johnck J, Lubbers J, Andersen N. 2018. Late Miocene climate cooling and intensification of southeast Asian winter monsoon. Nat Commun 9:1584.

Kitagawa T, Fujii Y, Koizumi N. 2011. Origin of the two major distinct mtDNA clades of the Japanese population of the oriental weather loach Misgurnus anguillicaudatus (Teleostei: Cobitidae). Folia Zool 60:343-349.

Saitoh K, Chen W-J, Mayden RL. 2010. Extensive hybridization and tetrapolyploidy in spined loach fish. Mol Phylogenet Evol 56:1001-1010.

Fig.1
How about C. pallasii in the Barents Sea?


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: PHYLOGENETIC RELATIONSHIPS, ORIGIN AND HISTORICAL BIOGEOGRAPHY OF THE GENUS SPRATTUS (CLUPEIFORMES: CLUPEIDAE)
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comments
Validity of the findings: The dataset should include more taxa to make the taxonomic and biogeographic results and conclusions more inclusive.
Note that all additional data that I suggest to combine with the current authors' data, are freely available (in GenBank). I "only" suggest to redo the same set of analyses that the authors did, but using an expanded dataset, as described below in the "General comments for the authors"
Additional comments: In this study, the authors examined the molecular systematics and biogeography of Sprattus and Clupea, two temperate genera of sardines, using several molecular markers. They found the genus Sprattus paraphyletic relative to Clupea, with the north hemisphere-distributed species, Sprattus Sprattus, more closely related to the genus Clupea than to other south hemisphere-distributed species of Sprattus. The authors, then, discussed the biogeography of the clade (Sprattus, Clupea) and concluded that the most recent common ancestor of this clade has a north hemisphere origin and the ancestors of the lineage (S. muelleri, S. fuegensis and S. antipodum) dispersed to the south hemisphere where they subsequently diversified.

This is an interesting paper which brings new information on the evolution and biogeography of this temperate group of sardines. To my knowledge, this is the first study dealing with the biogeography of this group of temperate sardines. The manuscript is well structured and well written and I have only few comments, but two of my comments are important:

Main comment 1 (about the origin of the clade [Sprattus, Clupea]): The clade (Sprattus, Clupea) belongs to a larger clade of temperate sardines including Ethmidium (already included in this study), Hyperlophus and Pomatalosa as found in Lavoué et al (2013) (but see a different hypothesis in Egan et al (2018)). The distribution of these three genera is restricted to the South hemisphere. It is very likely that the genus Ramnogaster belong to this clade as well (as shortly discussed by the authors see lines 289-293; see also Lavoué et al 2014 and Egan et al 2018 and Whitehead 1964). Ramnogaster is endemic to the marine southern region of South America. Moreover, it is also likely that the genus Strangomera belongs to this clade (the distribution of Strangomera is restricted to south South America and it occurs in commercial quantity along the coast of Chili according to Whitehead (1964, 1985)).
There are two possible consequences of this: 1) (phylogenetic consequence) the clade (Sprattus, Clupea) and the genus Sprattus are likely each not monophyletic relative to Ramnogaster and Strangomera and 2) (biogeographic consequence) if the south-distributed Ramnogaster and Strangomera are closely related to Sprattus and/or Clupea, and if the dataset includes the more distantly related genera, south hemisphere-distributed, Hyperlophus and Pomatalosa, this may significantly impact the ancestral area reconstruction towards a south hemisphere origin.

Main comment 2 (about the time calibration point used). Overall, the timescale of diversification inferred in this study is congruent with those of Lavoué et al (2013) and Egan et al (2018), as already noted by the authors. However, the calibration point used in this study is based on an extinct species (Clupea testis) which is only known by its otoliths. As discussed by Grande (1985) the phylogenetic positions of clupeiform extinct species that are only known from their otoliths (or scales) are difficult (often impossible) to determine. I could not find positive evidence in the literature to classify Clupea testis into the genus Clupea (but I am not a morphologist). It seems, unfortunately, there is no “good” fossil belonging, or closely related, to the clade (Sprattus, Clupea) that can be safely used to calibrate time of divergence of this group (see Whitehead 1985. Whitehead 1985 is a relatively old reference but it seems there is not so much more on this subject, subsequently published).

To overcome these two potential issues, I would like to suggest to expand the taxonomic sampling as following: Hyperlophus vittatus and Potamalosa richmondia (all gene sequences available in GenBank) and Ramnogaster melanostoma (only partial COI sequences [from specimens collected from the Lower Parana River; see Diaz et al 2016] and partial cytochrome b sequences [from specimens collected nearby the Río de la Plata estuary; see Garcia et al 2011 for identification in their Appendix 1] available in Genbank. The quality of the phylogenetic signal of these two genes is good and it should be enough to reliably infer the phylogenetic position of Ramnogaster melanostoma relative to Clupea and Sprattus). Unfortunately, there is still no sequence of Strangomera bentincki available.
As outgroups, it would be interesting (for rooting and time calibration purpose) to add two species of the subfamily Ehiravinae such as Gilchristella aestuaria and Ehirava fluviatilis (sequences available in Genbank). These two species should be constrained to form a monophyletic group (sister group to the rest of the taxonomic sampling) and the time divergence between these two species should be constrained by the age of the fossil species Lecceclupea ehiravaensis (with a strict minimum age of 74 My). Lecceclupea ehiravaensis has been shown to be a crown member of the clade (Ehirava, Gilchristella) (see Taverne 2011).
The ancestral area reconstruction should include all ingroup taxa.

Reference
Díaz J, Villanova GV, Brancolini F, del Pazo F, Posner VM, Grimberg A, et al. (2016) First DNA Barcode Reference Library for the Identification of South American Freshwater Fish from the Lower Paraná River. PLoS ONE 11(7): e0157419. https://doi.org/10.1371/journal.pone.0157419
García, G., G. Martínez, S. Retta, V. Gutiérrez, J. Vergara and M. de las M. Azpelicueta. 2011. Multidisciplinary identification of clupeiform fishes from the Southwestern Atlantic Ocean. Internat. J. Fish. Aqua. 2: 41–52.
Taverne (2011) Les poissons crétacés de Nardo. 33. Lecceclupea ehiravaensis gen. et sp. nov. (Teleostei, Clupeidae). Boll Mus Civ St Nat Verona, sez di Geologia, Paleontologia e Preistoria 35: 3–17.

I think the origin and biogeography of the genus Sprattus cannot be reliably solved without considering these other taxa (as listed above).

Other comments:

Introduction section, lines 75-76: Change “Sprattus genus” to S. sprattus”

Introduction section, line 77: please specify why it is important to indicate that Clupea is morphologically distinctive within Clupeinae (it seems to me that any genus within Clupeinae must be morphologically distinctive to others?)

Introduction section, line 91: maybe change “the same” to “similar”

Introduction section, line 98-101: Maybe this sentence could be reworded. Something like: “Experimental studies aiming to evaluate the thermal tolerance of two temperate species of Clupeidae (i.e. Clupea harengus and Sardinops sagax) evidenced their low tolerance for warm (tropical) water (Martínez-Porchas et al., 2009; Peck et al.,2012). These results are in favour of/reinforce/support the hypothesis that warm waters act as a dispersal barrier”

Introduction section, lines 103-105: Please add a reference supporting this assertion

Introduction section, line 106-107: the sentence part “…S. Sprattus was the earliest diverged species of the group” needs to be reworded

Material and methods, line 128, Sprattus in italics

Material and methods, line 139: please indicate the size of each molecular marker

Material and methods, line 181: please indicate the size of your phylogenetic matrix (characters*taxa)

Material and methods, lines 210-211: See my main comment 2 above: According to Grande (1985:324) Clupea testis is known only from otoliths. Because of that, Grande (1985) questioned its generic assignment/phylogenetic position.

Material and methods, lines 231-232: It seems that the method of ancestral area reconstruction is a method of ancestral character reconstruction which allows only dispersal events (no vicariant events; meaning that the inference only allows one state at node. For example, A or B but not A+B): This is fine but it should be indicated.

Discussion, line 281: change “S. sprattus is phylogenetically more like a Clupea species” to “S. Sprattus is sister to Clupea”

Discussion, line 296: Please change “Sprattus genus is not a monophyletic group, but it is paraphyletic” to “Sprattus genus is a paraphyletic group”

Discussion, line 313: Change “the valid species tree” to “the current generic classification”

Discussion, lines 380-387: I strongly disagree with this explanation for two reasons: 1) Whitehead (1985) who reviewed most of “Clupea” fossils clearly stated that none of these fossils are positively classifiable into the extant genus Clupea (see his detailed discussion on the fossil record of clupeiforms). At the best, “Clupea” fossils are only assignable to the family Clupeidae. 2) based on the timetree of the authors, it is expected to find north hemisphere fossils as old as 16 my (most of the “Clupea” fossils are younger). However, to support a north hemisphere origin of this group, it must be found older (>16my) Clupea/Sprattus-related fossils in the north hemisphere as evidence that this group was present there before the clade (Clupea, S. Sprattus) diversified.

Sebastien Lavoue


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: PHYLOGENETIC RELATIONSHIPS, ORIGIN AND HISTORICAL BIOGEOGRAPHY OF THE GENUS SPRATTUS (CLUPEIFORMES: CLUPEIDAE)
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Letter to Authors
peerj-53259-v1
Phylogenetic relationships, origin and historical biogeography of the genus Sprattus (Clupeiformes: Clupeidae)
Cristian B. Canales-Aguirre, Peter A. Ritchie, Sebastian Hernandez, Victoria Herrera-Yanez, Sandra Ferrada-Fuentes, Fernanda X. Oyarzun, Cristian E. Hernandez, Gloria Arratia, Ricardo Galleguillos

210524

Dear authors,
Revision with some reanalysis has made your MS more interesting. Many issues I pointed out last time were cleared, but some others remained or newly introduced. One more round of minor revision is necessary.
See below for detail.

L60
tropical the area -> tropical area

L65
However, there is still (unclear logical link) -> There is

L66
; such is -> such as [in]

L69
, are the important of (not a complete sentence) -> They are [important] components of (break sentence here)

L143
follows -> following

L157
i.e stochastic effects ??
This insertion does not make sense. You should state here why separately. Or otherwise, I do not think separate analysis is necessary. Mitochondrial genome constitutes a single heritable unit, and thus it is a single locus. Then, the longer-the-better rule applies. Concatenated four coding sequences may be the only and the best in your case.

L158
considering that ??
This insertion does not make sense.

L192
(Taverne, 2011) (Taverne 2011) -> (Taverne, 2011)

L202,203
LogCombiner v1.8 ?  TreeAnnotator v1.8 ?
Version information may not necessary unless it is not what is implemented in BEAST v2.

L203
Reference is necessary for FigTree v1.4, though I do not know how to cite a GitHub page.

L226,228,231
Consider omitting "(Figure 2)". I think it is enough citing at once in the top of this paragraph.

L236,238,239
Consider omitting "(Figure 3A)". I think it is better citing at once in the top of this paragraph.

L286
by comparing mtDNA and nDNA
How was this comparison in clupeids by Bloom & Lovejoy (2014)?

L287
such as it has been found in spined loach fish -> delete
Particular fish other than clupeids is not important. See above. Did this mitochondrial genomics deal with nDNAs?

L292
the sympatric species S. antipodum and S. muelleri from New Zealand (unclear) ->New Zealand S. antipodum and S. muelleri sympatric with each other

L298
Summarizing, the results in (verbose) -> delete

L306
that -> than ?

L315
2014)., -> 2014),

L322
Eoceno -> Eocene

L332
What does "lens" mean?

L334
a tropical submergence (uncountable) -> tropical submergence

L334-342
You should address an alternative parallel dispersal hypothesis of tropical MRCA to cool waters independently around 55.8 - c.a. 34 MYA.

L339,348
Grant, Leslie & Bowen -> Grant et al.

L366 reference
Reference list is still a den of errors. Check thoroughly again.

L375
Book title (not a series title)? Editors?

L386,394,etc
Paper titles should be in lower case.

L396
PloS one -> PloS One

L469
Journal titles should be in title case.

Fig.2 legend
L5-7
orange branches correspond to S. muelleri .. (verbose) -> orange to S. muelleri, light blue to S. antipodum, and green to S. sprattus


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: PHYLOGENETIC RELATIONSHIPS, ORIGIN AND HISTORICAL BIOGEOGRAPHY OF THE GENUS SPRATTUS (CLUPEIFORMES: CLUPEIDAE)
Review round: 2
Reviewer: 2

Output:
Basic reporting: English usage could be improved.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: Thank you to the authors for their thoroughly revision of their manuscript. I don’t have major comment on the content and I think the results of this study are particularly interesting for the biogeography of Clupeoidei to understand their antitropical distribution.

However, I noticed several minor typos/misspelling/inaccuracies (see the list below) throughout the manuscript. Also, I am not an English native speaker, but the English usage could be edited.

Minor comments:
Line 45: sometimes the authors use “MYBP” and sometimes “MYA”. Usage needs to be homogenised throughout the manuscript.
Line 46: “in THE southern…”
Line 61: species is misspelled
Line 65: change “is” to “are”
Line 66: change “studies” to “studied”
Lines 69, 75 and 79: publication date after van der Laan is missing
Line 69: please revised “…are the important of…”
Line 170: change “suitable” to “informative”
Line 181: This sentence needs to be reworded: how many “consensus trees” did you obtain?
Line 187: “run” without “s”
Lines 191 and 197: MYA or MYBP?
Line 192: delete one “(Taverne 1971)”
Line 193: the darter in front of the fossil name Lecceclupea is missing
Line 194: “Ehirava, Gilchristella” in italics
Line 202: how many maximum clade credibility trees?
Line 226: change “is a valid species from a phylogenetic perspective” to “forms a monophyletic group”
Line 230/231: change “the species within the genus Sprattus are a paraphyletic group” to “the genus Sprattus is polyphyletic” because S. Sprattus is closely related to Clupea AND S. fuegensis, S. antipodum and S. muelleri are closely related to Ramnogaster and Strangomera.
Line 247 (and elsewhere as lines 257 and 258): I think polyphyletic is better than paraphyletic for the reason given above (under the comment on Line 230/231, above)
Line 259: “add” without “s”
Line 267/268: Linnaeus could not have done this because the genus Sprattus was described in 1846. Please reword.
Line 269: delete “on”
Line 288/289: this sentence needs to be reworded.
Line 294: who suggested? Need reference.
Line 322: “Eocene”
Line 434: “WAS” or “WS” as written in the above and below references

Likely more minor typos I missed. Please check carefully.

Figure 1 is nice but it could include the distribution of Ramnogaster and Strangomera as well.

A last comment: Potamalosa, Hyperlophus and Ethmidium are also temperate species, that are distributed in the southern hemisphere. Therefore, the “southern distribution” of the whole lineage predated by about 50 million years the origin of the clade (Sprattus, Clupea, Ramnogaster, Strangomera). This is well shown Figure 3 but not very visible in the text. As far as I know, this is one of the oldest south-distributed groups of fish. They were able to cross the tropics but not to adapt to warm environment.


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: ATLAS OF TISSUE-SPECIFIC AND TISSUE-PREFERENTIAL GENE EXPRESSION IN ECOLOGICALLY AND ECONOMICALLY SIGNIFICANT CONIFER PINUS SYLVESTRIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors of the manuscript entitle “Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris” have analyzed the transcriptome of different organs/tissues from the Scot pine by RNA-seq determining the profiles and preferential gene expression in the different organs/tissues.
The manuscript is well written although there with several minor grammatical or form mistakes. For example:
Line 53: Change “as for example Pinus and Picea” to “as for example Pinus and Picea genres”.
Line 80: Change “Canas et al. 2017” to “Cañas et al. 2017”.
Lines 98-108: Change letter color to black.
Line 143: Change (Ojeda et al. 2019) from cursive to normal case.
Literature cited cover the subject of the manuscript and the structure, figures and supplemental data are correct.
Experimental design: The research is original, but the relevance is limited since transcriptomic studies now are easy to make and accessible for near every research group working on conifers. It is true that the variety of organs and tissues, and development and environmental conditions for this kind of plants is very high. For this reason, it is necessary to increase the transcriptomic data in coniferous trees, but the selected group of samples is limited and without a clear objective.
Methods are in general well described and the statistical approach is complex, more advanced than a simple K-means or a correlation clustering. However, I have some comments about some  methodological approaches.
Detailed comments:
Line 154: Please describe the initial quantification and quality controls of total RNA. Before to make polyA isolation from total RNA to make sequencing libraries the integrity of the RNA must be OK. For example, using a Bioanalyzer the RIN must be higher than 6.5-7.
Line 170: Please, describe the trimming process.
Line 171: Please, improve the sentence. It is difficult to follow, the reference must be in the journal format (not with a number). I have a problem with the assembly method. If you want to analyse for the first time the transcriptome of different tissues/organs it is not recommended to use a guided alignment with a previous transcriptome as reference (with a genome is OK). In this sense, you will loss new transcripts (splicing variants and transcripts for not identified genes) expressed in your samples. See in the line 282 that only the 76% of the reads are mapped in the reference.
Lines 181-187: The contaminant removal process is very complicated. Why have you removed contaminants from contigs and not from reads? There are different software that remove contaminant reads.
The number of contigs is very huge (1.2 millions). You must consider to use CD-HIT to reduce the sequence redundancy.
I think it will be necessary to use REVIGO tool to highlight the more important and non-redundant GO terms. Additionally, I miss RT-qPCR validation of the results.
Validity of the findings: Although new transcriptome data in conifers always is interesting, I think that in the present manuscript the main findings have been lost since de novo assembly has been made through a reference-guided approach. Additionally, an annotation based on a previous reference transcriptome limits the originality of the work. These are important concerns since a database containing transcriptome and annotation data (GymnoPlaza) from Pinus sylvestris is accessible for researchers
Additional comments: I have a concern about the use of the word “tissue” in the manuscript including the title. It is true that this term is clarified in the Discussion section. But I think this must be done before indicating that some of your samples are organs and not tissues, maybe in the Introduction.


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

Input:
Title: ATLAS OF TISSUE-SPECIFIC AND TISSUE-PREFERENTIAL GENE EXPRESSION IN ECOLOGICALLY AND ECONOMICALLY SIGNIFICANT CONIFER PINUS SYLVESTRIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is clear and unambigous, English is professional.

Wide background, well cited.

Figures and data are clear.

The hypotheses that tissue specific genes differentially expressed could be detected was confirmed. The megagametophyte was not the tissues with most tissue specific genes as hypothesized, rather needles.
Experimental design: The research contributes original new data, as previously fewer tissues had been sampled from a single stage or condition.

It completes previous studies, it provides a support for genome sequencing.

Yes, although I have some comments/questions below.

Standard methods were used for tissue collection and data analyses- but see comments.
Validity of the findings: Yes. Extensive and relevant results and discussions sections.

Stastistics are suitable.
Additional comments: Dear author,

The 'Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris' is an important contribution towards the genome sequencing effort of this tree.

I have a few comments/questions:

For the sampling: 6 non related individuals were sampled in the field, is there a reason for not using clones, which provide more statistical power for the reconstruction of the transcripts?

For the analysis first with Salmon (pseudo-alignment) and then Trinity, how did these two methods compare? I did not find it in the results-discussion, was this useful, did they correlate well with the number of transcripts?

Is there a reason for the authors not to use a single copy orthologous genes analysis to get an estimate of transcriptome completeness, like BUSCO?
This might provide additional relevant information.

Suggestions:

P. 14 line 213: please explain here PUR again, as it had only been explained in the introduction (and many readers might overlook it)

P. 28, lines 514-516: Might be useful to indicate which type of bias: i.e. underestimating genetic variation

Best wishes!


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

Input:
Title: ATLAS OF TISSUE-SPECIFIC AND TISSUE-PREFERENTIAL GENE EXPRESSION IN ECOLOGICALLY AND ECONOMICALLY SIGNIFICANT CONIFER PINUS SYLVESTRIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: After authors' reponse I have no additional comments. The authors have appropiately answered to my comments and revised the manuscript.
Experimental design: I only have a minor comment or opinion, not for a new round of revision. There is a generalized opinion that RT-qPCR validation is not necessary for RNA-seq experiments. It is true that RNA-seq is very robust technique but the analyses depend on reference sequences used for mapping. In the case of well stablished model such as human or Arabidopsis with extremely well annotated genomes this can be, they do not need RT-qPCR validation experiments (although I consider that is necessary to determine if the sample files have been used in the proper order and not inverted). But the RNA-seq analyses based on transcriptomes and assemblies this is different. You can find splicing isoforms, misassembled contigs, etc. In fact, the library synthesis can introduce some biases. In many cases Illumina results do not well correlate with PacBio or ONT sequencing of unamplified samples, in an intuitive manner it is easy to think that results of the 3rd generation NGS sequencing in this case are more closed to reality.
Validity of the findings: After authors' reponse I have no additional comments. The authors have appropiately answered to my comments and revised the manuscript.
Additional comments: After authors' reponse I have no additional comments. The authors have appropiately answered to my comments and revised the manuscript.


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

Input:
Title: ATLAS OF TISSUE-SPECIFIC AND TISSUE-PREFERENTIAL GENE EXPRESSION IN ECOLOGICALLY AND ECONOMICALLY SIGNIFICANT CONIFER PINUS SYLVESTRIS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Very professional sharing of the document via Google Docs, but please make sure that the reviewers can only read and not edit, as information can be wrongly deleted.

Else no comment.
Experimental design: Many ambiguities were cleared up.
I don't find sharing the contaminant list (https://figshare.com/articles/dataset/Data_S1_List_of_putative_contaminant_contigs_removed_from_quantification_files_txt/13121849) very useful. Please share the sequences (fasta) as well.
Validity of the findings: No comment.
Additional comments: Dear authors,

Thank you for addressing my concerns, there is a very significant improvement of the manuscript.

Best wishes!


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

Input:
Title: LEAF WATER POTENTIAL OF FIELD CROPS ESTIMATED USING NDVI IN GROUND-BASED REMOTE SENSING—OPPORTUNITIES TO INCREASE PREDICTION PRECISION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The study focused on the relationship between leaf water potential and normalized deficit vegetation index. The experiment is overall reasonable. However, there are still issues that need to be improved. The English writing must be improved before publishing since the current version is not professional. For the research, it is not clear how the WLS method could help with the analysis of the uncertainty. Please introduce more about this method because this part is important in the manuscript.

Detailed comments and suggestions:
L44 Misunderstanding statement
L51 In this paragraph, you mentioned NDVI could not represent LWP directly. So explain more how Elsayed did to exclude the effect.
L56 Following the previous comment, given the non-direct relationship with LWP and NDVI, what is the theoretic basis of the research in L57 to 58? Please read deeper in these studies, and give a more accurate review of LWP-NDVI relationship. Try to review these works considering their time scale.
L61-62. Unclear statement.
L83. Use “apply” or “improve” instead of “design”
L98. Delete the NDRE, since this part didn’t appear in the main result.
L106. Check the whole manuscript and make sure the phrase “Deficit- and Full irrigation” are the same (see L115 for the difference). And lowercase the initials of Deficit and Full.
L107. What is “A&M”
L123. Is there any difference between the top leaves of the canopy and lower leaves? If the answer is yes, how did you consider this uncertainty during analysis?
L157. As the major comments, please introduce the second method more to clarify how this method could describe the uncertainties.
L185. I strongly suggest dividing the result part into 2 part, to introduce the relationship and uncertainty analysis separately.
Table 1. Why there is no difference between full and deficit irrigated wheat?
L193. Check the manuscript, and avoid using the words like “surprising”.
L197. Analysis more why deficit irrigated wheat has a higher NDVI than full irrigated.
Figure 5. This figure is quite confusing. 1. Why there is a significant curve pattern within the first blue stage? 2. I think you just want to show the difference between full and deficit-irrigated NDVI, consider using a boxplot. 3. I am quite interested if there is a significant difference between NDVI within a single day? If the answer is yes, introduce is you are using a daily average.
Figure 7. Why use a linear fitting rather than using Beer-Lambert Law
Figure 8. Describe in chapter 2 more about the three dates. Describe the phenology of the crop at three times and the nearest irrigation event, to see if the unsatisfied result in panel a comes from irrigation.
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: LEAF WATER POTENTIAL OF FIELD CROPS ESTIMATED USING NDVI IN GROUND-BASED REMOTE SENSING—OPPORTUNITIES TO INCREASE PREDICTION PRECISION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well drafted and structured.
All figures, tables and graphs are relevant and of good quality.
Authors have submitted the associated data, codes and supplemental materials.
The language and overall content is well written for international readers.
Experimental design: Overall methodology and design of research is well laid and conducted.
Authors have explained all steps in detail along with any notes that were considered while capturing the data.
All steps and methods are well supported by graphs and figures.
Validity of the findings: Its a good research that will definitely add to the existing knowledge in this field.
This is a ground research based on actual survey that means a lot more than simply gathering data and analyzing it.
Authors have well justified their works with proper discussion and results.
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: LEAF WATER POTENTIAL OF FIELD CROPS ESTIMATED USING NDVI IN GROUND-BASED REMOTE SENSING—OPPORTUNITIES TO INCREASE PREDICTION PRECISION
Review round: 1
Reviewer: 3

Output:
Basic reporting: In this paper, a push-wheel cart was designed to collect field data and then the authors evaluated the potential of using NDVI as a proxy to calculate leaf water potential (LWP). Generally, the paper is well-constructed and I have some concerns about data collection and analysis.
Experimental design: The experiments are well designed as this may be the start point of a series of works. I suggest testing more variables as proxies and extend the work to the canopy level when calculating LWP using remote sensing data in future work.
Validity of the findings: It's fine.
Additional comments: 1. The canopy reflectance was collected to calculate NDVI, so that the NDVI used in this study is the canopy NDVI, while, the LWP used in the study is the leaf LWP, are these two variables match? As we know, the canopy is affected by the Leaf area index (LAI), leaf angle distribution (LAD), surface soil reflectance, and the fraction of vegetation cover (FVC), etc. So, could you comment on the effect of canopy characters on your LWP-NDVI correlations? And have you considered using leaf NDVI and LWP to analyze the correlation? Or is possible to collect canopy LWP and analyze the correlation of NDVI---LWP at the canopy level? This may be interesting as we may using remote sensing data to analyze canopy level LWP in this way.
2. I noticed that both NDVI and NDRE were calculated for the evaluation, and how about the performance of NDRE? Furthermore, there are some other indices that could be used to describe crop water stress such as the NDWI (https://www.usgs.gov/core-science-systems/nli/landsat/normalized-difference-moisture-index), I suggest considering more indices in your further 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: LEAF WATER POTENTIAL OF FIELD CROPS ESTIMATED USING NDVI IN GROUND-BASED REMOTE SENSING—OPPORTUNITIES TO INCREASE PREDICTION PRECISION
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment'
Experimental design: no comment'
Validity of the findings: no comment'
Additional comments: 1. The date information should also be added in the description of Figure 5.
2. Authors should have another round of grammar check to make sure the English language satisfies the requirement of the journal.


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: LEAF WATER POTENTIAL OF FIELD CROPS ESTIMATED USING NDVI IN GROUND-BASED REMOTE SENSING—OPPORTUNITIES TO INCREASE PREDICTION PRECISION
Review round: 2
Reviewer: 2

Output:
Basic reporting: I am satisfied with the revision.
Experimental design: The experiments are well designed.
Validity of the findings: It's fine.
Additional comments: I am satisfied with the 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: LEAF WATER POTENTIAL OF FIELD CROPS ESTIMATED USING NDVI IN GROUND-BASED REMOTE SENSING—OPPORTUNITIES TO INCREASE PREDICTION PRECISION
Review round: 3
Reviewer: 1

Output:
Basic reporting: Satisfied
Experimental design: Satisfied
Validity of the findings: Satisfied
Additional comments: No more comments


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

Input:
Title: A SYNTHESIS TREE OF THE COPEPODA: INTEGRATING PHYLOGENETIC AND TAXONOMIC DATA REVEALS MULTIPLE ORIGINS OF PARASITISM
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I enjoyed reading your manuscript since it is well written and matches my research interests. My comments are mostly minor in nature, and I am happy to recommend publication and revision.

Line 20 you wrote 14,397 species, but in line 40 “14,397 valid species”, please check.

Many citations are missing through the manuscript. For example, lines 48 and 53 in the Introduction.

Line 57, Please note there are some overlaps between these groups.

Line 75, If I understood correctly, these phylogenies/analyses were not for copepods. I would suggest to make a smooth transition with last paragraphs.

Line 94, why is interesting/important to study parasitic copepods? You need to introduce it.

Line 93-100, I would move them to the Method (how you identify the parasitic copepods).

Line 105, are you sure you did it on June 01, 2021?

Line 106 and others, I think you need citations for the software.

I would suggest to move the Figure 1 into supplementary material, as it is not your results. Otherwise, I would suggest you provide a paragraph to describe how you did the morphological analyses.

Line 465-466, why did the “transitions to parasitism” have important implication to understand the morphological evolution? Please clarify.

Line 476, as you did not touch anything about the morphology of copepods in this study, I would suggest you to be very carefully to discuss this issue.

I would suggest you to largely reduce the Discussion (the current version is too long): you can focus the “transitions to parasitism”, after a short discussion of “copepod phylogenies”.


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 SYNTHESIS TREE OF THE COPEPODA: INTEGRATING PHYLOGENETIC AND TAXONOMIC DATA REVEALS MULTIPLE ORIGINS OF PARASITISM
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript under revision is a nice piece of work dealing with evolution of parasitism in copepods. The work is based on published phylogenetic analyses merged to produce a synthetic phylogeny of copepods. On such a phylogeny, the possible transition/s to parasitism have been mapped.
The manuscript is very well written and it was a pleasure to read it, nonetheless, I am under the impression that the work is too preliminary. As the Authors state several times through the text, there is a non-negligible lack of knowledge for a conspicuous number of copepod species. The under-representation in terms of species within families and orders is the main drawback I see. The second issue I recognise in the work is a lack of statistical treatment of some results such as for instance the possible number of transitions to parasitism in copepods. PAUP was used to carry out parsimony analyses, but both analyses gave equivalent results. The Authors sublimely discussed this result, but indeed, to me, that is not a conclusive result. I would suggest to run other tests using other approaches (Bayesian statistics?) in order to validate one or the other hypothesis.
I feel that this work is too preliminary and it leaves more open questions than it addresses. What I learned from the work presented in the manuscript under revision is that our knowledge about copepod evolution and the evolution of parasitism is too scanty. The present manuscript looks more like a ‘position paper’ or the preliminary results of a grant application than a regular research paper. The Authors state (lines 531-533) ‘The Cyclopoida, Harpacticoida, and Siphonstomatoioda require the greatest additional sampling effort (Table 2), and, coincidentally, these orders contain nearly all of the parasitic copepods.’ This made me think that the bulk of data in molecular phylogeny is too weak to carry out a work like that presented in the manuscript. In the manuscript, contrasting hypotheses are validated and rejected in the same sentence, which is good and reveals a strong thinking effort the Authors have carried out to draw conclusions. Nevertheless, this weakens the conclusions in my opinion.
Experimental design: The research question is well defined and an investigation on transition to parasitism in copepods is needed. Nevertheless, as stated above, I think that the knowledge available to date to carry out the analyses in the present manuscript is too scanty.
Validity of the findings: See the comments in section 1
Additional comments: Lines 49-51. DNA extraction from formalin preserved samples is rather tricky, although a paper was published 17 years ago describing a protocol to extract DNA from formalin samples. The yields are somehow low (70% of gDNAs produced a PCR amplification on 91bp fragments and 40% on 181bp fragment; n=20; https://doi.org/10.1016/j.ympev.2003.11.002). For other organisms, DNA extraction from formalin preserved samples is almost a routine (DOI: 10.2144/97223bm03; https://doi.org/10.1186/s13104-016-2140-1; etc.) I think that this is worth a mention otherwise the reader would have partial information about that.
Lines 52-54. References are needed here.
Lines 55-56. I do not understand what the Authors mean by this sentence: ‘Overall, there are few accurately identified reference sequences of copepod taxa.’
Lines 59-60. I do not understand the correlation between the five ecological groups and the ‘[…] limited the integration of copepod phylogenies into a cohesive tree of life.’
Line 106. Mosquite was updated to V3.61 in December. Which version did you (3.31 if I am right) use and why? Mosquite website suggests several citations for the software, please have a look at that and cite Mosquite as requested (https://www.mesquiteproject.org/How%20to%20Cite%20Mesquite.html?PublishingResultsPanel=open)
Lines 135, 196, 236. Figure 3 does not contain panels, so I do not understand what do Fig.3A and B mean.
Lines 141-156. I do not understand how the Authors chose the published studies to be included in their synthetic phylogeny analyses. There are some recent papers that have not been included although morphology and multi-locus BI and ML phylogenies were carried out, especially within Cyclopoida. Five Oncaea and one Triconia species were relatively recently investigated by COI and ITS1-5.8S-ITS2 rDNA (https://doi.org/10.1371/journal.pone.0175662). Even more interestingly, Cyclopoida contain the debated suborder formerly known as Peocilostomatoida and I would be curious to see where Oncaea would sit in your synthetic phylogeny. If it would cluster together with Poecilostomatoida then some more debate can be done on the monophyly of Poecilostomatoida.
Line 242. There are no black branches in Fig. 3 (A ???)
Lines 285-295. I think that if parsimony is not completely resolving, other statistical methods may be used (?). This part is the real core of the work and upon this result conclusions are drawn. I would try to make this part more robust.
Lines 298-301. The disclaimer about the number of molecular markers and number of studies on

I would suggest to turn the manuscript into a position paper and to dim conclusions on the evolution of parasitism. I do not know whether the Authors intend to follow-up this topic in their laboratories, but reading the manuscript it looks like.


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 SYNTHESIS TREE OF THE COPEPODA: INTEGRATING PHYLOGENETIC AND TAXONOMIC DATA REVEALS MULTIPLE ORIGINS OF PARASITISM
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The article gives valuable insight and significantly improves our understanding of the evolution of parasitism within copepods. The article is well composed and gives a solid overview of the current knowledge on evolutionary pathways into parasitism in the taxon.

Below are detailed comments that should be addressed:

Line 51 - 53: A limited assortment of markers and the use of a selected gene set is not unique for studies on copepods. As important as the number of markers is the selection of the right markers based on how conserved they are and what phylogenetic level is investigated.

Line 103 - 105: It should be added how the final selection of 26 publication was done from the 178 search results from Google Scholar.

Line 114, 116, 119: File names are given, but they do not seem to be linked to accessible files. Those names (e.g. labelled_supertree_simplified_ottnames.tre) should not be included in the text if not published as supplementary data.

Line 132: Repetition from Materials and Methods.

Line 135: “(Fig 3A, B)” There is no separation into A/B in this figure.

Line 148/149: “The species-poor orders Gelyelloida, Misophrioida, and Monstrilloida, have been relatively well-sampled.”
According to Table 2, no Gelyelloida or Misophrioida are included in the synthesis tree, and while constituting 1.7% of species diversity in Monstrilloida, only a low number of 3 monstrilloid taxa are included in the synthesis tree.

Line 207: The word “although” is not fitting here. I suggest to split the sentence up into two. E.g.: “Another species rich group are the…”.

Section line 285 - 306: The authors consider the non-parasitic taxa within the parasitic poecilostome cyclopoids unlikely to be derived from parasitic forms, following the hypothesis of parasitism being an irreversible transition, related to Dollo’s law of irreversible evolution. However, more recent studies than cited found exceptions to this rule, and copepods might include further exceptions. This scenario should in particular be considered since parasitic copepods in this group do not display the most extreme morphological modifications due to parasitism compared to other parasitic copepod taxa such as for example those shown in figure 1.
e.g.:
Klimov, P.B. and OConnor, B., 2013. Is permanent parasitism reversible?—Critical evidence from early evolution of house dust mites. Systematic biology, 62(3), pp.411-423.
Weinstein, S.B. and Kuris, A.M., 2016. Independent origins of parasitism in Animalia. Biology Letters, 12(7), p.20160324.

Line 323 - 324: It is unclear what “80 mm land crabs” refers to. Presumably this is carapace width, but this should either be explained or just left out since not really relevant here. “Found with high infection rate at 100% prevalence” might be sufficient.

Line 372: Missing “of” between “none” and “the”.

Line 466 - 472: From this sentence it appears that all the exemplified morphological changes, including the most extreme examples such as loss of all appendages, have happened convergently in all 14 transitions. This sentence has to be rewritten in order to clarify that not all modifications appear in each parasite clade.

As a more general comment; it is striking that that Calanoida do not contain any parasitic forms, despite being one of the most speciose copepod orders. It could be interesting to discuss why parasitism evolved multiple times in all other major copepod clades but not in calanoids, such as ecological or morphological preadaptations to parasitism. However, this is not crucial to the quality of the paper.

Table 3: Species numbers for Siphonostomatoida and Monstrilloida should be given individually instead of combined. In addition, the combined species numbers for these two orders slightly deviate from the numbers in table 2.


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 SYNTHESIS TREE OF THE COPEPODA: INTEGRATING PHYLOGENETIC AND TAXONOMIC DATA REVEALS MULTIPLE ORIGINS OF PARASITISM
Review round: 2
Reviewer: 1

Output:
Basic reporting: I am happy with the revisions. Thank you.
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: A SYNTHESIS TREE OF THE COPEPODA: INTEGRATING PHYLOGENETIC AND TAXONOMIC DATA REVEALS MULTIPLE ORIGINS OF PARASITISM
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have clearly addressed all my points and, although I still find some criticisms to the procedure (e.g. the criteria for exlusion or inclusion based on e.g. concatenation https://doi.org/10.1080/10635150601146041), I am happy to support publication. I would have appreciated a more thorough investigation on the ancestral state but, because one of the aims of the work is to quantify the lack of knowledge in order to stimulate more phylogenetic studies in copepods (the Authors state) then I am happy to promote its publication.
Experimental design: .
Validity of the findings: .
Additional comments: .


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

Input:
Title: A SYNTHESIS TREE OF THE COPEPODA: INTEGRATING PHYLOGENETIC AND TAXONOMIC DATA REVEALS MULTIPLE ORIGINS OF PARASITISM
Review round: 2
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: All comments from the first review have been well addressed.


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: INTEGRATED BIOINFORMATICS ANALYSIS OF THE NEDD4 FAMILY REVEALS A PROGNOSTIC VALUE OF NEDD4L IN CLEAR-CELL RENAL CELL CANCER
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: There are thousands of differentially expressed genes in cancers as compared to normal tissue. The authors did not show how NEDD4L-related genes are important in this background. The authors could develop a prognostic model that was derived from NEDD4L-related genes, but it can be speculated that this prognostic model is not the best one (although the ROCs with AUC seem to be good). A good prognostic model should be generated from the genes screened by survival analysis of all candidates.  The authors did not show the advantage of NEDD4L-based prognostic model over other models primarily aimed to predict prognosis, and this would limit the use and follow of this model.
Validity of the findings: no comment
Additional comments: This study conducted an integrated bioinformatics analysis using public datasets and identified NEDD4L as the differentially expressed gene in ccRCC compared with normal samples. The gene this study identified may have potential role in tumorigenesis and values of diagnosis and target treatment for ccRCC. This study suffers from some limitations that need to fully addressed.

Major concerns:
There are thousands of differentially expressed genes in cancers as compared to normal tissue. The authors did not show how NEDD4L-related genes are important in this background. The authors could develop a prognostic model that was derived from NEDD4L-related genes, but it can be speculated that this prognostic model is not the best one (although the ROCs with AUC seem to be good). A good prognostic model should be generated from the genes screened by survival analysis of all candidates.  The authors did not show the advantage of NEDD4L-based prognostic model over other models primarily aimed to predict prognosis, and this would limit the use and follow of this model.

It's not usual to divide the tumor stage into stage I vs. stage II-IV in survival analysis. Stage I-II vs III-IV may be a better choice.

Prognostic value of dichotimized NEDD4L seemed to be tested in a single cohort (TCGA).  How the cutoff of NEDD4L was determined? The prognostic value needs to be validated in other cohorts with public survival information and gene expression data.

The authors discovered NEDD4L as a critical gene in ccRCC. However, they should validate it in the author's in-house cohort and tumor samples.

Figure 8C, the workflow and method for generating nomogram are not reliable. In the nomogram, both M-stage and TNM stage are included in the model. However, M stage is a part of TNM staging system. It's werid to see 'Tumor-free' and 'with tumor' in the nomogram. How these two end-point status could be selected as predictive variables for survival?

line 105, "The correlation between NEDD4L and fatty acids has rarely been studied. One study showed that 20‑hydroxyeicosatetraenoic acid regulates NEDD4L expression in kidney and liver[30]." GSEA analysis support this one. However, the authors did not show how their GO, KEGG, and GSEA results could support the other popular roles of NEDD4L in ccRCC. This is important, since it could verify the robust of authors' methodology in this manuscript.

The authors defined NEDD4L-related genes using correlation analysis. However, interaction network analysis would be more robust, as they seemed to find a set of genes regulated or impacted by NEDD4L and take them to downstream enrichment analysis.

Minor concerns:
More details on quantification of gene expression should be provided. Is RNA-seq or microarray was used in the analysis?
Table 3 and Figure 7 need to be edited, the terms should not be presented as a computer input way. The p values and enrich scores should be shown in each panel of figure 7.
line 221, q value or adjusted p values in multiple correlation test should be shown there.
Legend of figure 5 did not describe the panel of heatmap and dotter plot on the right bottom.
The bulk survival plots in figure 2-3 need to be edited and cut.


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: INTEGRATED BIOINFORMATICS ANALYSIS OF THE NEDD4 FAMILY REVEALS A PROGNOSTIC VALUE OF NEDD4L IN CLEAR-CELL RENAL CELL CANCER
Review round: 1
Reviewer: 2

Output:
Basic reporting: This study proposed a bioinformatics analysis to understand the role of NEDD4 family in clear-cell renal cell cancer. The authors finally convinced that this gene may be a prognostic biomarker for ccRCC. The idea is reasonable; the use of clear and unambiguous English. There are some major points that need to be addressed:

- Literature review is weak. There must have some related works on bioinformatics analysis on CcRCC.

- Quality of figures should be improved.

- "Abstract" should not be broken into two paragraphs.

- There should have space before reference number.
Experimental design: - It is unclear how did the authors divide/separate their datasets. How did they use GEO datasets since they only mentioned that analyzed 526 tumor samples from the survival data of the TCGA_KIRC data set.

- Methodology has not been explained clearly.

- Number of control samples is much lower than patients.

- Did the authors concern about the batch effect removal among the datasets?

- ROC curves have been used in previous bioinformatics studies i.e., PMID: 31750297, PMID: 31362508, and PMID: 33260643. Therefore, the authors are suggested to refer to more works in this description.
Validity of the findings: - The authors should show p-values on GO analysis.

- According to the ROC curves and AUC values, the performance results were not too high.

- The authors should compare the predictive performance or the finding biomarkers to previous works on the same problem/data.
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: INTEGRATED BIOINFORMATICS ANALYSIS OF THE NEDD4 FAMILY REVEALS A PROGNOSTIC VALUE OF NEDD4L IN CLEAR-CELL RENAL CELL CANCER
Review round: 2
Reviewer: 1

Output:
Basic reporting: NA
Experimental design: NA
Validity of the findings: NA
Additional comments: I still have multiple major concerns that may impact the reliability of this manuscript:

1. As the author declaimed in the revised Methods, they used HTSeq-FPKM. Unfortunately, this reviewer highly suggest HTseq-counts as an optimal method to quantify the mRNA expression. They may check the difference between FPKM and counts in the differential expression analysis across samples. This reviewer highly suggest the authors work closely with statisticians and data scientists to check their data analysis, re-analyze the dataset and revise the whole text to present reliable results.

2. Why skin melanoma from TCGA-SKCM was used in figure 7?

3. The results and discussion need to be more relevant to their hypothesis that NEDD4L is assoicated with fatty acids. In GSEA, GO, and KEGG analysis, they need to illustrate how fatty acids-related genes and pathways were critical and outstanding among others in NEDD4L-related differentiation.


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: INTEGRATED BIOINFORMATICS ANALYSIS OF THE NEDD4 FAMILY REVEALS A PROGNOSTIC VALUE OF NEDD4L IN CLEAR-CELL RENAL CELL CANCER
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: My previous comments have been addressed well.


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: INTEGRATED BIOINFORMATICS ANALYSIS OF THE NEDD4 FAMILY REVEALS A PROGNOSTIC VALUE OF NEDD4L IN CLEAR-CELL RENAL CELL CANCER
Review round: 3
Reviewer: 1

Output:
Basic reporting: NA
Experimental design: NA
Validity of the findings: NA
Additional comments: I appreciate the authors' response. My concerns have been addressed.


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: PROGNOSTIC SIGNIFICANCE AND TUMOR-IMMUNE INFILTRATION OF MTOR IN CLEAR CELL RENAL CELL CARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: This paper discussed the expression and prognosis of mTOR and phosphorylated mTOR (p-mTOR) in clear cell RCC (ccRCC) patients, and explored the interactions between mTOR and immune infiltrates in ccRCC. This paper is reading friendly. The overall structure and results are clear.
Experimental design: The design of this experiment is simple and clear. After collecting the data, the author performs correlation analysis and survival analysis by using two existed databases including TIMER and TISIDB to show the relationship between mTOR, p-mTOR and immune infiltrates.
Validity of the findings: 1)	The correlation between mTOR expression and tumor infiltrating immune cells is too general which just contains the correlation plot. It would be helpful if the author could find other validations through literatures. The mechanism behind the association between mTOR expression and immune cells is still unclear. For example, the author just mentions the statistical results of the correlation in the section of TIMER and TISIDB analyses revealed the relationship between mTOR and immune infiltrates in ccRCC. I think that more biological evidence is needed to validate the statistical results.
2)	The survival plot shows that the p-mTOR was identified as an independent predictor of poor CSS with significant p-value (0.002). The author also shows that the p-mTOR is significantly correlated with metastasis, tumor size, and stage. However, the sample size for this plot is pretty small, which is around 150. It’s doubtful whether the conclusion is generalizable to other datasets.
3)	As mentioned by the author, controversial conclusions were made by different studies. The role of p-mTOR on the survival is totally reversal. This means that more evidence is needed to validate paper’s conclusion.  For example, is there any group showing the negative p-mTOR role on the patient’s survival? Besides, is the conclusion of mTOR consistent with other studies? For example, is there any study showing the significant relationship between mTOR and patient’s survival?
Additional comments: None


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

Input:
Title: PROGNOSTIC SIGNIFICANCE AND TUMOR-IMMUNE INFILTRATION OF MTOR IN CLEAR CELL RENAL CELL CARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written, authors have shared all the relevant data associated with the experiments. There is need to clarify the figure 5 and 6 and need to better address them in the reporting and discussion.
Experimental design: The research is thought-out and would add more information to the field of Renal cell carcinoma. There are some gaps in the studies that need to be filled
Validity of the findings: The authors have validated their data in human samples and have utilized the available data to validate their findings using a larger data set. However, the authors need to validate some of it in their 145 ccRCC patients as well as in the 3 patients that they chose to show mTOR staining
Additional comments: The authors have a well written and thoughtout manuscript. They have used a small data set to generate the hypothesis and validated it on a larger model.


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: INFLUENCE OF TIED-RIDGE-FURROW WITH INORGANIC FERTILIZER ON GRAIN YIELD ACROSS SEMIARID REGIONS OF ASIA AND AFRICA: A META-ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors of the paper Influence of tied-ridge-furrow with inorganic fertilizer on grain yield across semiarid regions of Asia and Africa: a meta-analysis propose a relevant theme because droughts and soil erosion has been attributed to the problem of appropriate soil moisture conservation practices and lead to lack of crops produced in the mentioned region of this studied.
Experimental design: Given that this is a meta-analysis, before the last paragraph of introduction needs to establish the following:
-What is a meta analysis and how and why is it used?
-Has there been any metaanalysis /systematic review performed in this area of research ? The reason is to clearly justify why this meta analysis is needed, as well as help establish a clear gap that this current work aims to fill
Information written about metaanalysis in the data analysis section Lines 112-117 should be brought here, and further information supplemented, with adequate references
Methodology
The aim of this paper is very interesting. The research design appears well built. However, kindly remove authors names from data collection. Kindly break down the methodology section into the following below, making sure to refer effectively to the flow chart at each stage
- The protocol followed to achieve this meta analysis
-The search strategy must stand out alone, here feel free to engage the challenges encountered in conducting the search itself
-Inclusion and exclusion criterion must be clearly explained
-How was the data extracted, kindly describe this step-wise and succinctly
-Data analysis’ should be changed to ‘statistical analysis and meta analysis’
Results
Given that this is a metanalysis, it is useful to start the results and discussion with:
-Process of conducting the review , this should be the start of line 163 . Kindly
-Characteristics of studies, that has been meta-analysed. These should form the  components that have built the meta analysis, it is essential that this has to be characterized
- Meta analysis should then follow, where the influence and yield can be presented
Please clarify and consider if it is possible to provide a short description of parts of Asia and Africa countries that applied the specific approach comparatively. For Instance, West Africa Countries, Line 164 – 165.
These are essential aspects of meta analysis, authors are encouraged to follow this, to improve clarity of this work
Validity of the findings: This work appears to present very valid results. Authors are encouraged to elaborate more on the discussion, and add more information from Tabulated data herein.
The conclusions are properly presented by the authors of the research, reflecting the final results of the comparisons with the existed studies.
Additional comments: Authors have made very strong effort in this work. However, major revisions are required to improve it, towards potential acceptance.


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: INFLUENCE OF TIED-RIDGE-FURROW WITH INORGANIC FERTILIZER ON GRAIN YIELD ACROSS SEMIARID REGIONS OF ASIA AND AFRICA: A META-ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: The hypothesis authors made "using inorganic fertilizers and mulching in semi-arid areas is the best agronomic method for reducing drought's negative effects and avoiding runoff and soil erosion.". I just wandering how authors test a method is best?
Validity of the findings: No novel finding was presented in this MS.
Additional comments: In the MS, authors tried to compare the impact of different cultivated systems for cereal crop yield using a meta-analysis based approach. But the results were not any new discovery and the conclusions were not strongly supported by the results.

In row 82-84: "As such, we hypothesized that using inorganic fertilizers and mulching in semi-arid areas is the best agronomic method for reducing drought's negative effects and avoiding  runoff and soil erosion.", authors need to check the "best", how do authors test "inorganic fertilizers and mulching in semi-arid areas is the best agronomic method"?

In the row 165-167, authors presented " temperatures are mostly greater than 20°C (Table 4). Results from the studies revealed there was  no significant difference between grain yields in tied ridge with mulching compared to flat planting ", but in row 174-177, authors showed tied-ridge-furrow system significantly increases sorghum yield. The results were different, authors need to explain it.

I don't think the results support the author's conclusion. Such as in row 255-257 "Based on the results of this study, it can be concluded that the combination of tied ridge rainwater harvesting system with mulching treatment was the best technique in retaining soil moisture and can be adopted by farmers in semiarid areas to increase crop yields.", but the results part (row 165-167) showed "Results from the studies revealed there was no significant difference between grain yields in tied ridge with mulching compared to flat  planting (p > 0.05)."

In total, there is no difference from previous research, or authors need to figure out what is the new discovery of the MS.


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: INFLUENCE OF TIED-RIDGE-FURROW WITH INORGANIC FERTILIZER ON GRAIN YIELD ACROSS SEMIARID REGIONS OF ASIA AND AFRICA: A META-ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors of the paper Influence of tied-ridge-furrow with inorganic fertilizer on grain yield across semiarid regions of Asia and Africa: a meta-analysis propose a relevant theme because droughts and soil erosion has been attributed to the problem of appropriate soil moisture conservation practices and lead to lack of crops produced in the mentioned region of this studied.
Experimental design: How meta analysis and why it was used, was  properly described by the authors before the last paragraph of introduction as requested, appears to clearly justify its  relevance for the study. Gaps that also justify the need for the study has been presented.
Validity of the findings: The experiment appear valid.

The methodology has improved. However, it is important that authors further elaborate on the following:
- The methods section has to be broken down into its relevant subsections
An example, sections like inclusion and exclusion criteria, search strategy should all stand out in a subsection.

Results have improved. However, in the discussion, more literature is required to strengthen the discussion. Example, in areas where meta analysis results are being compared.
Additional comments: Look forward to the revised manuscript.


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

Input:
Title: DIVERSE METHANOGENS, BACTERIA AND TANNASE GENES IN THE FECES OF THE ENDANGERED VOLCANO RABBIT (ROMEROLAGUS DIAZI)
Review round: 1
Reviewer: 1

Output:
Basic reporting: This paper by Montes-Carreto et al investigated the faecal microbiome by metagenomic sequencing from four faecal pellets thought to be from the endangered Volcano rabbit in Mexico.

Although I originally accepted this article for peer review, on reading the article I do not feel that I have appropriate expertise to review this paper. I have expertise in some lagomorphs, but not the ecology of the volcano rabbit. I have some expertise in metatranscriptomics for virus discovery. But I feel that the bacterial ecology and bioinformatics used in this manuscript go beyond my area of expertise.

I have tried to provide some useful comments below but I really struggled to understand the manuscript, analyses, and conclusions, presumably because of my lack of expertise specifically in bacterial ecology.
Experimental design: Based on my experience with metatranscriptomic sequencing, I would not typically consider an analysis of four animals to be robust. I do not know if this is acceptable in the microbial ecology field. I would also have concerns about assigning animal age based on faecal size, assigning species based on faecal appearance, cross-contamination with two samples being collected from the same latrine, representativeness of faecal samples that were not collected fresh (e.g. were samples degraded due to environmental/UV exposure?).
Based on my experiences, I have some concerns about the external validity of these findings and extrapolation from the small sample size. For example, the authors make conclusions about all young volcano rabbits, and differences between young and adult volcano rabbits, based on a single faecal sample that may be from a young animal based on faecal pellet size.
Validity of the findings: I had difficulties assessing the validity of the findings, likely due to my lack of specific expertise. This paper should be reviewed by an additional reviewer with more microbial shotgun bacterial metagenomics expertise.

However, I did note some inconsistencies in the manuscript.
For example, Lines 86-88 – The author's interpretation and summary of these papers is not how I read these papers. Velasco-Galilea found that Firmicutes, followed by Bacteroidetes and Tenericutes, were the most abundant phyla. Crowley found that Firmicutes and Bacteroidetes were the most abundant. North found that Firmicutes, followed by Bacteroidetes and Proteobacteria were the most abundant but they also looked at caecal samples, which may differ from faecal samples investigated in many of the other papers. Shanmuganandam found that Illumina 16S v3-v4 sequencing underrepresented Tenericutes.
For example, in Figure S1 I would typically look for a more comprehensive Leporidae tree.
For example, I interpreted figure S2 as not supporting Figure 1 e.g. I could not see any Actinobacteria in Fig S2. However, the authors state in line 315 that the same 9 phyla were found by 16S and shotgun analysis. I am not sure how much correlation there should be between shotgun and 16S datasets.
Additional comments: After reviewing this article I found that I did not have the relevant expertise to review this appropriately. This paper should be reviewed by an additional reviewer with more microbial shotgun bacterial metagenomics expertise. Since I work mostly with viruses, I can't really think of anyone with specific bacterial metagenomics expertise. I'm sorry that I could not be of more help.


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: DIVERSE METHANOGENS, BACTERIA AND TANNASE GENES IN THE FECES OF THE ENDANGERED VOLCANO RABBIT (ROMEROLAGUS DIAZI)
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English language should be reviewed to ensure that an international audience can clearly understand your text. I suggest you contact a native colleague or a professional service that help you to improve the English of your manuscript.
Experimental design: Your research aims at characterizing the fecal microbiota of the volcano rabbit and assessing the role of microorganisms in the degradation of plant fiber and tannin. I found it a meaningful objective since you sed light on a Mexican endemic rabbit species, which, moreover, is critically endangered. However, you should remove the last sentence of the introduction section "Indeed, we found abundant genes with such putative functions, especially endoglucanase genes, but also β-glucosidases, arabinofuranosidase and endo 1,4 β-xylanase." because this is an output of your study.

My main concern in your study is its limited sample size. This constraint, however, could be justified by the difficulties in collecting feces of an endangered species. Moreover, this study is of interest because it covers a topic in a species which is still relatively poorly understood.
Validity of the findings: The limited number of samples is the main limitation of this study, specially in terms of providing results statistically sound.
Additional comments: I think microbial names should be italicised.

L30: citations should not be provided in the abstract.
L57: it should be "interacting between them".
L58: remove "or disease".
L63-65: please add references of previous studies in rabbits that demonstrate how age, genetics, diet, breeding conditions or the administration of antibiotics shape gut microbiota over the life of the animal.
L74: which species?
L87: "dominated by phyla..."
L103: please explain the importance of finding microorganisms involved in tannin degradation.
L119: how much time were samples stored until DNA extraction?
L127: please provide more detail about the process of library generation.
L170: how did you compute Shannon index? Specify at which number of reads you rarified your samples.
L175: please explain why you used nonparametric Friedman test with 10,000 Bootstrap.
L178: did you conduct any additional filtering by low abundant genera?
L201: please specy the range and the average number of raw and filtered reads per sample.
L209: At which taxonomy level does it refer? please provide an explanation for this low percentage of classification.
L212: you should provide some descriptive statistics in this table.
L323: you should mention that these differences could be due to different strategies to characterize microbiota (shotgun vs 16S amplicon sequencing).