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: NUTRIENT AVAILABILITY INDUCES COMMUNITY SHIFTS IN SEAGRASS MEADOWS GRAZED BY TURTLES
Review round: 1
Reviewer: 2

Output:
Basic reporting: In the manuscript Nutrient availability induces community shifts in seagrass meadows grazed by turtles López et al seek to add to the growing literature on the effects that increasing and range-expanding populations of herbivorous green sea turtles can have on seagrass meadows. In this manuscript Lopez et al report that increased grazing pressure induced by both simulated and natural green turtle grazing led to increased pore-water ammonium concentrations and shifts in seagrass species composition from a long-lived (turtlegrass Thalassia testudinum) to early successional species (manatee grass Syringodium filiforme & rhizophytic algae). They also found no differences in organic sediment content among grazing treatments.
While there is a need for additional information on the effects on sediments and pore water nutrient content affected by green turtle grazing, the flaws in this study’s experimental design prevent sound conclusions from being drawn. Below we consider only a few of our concerns, but they are sufficient to support our assessment that the paper is fatally flawed.
Experimental design: Among the complicating factors in the experimental design, the active turtle grazing that occurred in the simulated grazing plots while the experiment was in progress negates the use of results from this treatment and is only one example of uncontrolled treatments. In addition, there was no justification provided for initiating simulated grazing in abandoned, naturally grazed patches (Long-term treatment). Because turtles don’t return to abandoned patches until they have recovered, this treatment and its results seem biologically irrelevant. It is also unclear why the authors clipped Syringodium and calcareous green algae, for which there was no evidence produced that these species are food resources for green turtles.
We also note that additional statistical analyses (the ANOVA table and post hoc results) are needed to further explain the densities and biomasses of each species. Post hoc tests carried out with their results shown on Figure 2 B would unlikely provide justification for the claim that grazing drives the shift seen in species composition, because the low p value for the ANOVA reported in the text has to be primarily due to the high value of the control and not differences among the grazing treatments.
Validity of the findings: Among the complicating factors in the experimental design, the active turtle grazing that occurred in the simulated grazing plots while the experiment was in progress negates the use of results from this treatment and is only one example of uncontrolled treatments. In addition, there was no justification provided for initiating simulated grazing in abandoned, naturally grazed patches (Long-term treatment). Because turtles don’t return to abandoned patches until they have recovered, this treatment and its results seem biologically irrelevant. It is also unclear why the authors clipped Syringodium and calcareous green algae, for which there was no evidence produced that these species are food resources for green turtles.
We also note that additional statistical analyses (the ANOVA table and post hoc results) are needed to further explain the densities and biomasses of each species. Post hoc tests carried out with their results shown on Figure 2 B would unlikely provide justification for the claim that grazing drives the shift seen in species composition, because the low p value for the ANOVA reported in the text has to be primarily due to the high value of the control and not differences among the grazing treatments.
Additional comments: Specific comments:
Introduction
●	Line 49: Lal et al. 2010 also reports changes in seagrass bed composition due to turtle grazing
●	Line 102:  “Sensu Williams (1990)...” into “Williams (1990) reported...”
Materials and Methods:
●	Combine Simulated grazing and “Seagrasses and rhizophytic algae” sections
●	Line 133: i.e.instead of “species like”
●	Lines 141-142: unnecessary capital letters in treatment names
●	Lines 142-143: Grazing an abandoned patch is not a realistic treatment
●	Line 146-147:there is no evidence turtles graze on Syringodium is a primary food source, most likely just occasional, incidental grazing (Molina-Hernández & van Tussenbroek (2014)), clipping it does not mimic natural grazing
●	Line 154-156: time needed for seagrasses to grow enough would depend on the time of year. References show no evidence of Thalassia needing 15 days to regrow >5 cm in any of the references except Moran & Bjorndal 2007 says “Clipping interval ranged from 12 to 38 days because growth rates varied with temperature”
●	Line 156: replace “during” with “for”
●	Line 161:  “...the leaves in these patches did not have bite 161 marks of the turtles which are clearly visible” reconsider sentence structure
●	Line 168: “...in February 2016.” say what this means timeline-wise
●	Line 175-176: again, tell us what this means for your timeline. Halfway into the experiment? 3 weeks in?
●	Line 190-191: replace symbols for meaning
●	Line 233: lowercase o in “One-way ANOVA”
●	Line 240-241: leverage is not used correctly. Stop sentence after “...were removed” The term “outliers” is enough justification.
●	Line 244: same as line 210-241

Results
●	Combine Simulated grazing and “Seagrasses and rhizophytic algae response to grazing pressure” sections
●	Lines 251-252: natural grazing co-occurring with simulating grazing would negate the results as the grazing regime is not followed
●	Line 247: if there are no results to report in the simulated turtle grazing results section, don’t include the section
●	Lines 273-277: There are no significant differences, and the differences are not enough to assert this trend. Include ANOVA table and post hoc results because low p value reported in the text can be driven mainly due to the control
●	Line 278: Fig. 2
●	Line 283: two-way
Discussion:
●	Line 307: write out the full scientific name and common name every time you start a new section
●	Line 382-386: irrelevant because turtles only incidentally graze Syringodium
●	Line 388-390: Lal et al. 2010 reported the same for turtle grazing
Tables:
●	1
○	“ ...undisturbed until the end...”
○	“Experimental grazing (clipping maintenance)” as the column header is unclear, suggest Experimental grazing duration
○	If “Does not occur naturally in patch rotational grazing because turtles do not return to abandoned patches” is true of the long-term treatment in previously grazed grass, what is the justification for this treatment?
●	2: Include what the error value is
●	4: nitrogen (N) and carbon (C)
Figures:
●	1: include an explanation of the dotted line
●	2: extra parenthesis
●	3: include legend on the graph
●	4: graphic is too complex and not understandable

Overall recommendation: Clearly, a great deal of work was done to gather the data reported in this manuscript. However, the lack of proper control of treatments, along with other issues noted above, render the results and conclusions in this paper unreliable, and a recommendation that the paper be rejected the only one possible. There may be a way to use portions of the data to produce a more qualitative, narrative type manuscript but this will require a significant amount of 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: THE ADIPOKINETIC HORMONES AND THEIR COGNATE RECEPTOR FROM THE DESERT LOCUST, SCHISTOCERCA GREGARIA: SOLUTION STRUCTURE OF ENDOGENOUS PEPTIDES AND MODELS OF THEIR BINDING TO THE RECEPTOR
Review round: 1
Reviewer: 1

Output:
Basic reporting: This work is primarily a modeling study aimed at elucidating the binding of three different AKH peptides of Schistocerca gregaria to its only AKH receptor. While the article in general addresses the modeling aspect, there are several issues which would need to be addressed before the manuscript can be deemed publishable:
1. The English language remains a primary concern and needs to be vastly improved. The target audience is likely from the entomological community so certain terms and abbreviations which are more appropriate for molecular modeling studies have to be adequately explained.
2. The title is a bit strange sounding "...solution structure of agonists...". The authors employed the three AKH peptides that are found in S. gregaria but not agonists that would mimic the AKH peptides, so I am confused why they prefer the term agonists in such a case. I would probably rephrase the tile as "...ligand-receptor binding modeling studies".
3. Table and Figure legends are very brief. More explanations are required. In general, I would expect stand-alone legends which would sufficiently explain what is being depicted without the need to have recourse to the text.
4. What was the hypothesis being tested?
Experimental design: 1.One of the concerns I had about the experimental design was that while all three peptides were synthesized and purified, they were not sufficiently soluble in water (Line 105). What was the solubility?
2. Within the insect body, how would these peptides behave? Were these synthetic peptides checked to determine if they actually mobilized lipids in S. gregaria?. Some information on this should be provided otherwise the relevance of this work remains doubtful.
3. The M&M section is replete with terminology which probably would be easier comprehended by specialists in molecular modeling studies but would be difficult for the average entomologist or insect physiologist to understand. The authors would need to provide a more lucid account of the techniques used. For example Line 115: "using the dipsi2esgpph pulse sequence" What does this mean? Also, line 117: "and noesyesgpph". This is incomprehensible.
4. What was the statistical treatment of the data generated?
Validity of the findings: 1. This study is primarily a modeling study with a view to provide information on how putative agonists or antagonists can bind to the AKH receptor with the eventual goal of designing novel pesticides. However, its validity is in doubt because the authors could easily have designed an antagonist (since they already used synthetic ligands) and checked it for binding competitively to the AKH receptor.
2. It is unclear from the studies which of the three different AKH would show preferential binding to the receptor (i.e. competitive binding). If all three bound to the same receptor with the same efficiency, do the authors hypothesize that the constraint is on which of the neuropeptides are being synthesized and released?
3. What is the statistical validity of the findings?
Additional comments: The English language remains a matter of primary concern along with all other points raised above.
1. Line 21-22: "currently discussed as targets to" could be rephrased as "being considered as a novel target to".
2. Line 23 and 26: I do not like the term "AKH system". Why do the authors refer to this neuropeptide as a "system"?
3. Line 30 Replace "Next" with "Further".
4. Line 58 Aedes aegypti should be in italics.
5. Line 63: Rephrase, it sounds clumsy. I suggest : "which occurs not only in insects and crustaceans".
6. Line 64: Codes "an mRNA".
7. Line 76 "are currently fiercely discussed" replace with "are currently being considered".
8. Line 86 is essentially a rehash of line 84-86.
9. The term ligand and agonist are referred to interchangeably. Since these are actually peptides endogenously synthesized, should they not be referred to as such?
10. Line 152 S. gregaria should be italicized.
These are just some of the edits, I suggest a more thorough revision of the manuscript along these lines.


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 ADIPOKINETIC HORMONES AND THEIR COGNATE RECEPTOR FROM THE DESERT LOCUST, SCHISTOCERCA GREGARIA: SOLUTION STRUCTURE OF ENDOGENOUS PEPTIDES AND MODELS OF THEIR BINDING TO THE RECEPTOR
Review round: 1
Reviewer: 2

Output:
Basic reporting: I found this manuscript written in a lucid manner allowing otehr researcher for both understandings and repeating of the reported procedures.
Although the authors refer to structural study (molecular dynamics) on insect adipokinetic hormones (L 617: Zubrzycki IZ. 2000. Molecular dynamics study on an adipokinetic hormone peptide in aqueous solution. Zeitschrift für Naturforschung C, A Journal of Biosciences 55:125-128. ) I think that it should be stressed that the first 3D-structure derived by NMR spectroscopy has already been published: Zubrzycki IZ, Gäde G. Conformational study on an insect neuropeptide of the AKH/RPCH family by combined 1H NMR spectroscopy and molecular mechanics. Biochem Biophys Res Commun. (1994) 198:228–35. 10.1006/bbrc.1994.1032.
The molecular dynamics study section unfolds the three approaches i.e., "NMR restrained molecular dynamic simulations in vacuum, water and DPC." (please put a comma after water...)  Here I have the following question to the authors; 1) what is the logic using three different environments. Could the authors justify this decision especially vacuum simulation? 2. How many water molecules were used in the simulation? The authors put there ~700, but they, in my opinion, say explicitly how many: 703 ... 721..

L 188: How many CL- ions were added for zeroing total charge.

L 198: "Berjanskii and Wishart (Berjanskii & Wishart 2006) and Tremblay (Tremblay 2010) have shown that by comparing the measured chemical shifts to literature values for a random coil structure, some idea as to the structure and flexibility of the peptide can be obtained" - I have a problem with "some idea" statement. In my opinion, It is simply too vague. Please state clearly as to the kind of conclusions that can be derived.

L 436: "Our results show that the three endogenous peptides, Schgr-AKH-II, Aedae-AKH and Locmi-AKH-I, all bind to the same receptor binding site and with very similar binding constants. This may be surprising, as the three ligands are very different." - can the last statement be clarified i.e., ligands are very different - structurally or charge wise?

Conclusions; The first statement "In this paper, we have shown that the putative receptor, Schgr-AKHR, is a member of the Class A superfamily of G-protein coupled receptors." which is a derivative of the statement provided at L 245 The sequence identity between the Schgr-AKHR and the h-OR was 26.33% The h-OR structure belongs to the class A... " 26% of sequence identity is, in my opinion not enough to judge on structural and functional similarities between proteins or peptides. I may cover 26% right from the N-terminal amino acid to, let say 26th amino acid, in case of 100 residue peptide. Please provide the overlay of these sequences to justify your statement that the studied structure renders analogous biological functions.

Figure 1. The authors provide a graphical representation of chemical shifts. Although it is a nice picture it is not very informative without knowing, in depth, what are the relations between chemical shifts and randomness of the structure. There are also colors on the picture but without proper description it simply meaningless.

Figure 2: The superposition of so many conformers make it nearly impossible to deduce the overall shape of the peptide. The authors tried to clarify this be providing stick representation. Nevertheless, in my opinion, if the average cartoon representation would be overlayed on the stick representation the reader would get a much better feeling of the shape of the peptide (it is done in figure 4).

Figure 6. The authors show the surface representation of the binding pocket using unknown to the reader coloring scheme. I presume that this does not reflect the charge. If my presumption is correct I would appreciate changing it to charge coloring scheme for both the surface and the molecule.
Experimental design: The research is within the aims and scope of the journal.
The research questions are well-defined and meaningful. There are some problems that should be addressed (listed in the basic reporting).
The study is of the top technical standard. Methods are generally sufficient to replicate (the problems have been addressed  in basic reporting)
Validity of the findings: It is the novel study employing state of the art technology, including both NMR spectroscopy and molecular modeling. Conclusions are well stated although as outlined in basic reporting I have a problem with the non-discussable statement "In this paper, we have shown that the..."
Additional comments: The paper is generally well written. There are some issues with figure legend and this must be addressed. The same applies to the final conclusion. In my opinion, the authors should "weaken" the first sentence of the Conclusion section and indicate it as more speculative.


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 ADIPOKINETIC HORMONES AND THEIR COGNATE RECEPTOR FROM THE DESERT LOCUST, SCHISTOCERCA GREGARIA: SOLUTION STRUCTURE OF ENDOGENOUS PEPTIDES AND MODELS OF THEIR BINDING TO THE RECEPTOR
Review round: 2
Reviewer: 1

Output:
Basic reporting: No Comment
Experimental design: No Comment
Validity of the findings: No Comment
Additional comments: The authors have adequately addressed all issues raised by reviewers.


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: EXPANSION OF SANDHILL CRANES (GRUS CANADENSIS) IN EAST ASIA DURING THE NON-BREEDING PERIOD
Review round: 1
Reviewer: 1

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: [Also see attachement]

Lines – statements

14.  “Historically, the distribution of Sandhill Cranes included much of North America and extending in summer into northeast Russia.”
18. “spread south into East Asia”.
19. “and to assess…”
31. “with five other species of cranes”.
32. “that the range and numbers of Sandhill Cranes have expanded”.
33.  “were mixed with five other species of cranes”
35.  “ advantages of these other species”
36.  “other species of cranes”
37.  “current perhaps the most abundant of th 15 species of cranes”.

Figure 1. Sandhill Cranes are with both White-naped and Red-crowned on the Korean DMZ, with both Siberian and White-naped at Poyang Lake. Perhaps there are other species in contact with them at the other locations indicated. There is much overlap with the distribution of many crane species during migration and in winter in East Asia, with the exception of Red-crowned in Hokkaido.  If the data show association with specific species, that should be discussed if possible as selective or opportunistic.

Figure 2. It should be mentioned that the number of bird watchers has also increased since the 1960s (China was in the throes of the Cultural Revolution then). The bird watching groups in the three nations might have information on their numbers to graph with the sightings of Sandhills.


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: EXPANSION OF SANDHILL CRANES (GRUS CANADENSIS) IN EAST ASIA DURING THE NON-BREEDING PERIOD
Review round: 1
Reviewer: 2

Output:
Basic reporting: The structure, figures, and table are good, and the raw data supports the results and discussion.  The abstract provided a succinct summary of the results.   References are appropriate and complete, and provide good background and context.
Professional, technical English is used, but there are a number of areas where better word choice or wording is needed for clarity.  Some suggested wording changes and problematic areas:
Line 25 and in abstract: Replace ‘Python” (the software) with regression analysis; specifics of the software seems unnecessary since this is a common statistical method.
Line 27: insert “during the non-breeding season in Asia” following sandhill crane to clarify the distribution details and season.
Line 34-35: During the nonbreeding season, most species of cranes have fairly similar foraging habits (grains, seeds, tubers), and sandhill cranes are known to be one of the more generalist species.  Suggest changing / simplifying this statement to ~ “indicating their adaptability to a range of habitat types and food resources.”
Line 36: “Future development trends” could refer to human developments.  Recommend changing wording of this sentence to “The implications of these trends in sandhill cranes in East Asia for this and other crane species warrants further research”
Line 51:  Phymer et al. should be Rhymer et al.
Lines 47-61:  Data in this paper deals sandhill cranes associated with the Midcontinental Population, and specifically the less subspecies; it not necessary to name the other North American populations. I think this pargraph could be rewritten to indicate that it is the lesser sandhill crane subspecies that migrates to Asia from central North America, that it is part of the largest population of sandhill cranes, and that population continues to increase in number and its breeding range in Asia.
Line Lines 63-64:  Should clearly indicate in this sentence that these are birds that fly to Russia for the breeding season.
Line 76:  Clarify what region here – time of arrival to different breeding grounds generally, or here specifically about North American breeding grounds?
Line 89:  “Sandhill cranes wintering in East Asia has long been reported.” Do you mean back to 1963, or were there earlier anecdotal reports?  If back to 1963, these first 2 sentences could be merged to “have been reported since 1963, with first reports in Izumi….”
Lines 168 and 174:  suggest it is more appropriate to use “created” rather than “obtained” as the data were used to create or generate maps and table.
Lines 208-212:  suggested revision for better flow:  “In recent years, there were 2 records showing that there were already sandhill crane family groups in Asia during the non-breeding period. One family group was recorded in Yancheng National Wetland National Nature Reserve for Rare Birds, Jiangsu, China on December 4, 2013, with 2 juveniles in the reserve. The second was recorded in Kagoshima, Japan, on November 7, 2014, also with 2 juveniles recorded.”
Line 262:  “Previous reports” – previous to when? 1963 or a report before this paper?
Lines 288-291:  Based on my assumption that “subadult” means a bird <1 year old (‘young’ in the raw data), I suggest the following revisions for this paragraph:  “There were four clear records of subadults individuals wintering alone with other crane species in Asia, the earliest in 1969. There may have been additional occurrences of subadults wintering in East Asia that were not detected because of limitations of field identification abilities.  That most of the records of subadults were sporadic (1969, 1984, 2011, and 2014) may also reveal the role of subadults in the winter range expansion of sandhill cranes.”
Line 301: Insert “that breed in Russia” after sandhill cranes to differentiate from North American breeding cranes.
Lines 304+:  As indicated for the Introduction, worth noting that sandhill cranes are generalists in food habits, and therefore are likely to overlap in habitat and foraging with other crane species.
Lines 315:  Recommend dropping “dangers”; simply” potential problems” is sufficient here.  When cranes are beginning the courtship and pairing relative to their associations with other crane species or their own will be important in evaluating to what extent this is a real risk to Asian crane species.
Lines 345-347: Duplicated sentence to the following sentence; delete one of the 2
Lines 347-348:  “In two recent years, a family of sandhill cranes…”  Recommend dropping “and not just as a single individual mixed with other cranes” as this phrase is confusing.
Throughout:   Often the authors refer to ‘other kinds of cranes.’  Recommend consistently referring instead as ‘other crane species’, to differentiate from types of groups (e.g, singles, family, grouped adults). Also, please change “common crane” to “Eurasian crane” throughout – this is the accepted common name.  Siberian should always be capitalized in the name of that species.
Experimental design: This is an observational study, but one which takes full advantage of a range of reporting sources as well as recent field work.  The research question is clearly stated and then addressed in the results and discussion.  The statistics applied were appropriate to elucidate the temporal pattern of numerical increase. Additional clarification is needed to demonstrate rigor in terminology, how some of the data sources were assessed, the data filtering for analyses, and to be able to replicate both field and searches for existing records.
Lines 139-140:  More explanation is needed to demonstrate how your “understanding of cranes” was used to filter information from news and bird watching sites when photographs were not available.  For example, how could you determine if there was a mis-identification of a species when reported as a sandhill crane but no photograph was available?
Lines 152-169 – Data Filters:  Several points need to be clarified here --
1)	Subadults (first used on line 161):  Please define subadults and how this age was identified in observations. Is a “subadult” defined a bird between 1~3 years? Or a bird <1 year old? How was the age determined -- based on plumage, social grouping, behavior?  In the raw data there is no “subadult” column, but there is a “Young” column, which I am assuming for this review is equivalent to “subadult” in the text. But families are described as adults and 2 “juveniles” – what is the difference if subadults are <1 year old? Clarifying terms for subadults and juveniles here and throughout the ms is very important to understand the differences and understanding how sandhill cranes are ending up wintering in East Asia. Review the paper throughout to be clear and consistent.  In my review of the results and conclusions, I came to assume subadult = young = a sandhill crane <1 year old.
2)	Year:  How year was assigned was not immediately clear to me until I reviewed the data.  I recommend changing the wording to indicate that if the month of observation was in January-May, then the record was assigned the previous year, to indicate the bird(s) was considered to have been present in East Asia that entire winter (fall-spring).
3)	Mixed With – the data indicate either other crane species that the sandhill crane(s) were observed with, or “NA”.  NA accounted for 139 of 168 observations. NA could be interpreted as simply no data, or (considering the general interest in cranes for most of these sources) that the sandhill cranes were not with other cranes. Please clarify so readers can appropriately interprete these records.
Line 199:  It is not clear what is meant by “no separate activity records”.  Since this in the section about misxed, subadult, adult and family records, you mean sandhill cranes were only observed with other cranes, and never reported away from other birds (on their own)?  Or were never observed as a solitary sandhill crane – e.g., “…with other cranes” or other crane species?  Review other sentences in the results and discussion to ensure clarity of other species versus simply other cranes.
Lines 214-215:  In reviewing the data table, I am confused on how these numbers were derived. There are 144 records with the number of cranes recorded (remainder are NA). In this sentence, the second number (98) – after the filter was applied – is higher than the original number of data (86).  How is that possible? Please explain the filter used to achieve the 86 and 98 records for regression analysis, and what each number represents.
Supplementary materials:  In Table 1-- 1) Recommend dropping the parentheses in the right column around the citations, as they are unnecessary here.  2) “Bird Talker 2018” appears to be “Talker, B.” in the reference list; recommend changing in the references as Bird Talker”.  3) NaverBlog 2006 is not listed in the references.
Validity of the findings: The data is robust and support the results and main conclusions The paper provides valuable insights, and foundational information, about an expanding species, which is shifting from ‘winter vagrant’ toward a more common wintering species in East Asia.  The risk of greater disease transmission is probably the most important challenge to Asian cranes during the nonbreeding season; suggest elevating that to be the main part of that portion of the discussion. Implications of hybridization is likely less serious to the future overall health and success of native Asian cranes, and will likely be uncommon.  Some other suggestions for improvement:
Lines 224-224:  Please express the increase as percentages rather than simply “significantly” to more clearly demonstrate the magnitude of change.
Lines 234-244:  Would be helpful to indicate, in each time period, the number of areas where sandhill cranes were observed (e.g., 7 areas before 2000, an additional xx records in the following periods).
Line 255: as noted above, would be helpful to indicate percent increase (ie magnitude of change), and give numbers – increasing from individual cranes in a single area before 1980 to as many as 8 birds ….
Lines 349-305:  Confusing sentence that has little value beyond the obvious; recommend deleting.
Additional comments: The paper lays out the historic and ecological background for the research question in the introduction, and the appropriate literature are referenced. The raw data provided were clear and very useful in reviewing and understanding the results.  Results support the main conclusions. The pattern reported of progressive increase in numbers and social groups is valuable to understanding how these birds may be shifting their migratory habits, with longer term implications for the development of a new migratory pathway and tradition.  This paper will provide useful foundational information about the status and trends of sandhill cranes wintering in East Asia.
Below are more specific questions and comments on parts of the text. Generally, key points to address are:
1.	Define or clarify terms used there, in particular subadult versus juvenile.
2.	Improve the explanation of how the raw data were filtered to obtain the final set used for regression.
3.	Ensure consistency in the use of terms throughout the paper (e.g., subadult, young, amount; other cranes versus other crane species) and be sure it matches the raw data table (young = subadult? amount = number).


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: EXPANSION OF SANDHILL CRANES (GRUS CANADENSIS) IN EAST ASIA DURING THE NON-BREEDING PERIOD
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed all my earlier concerns and questions with appropriate changes. While some of the English phrasing is a bit awkward and might benefit from some minor additional editing, the meaning is clear.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: No additional comments


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

Input:
Title: SARGASSUM BLOOMS IN THE CARIBBEAN ALTER THE TROPHIC STRUCTURE OF THE SEA URCHIN DIADEMA ANTILLARUM
Review round: 1
Reviewer: 1

Output:
Basic reporting: I appreciate how difficult it can be to write a technical paper in another language, and the authors have made a good effort. However, grammar and sentence structure need to be much improved throughout the paper. Many sentences are too long and could be split into two (or three) sentences. Other sentences are fragments.

Additional major improvements (in order of importance) include:
1.	Consider possibly narrowing the focus of the study. The study measures numerous values that make it hard to remember the overall aims of the study. Is it to determine how Diadema’s diet changed after the influx of Sargassum on the coast? Is it to quantify the trophic or niche breadth of Diadema? Is it to measure how Sargassum decomposition resulted in hypoxia in lagoonal backreef environments? Each of these questions are valid, but together, the various measurements reported in the study do not tell a cohesive story.
2.	Clearly state a hypothesis/hypotheses in the Abstract and Intro. Currently, the wording is very vague and no specific predictions are made about the impact of Sargassum on Diadema. This leaves the reader with many unanswered questions: (a) Why did the study focus on Diadema? It was a keystone herbivore on Caribbean reefs whose mass dieoff seems to have precipitated a coral/algal phase shift - is this why? (b) how would Sargassum be expected to impact Diadema’s diet? Would it limit benthic macroalgal resources by shading? No mechanisms are provided for how Sargassum would be predicted to impact this urchin.
3.	The Introduction needs to be re-written so that it clearly and succinctly sets up the study. The intro should explain the (a) overarching aims of the study (there seem to be too many – see comment #1), (b) how each of the stated study questions were investigated (currently, the rationale for collecting each specific measurement is not clearly stated), (c) how the various measurements can be integrated or considered together to arrive at a specific conclusion. The order of the paragraphs needs to be rearranged so that the rationale for using a particular technique (for example, stable isotopes) is clearly explained before going into the technical details of the technique. The aims are also stated at the end of the Intro, and should be moved up towards beginning of Intro.
4.	The paper says it is measuring how Sargassum has impacted the “natural” trophic structure of Caribbean reefs. But modern reefs have been significantly altered by human and (maybe) natural disturbances. Diadema populations are currently a tiny fraction of their pre-dieoff abundances. This needs to be acknowledged and discussed in the Intro and Discussion.
Experimental design: Significant efforts need to be made to clarify the specific research questions being asked, and why (currently, it appears to be a general “how did Sargassum affect numerous measures of Diadema’s diet and trophic position”, without any context for why this is relevant and meaningful). In addition, the statistical analyses should be modified to be more informative. Specific suggestions include:

1.	The Methods section needs to be re-worded to more succinctly provide the details of the study design and laboratory and statistical analyses. The first paragraph in Methods should be moved (the first sentence should go in Study Sites section, and the rest should go in Discussion). The Study Sites section should give more detail about the relative level and type of human disturbance at each site (and this should also be indicated in the table within Figure 1. Figure 1 should also have the boundaries of the Marine Protected Area). Collecting and Processing Data section should have more detail about: (a) choice of July/Aug 2016 for period without Sargassum effect (WSU) – were all Sargassum gone by then? What happened to it – did it get swept offshore, decompose, was removed by managers? Was water clarity back to pre-Sargassum levels?, (b) how were algae sampled – ALL taxa that were collected within a quadrat, or only fleshy, turf, and erect calcareous (were CCAs excluded?) Did a taxon have to be present in a certain abundance to be included in analyses? Were algae collected by scraping (and were any corals harmed in this process)? Why were Sargassum and turf on Sargassum included – how could a benthic urchin eat pelagic macroalgae?, (c) a figure needs to be added to show the study design for collection of algae and urchins. The Data Analyses section needs to include a figure or table showing how isotopic results from the algae were translated into relative contributions of each taxon to Diadema diet. Currently, this is a bit of a black box. How certain were these results?
2.	It is stated that no species that were collected are threatened, but Diadema is severely depleted across the Caribbean… was it ecologically damaging to collect these urchins? Or is Diadema is making a comeback on these reefs? Please provide information on the status of this urchin in Quintana Roo.
3.	Much more information is needed in Data Analysis section to be able to interpret the results/replicate the study. Rationale needs to be provided for choosing certain fixed values for parameters within the various models. For example, how were the “isotopic discrimination factors” and “theoretical geometric assumptions” chosen for this study determined to be valid for this data? (And what is the definition of these factors?) Why were certain macroalgal taxa/functional groups pooled for the mixing models analyses? For the SIBER analyses, what are the “metrics” that this analysis performs? And what is a “burn in”? What were the results of the tests for homogeneity and normality?
4.	The statistical analyses need to be modified to explain the differences among sites. The Methods states that the sites differ by (a) the amount of Sargassum accumulated, (b) the management strategies for removing Sargassum, and (c) the width of the lagoon. The Results show significant differences among sites. Therefore, analyses should include those characteristics of each site (a, b, and c above) as predictor variables of changes in algal community composition or changes in niche breadth before and after Sargassum.
Validity of the findings: Because there are so many different types of analyses that are performed and the results are reported in a somewhat disorganized manner, it is difficult to interpret the results and draw a cohesive message from them. This is compounded by the fact that mechanistic explanations for results are very rarely given. Lastly, confusing or contradictory results are often not properly interpreted in the conclusions, or conclusions are not supported by the results. Some suggestions for improvement:

1.	Consider narrowing the set of research questions/analyses. For example, why does algal composition of Diadema diet, Diadema trophic level, AND Diadema niche breadth all need to be measured? The authors do not consider what all three of these measures together might tell us about Sargassum impact on Diadema diet.
2.	Consider re-framing the research questions. This study provides a good description of Diadema trophic characteristics, and it also provides valuable data on oxygen limitation due to Sargassum decomposition. Either of these findings could make up its own paper.
3.	It is difficult to be certain that changes in each of these measures is directly caused by Sargassum, because the results differ by site. There could also be many other factors at play, such as differences in SST, precipitation, land-based runoff, etc. between the two years. These factors need to be included in analyses of change in Diadema trophic position and diet.
4.	The authors appear intent on showing the negative impacts of Sargassum on Diadema, but the results don’t seem to support this conclusion. Benthic macroalgae was higher when Sargassum was present – wouldn’t this be a good thing for Diadema? At 2 out of 3 sites, Diadema trophic level increases with Sargassum presence. Could this mean that Sargassum results in higher quality food for Diadema? Or did Sargassum presence somehow reduce the abundance of Diadema competitors? For one site, Diadema niche breadth increases under Sargassum presence. Overall, the results seem to indicate that Sargassum either has a neutral or positive effect on Diadema (although these differences cannot be conclusively attributed to Sargassum – see above). Wouldn’t a more straightforward measure of the effect of Sargassum on Diadema be to measure Diadema abundance or body weight before and after the presence of this algae?
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: SARGASSUM BLOOMS IN THE CARIBBEAN ALTER THE TROPHIC STRUCTURE OF THE SEA URCHIN DIADEMA ANTILLARUM
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper has a good structure, in fluent (except the discussion, which is a little bit confusing) and sound. The English can be improved, basically shortening some sentences and making clearer some concepts. The references cited are appropriate for the approach made by the authors, and the main hypothesis is correct, from my point of view.
Experimental design: The experimental design has some problems highlighted in the attached document.
Validity of the findings: In general, the findings are novel and deserve publication. The methods used and the stable isotope approach is correct, and the results found are in line with previous work done in other places under other or similar conditions. The authors highlight the limits of their own study, which is a very good approach. Statistics are in line with what we expect from this kind of treatment, but there are some particular points that could improve the approach made by the authors (see attached document).
Additional comments: The paper has a good novel approach of how the Sargassum blooms are impacting coral reef ecosystems and how. In fact, such recurrent biomass degradation in the Caribbean coasts has to have an impact on the trophic relationships in the already stressed coral reef ecosystems. I made some questions and recommendations in the manuscript to be considered by the authors that may help to clarify to the future readers the comprehension of your findings.


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: SARGASSUM BLOOMS IN THE CARIBBEAN ALTER THE TROPHIC STRUCTURE OF THE SEA URCHIN DIADEMA ANTILLARUM
Review round: 1
Reviewer: 3

Output:
Basic reporting: The English language is clear and I did not identify any major problems. I would be careful using the term “shoals”. "Shoals" does not seem appropriate for the pelagic Sargassum (line 18). I assume that shoal can be used to things you can count individually, as fishes and crabs. I suggest you to use “mats” instead.

In the line 52, the reference Sissini et al. 2017 is about extensive masses of Sargassum in 2015. Check the others references. You could replace "in 2011" for "Between 2011 and 201x".

Figure 4 – Add the local in the figure instead of the caption.

Caption Figure 5 – I suggest giving more information about the data. For example, specifying which analysis was made.
Experimental design: Lines 368-369 “We found that the composition of benthic macroalgae assemblages were different among both conditions (WSE and USE).” How was the comparison of benthic macroalgae assemblages between years if the quadrats were not fixed? Nine quadrats is enough to characterize the assemblage?
Validity of the findings: This paper shows the physical and ecological effects of the pelagic Sargassum in near-shore coral reef communities. How the benthic macroalgal community responds to the increase of carbon and nutrients and the nutrient flux in the food web under and without the Sargassum effect. It is well delineated and the approach to trophic structure give us a complementar understanding about the impact of pelagic Sargassum on coastal environments.
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: SARGASSUM BLOOMS IN THE CARIBBEAN ALTER THE TROPHIC STRUCTURE OF THE SEA URCHIN DIADEMA ANTILLARUM
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have made significant improvements to better clarify the aims of the paper and the methods they employed. I appreciate that in their rebuttal letter, the authors answered several of my questions about ecological inferences that can be made from their reported results. But they now need to add these explanations in their manuscript as well! In conclusion, two areas still need improvement before the paper is ready for publication:

(1)	Wording is still unnecessarily vague throughout the manuscript, and much clarification is still needed (for example, “trophic dynamics”, “negative effects”, and similarly vague phrases need to be replaced by statements that describe the specific effects they are trying to measure and the specific ecological mechanisms to be inferred from their observed results). This vague wording and lack of mechanistic explanations makes it difficult to draw coherent links between the specific analyses conducted, the results, and conclusions that can be drawn from these results. In the attached annotated manuscript, I have pointed out areas where vague wording needs to be replaced by specific wording that explicitly states what ecological information will be provided by an analysis and what a result means ecologically.

(2)	Grammar, sentence structure, and flow of the manuscript still need to be improved to provide sufficient clarity. There are many instances of redundant statements, numerous statements that could be simplified/made more succinct with fewer words/sentences, and many run-on sentences that need to be shortened. In the attached annotated manuscript, I have pointed out specific suggestions for improvement.
Experimental design: The experimental design appears solid. However, as noted above, more justification is needed for the specific sampling design chosen (why these three reefs? why sample each reef at different distances from shore? why take dissolved oxygen measurements?). None of these are explained in the Intro or Methods - please add justification for each aspect of the study.
Validity of the findings: I honestly am still finding it difficult to assess the validity of the main conclusion that Sargassum was found to be detrimental to Diadema. Is this because the taxonomic richness of the algae found in sampled Diadema declined after Sargassum influx? Is this unequivocally a negative for Diadema - does this necessarily mean that Sargassum "limits available resources" for Diadema as stated in the manuscript? What if Sargassum leachates and decomposition increased some of the preferred algal food sources for Diadema and limited some less preferred algae?

I am still not convinced that this study conclusively demonstrates a negative effect of Sargassum on Diadema. But I may be mistaken in this conclusion - it is hard to know, because the specific inferences and conclusions being made from each result are not clearly stated in the Results and Discussion. The above suggestions to add more explanation of inferences from results might help clear this up. Another possibility is that the results are ambiguous with respect to impacts on Diadema. If this is the case, the narrative needs to be modified to "Sargassum caused changes in diet/trophic characteristics of Diadema and caused reef hypoxia, the latter which could be bad for overall coral reef ecosystem functioning".

Please see the attached annotated manuscript for some suggestions for clarifying study results and conclusions.
Additional comments: Thank you for your revisions. This study is definitely interesting and worthwhile from a conservation and scientific standpoint. If a major effort can be made to: (1) use more precise wording, (2) add statements providing why each analysis was undertaken - exactly what information does each analysis provide, (3) add explanation of the precise ecological mechanisms that could explain your results, and (4) proofread for correct grammar and sentence structure, your manuscript will be ready for publication.


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

Input:
Title: THE COMPLETE CHLOROPLAST GENOME OF THE JERUSALEM ARTICHOKE (HELIANTHUS TUBEROSUS L.) AND AN ADAPTIVE EVOLUTIONARY ANALYSIS OF THE YCF2 GENE
Review round: 1
Reviewer: 1

Output:
Basic reporting: Dear Editor,

Authors report the first chloroplast genome of Jerusalem artichoke and presents its comparison with other members of the family They have observed some differences at the ycf2 gene level. The artichoke plastome showed high synteny to the other plastomes of the same genus and clade.
Experimental design: Experimental design and methods are the standard methods.
Validity of the findings: Submitted version of the paper reports the findings on the CP genome and the authors have compared the assembled chloroplast to the other CP genome chloroplast and observed conservation. The assembled CP genome is in lengthwise similar to the other CP genomes of the same species and also the gene conservation has been observed except with the deviation in ycf2.
Additional comments: We recommend authors to look at the ycf2 functions and the surrounding regions of the ycf2. In the MS, they have mentioned that the ycf2 showed several amino acids missing and also reported deletions in the ycf2. Therefore, taking into account the recent use of the ycf2 in phylogenetic studies it would be necessary to ascertain that whether this gene or better a pseudogene can be used a phylogenetic marker for these species. Hence we recommend authors to plot the rates of the evolution along with the missing of the deletions/insertions and then calculate the correlation. If the correlation is positive at an 0.05 level or 0.01 level then it is obvious that the deletions or the observed insertions has a role to play in the selective differentiation of this gene in these species.


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 COMPLETE CHLOROPLAST GENOME OF THE JERUSALEM ARTICHOKE (HELIANTHUS TUBEROSUS L.) AND AN ADAPTIVE EVOLUTIONARY ANALYSIS OF THE YCF2 GENE
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript reports the complete chloroplast genome of Jerusalem artichoke (Helianthus tuberosus) from a Chinese cultivated population. This is simple and straight forward genome report paper rather than in depth genome application paper.

Furthermore, the three plastid genomes of Helianthus tuberosus was already published at four years ago (Bock et al., 2014, New Phytologist 201: 1021-1030) and they are available from NCBI database.
Experimental design: The authors follow the well-established NGS sequencing and annotation procedures.
Validity of the findings: This manuscript reports the approximately 150 bp deletion mutation at the 5’ portion of ycf2 gene. But, the deletion is not unique in this report but share by all published Helianthus species and populations.
Additional comments: This reviewer recommends to the authors to publish the manuscript to some simple genome report journal such as Mitochondrial DNA Part B resources or other journals rather than PeerJ.


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 COMPLETE CHLOROPLAST GENOME OF THE JERUSALEM ARTICHOKE (HELIANTHUS TUBEROSUS L.) AND AN ADAPTIVE EVOLUTIONARY ANALYSIS OF THE YCF2 GENE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors report on the sequencing, assembly, and annotation of the chlroplast Helianthus tuberosus L. The authors also present an evolutionary analyisis of its ycf2 gene.

The manuscript covers the sequencing and annotation of the mentioned chloroplast and compares it to other sequenced species of the same genus (Heliantus) as well as related crops, and plastids of the same species previously reported. It is a well organized manuscript but it would improve if it was thoroughly proof-read for incorrect English expressions used (I´m attaching a track-changes word document with some -but not all- of these).

To the best of my knowledge, the Introduction and background cover the relevant literature, although there are a few citations on the text that are not present on the references section.
Experimental design: There are some oversights on part of the authors regarding the availability of their data that hinder the full reproducibility of their work.

1.	The authors should deposit the original short reads from their NGS experiments on an appropriate database (for example the SRA at NCBI).

2.	The Multiple Sequence Alignments (MSA) used for the phylogentic trees and other analysis should be included as supplementary files as plain-text files in an appropriate format (FASTA aligned, Clustal, nexus, phylip, for example).

3.	The parameters used on all bioinformatics software should be reported. If defaults were used this should be clearly stated on the corresponding methodology section. This is specially important on the assembly software, since the comparison with a previous plastid genome is noted to differ due in part to the method used.

4.	The accession number for the previously reported Heliantus tuberusus plastid genome is incorrect. It reads NC023112 but should be NC_023112.
Validity of the findings: As the authors state on the first paragraph of the discussion, the differences on the sequencing technology and assembly methodology are more than likely the reason there is an 384 bp difference between the chloroplast genome presented in this manuscript and the plastid genome of Bock et al. Since the length variation on the chloroplasts of the 8 species of the composite family are in this same range (200-400 bp) I’m not so sure that the statement on lines 364 to 366 are actually valid (as this may be very well just an artifact of the different methodologies used):
“The length variations of the chloroplast genomes of 8 species of the composite family correlated with the lengths of the IR regions, indicating the length of IR region had a significant effect on the length of genome (Guo et al. 2017).”
Additional comments: Regarding the 152 amino acid sequence deletion at the ycf2 gene, it is quite interesting that is only observed on Heliantus species. Has it been corroborated by PCR or has just been observed by the assembly through NGS?


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: COMPARATIVE AND EVOLUTIONARY ANALYSIS OF THE REPTILIAN HEDGEHOG GENE FAMILY (SHH, DHH, AND IHH)
Review round: 1
Reviewer: 1

Output:
Basic reporting: •	The English needs significant improvement throughout. The overall structure of the manuscript is good and hypotheses somewhat clear, but could be better defined.
•	The papers for the genomes used to obtain sequences for the study need to be cited.
•	The figures are adequate, but formatting and readability could be improved.
Experimental design: •	Overall research question is relevant and generally well defined; however, there are some methodological flaws.
•	The exclusion of birds from the study is a serious flaw since birds are the sister group to crocodylians. There are, however, plenty of bird genomes that these sequences can be obtained from. I would recommend using a representative sampling of birds so as not to taxonomically bias the analysis by using all available bird genomes. There are also other reptile genomes that would be included to further increase the sample size, which will provide additional power to the selection tests.
•	The authors seem to have two main hypotheses about the evolution of the hedgehog genes: that reptiles may be evolving differently than other vertebrates and that limbless species may also be under different selective pressure. I think these are reasonable hypotheses but they could be better tested. To test whether reptiles are evolved differently than other vertebrates the authors would need to include a representative sample of other vertebrates for comparison. The basis of the hypothesis could also be better explained. To test for an effect of limb loss it would be useful to include other limbless lineages besides snakes. There is at least one limbless lizard genome (Ophisaurus gracilis) that could be utilized for this purpose. Additionally, the PAML clade models would be better suited for these tests. See Baker et al Genetics 203:905–922 and Schott et al. MBE 2018 35:1376-1389 for examples. There are also additional HYPHY models that could be utilized as well, although the addition of the clade models would be sufficient. It is unclear why several of the lineage tests were performed and this should be explained.
•	PAML sites model M8a should be compared to M7 to test for positive selective (not just the M8 vs M7 test, which only tests for addition of a site class)
•	Datamonkey is a webserver that hosts various HYPHY programs. The names of the specific programs should be used (fine to indicate that they were used as implemented on the Datamonkey webserver)
•	MEGA should not be used to estimate phylogenetic trees. Please use a more robust phylogenetic program (e.g., RaxML or PhyML for maximum likelihood)
•	Reptiles did not arise from the amphibian ancestor. I believe the authors mean to say that the split between the two ancestors occurred roughly 330-310 mya
Validity of the findings: I expect the findings may change significantly after the methodological issues are resolved.
Additional comments: Overall I found this to be an interesting paper on the molecular evolution of the hedgehog genes in reptiles, a group that is severely understudied.


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: COMPARATIVE AND EVOLUTIONARY ANALYSIS OF THE REPTILIAN HEDGEHOG GENE FAMILY (SHH, DHH, AND IHH)
Review round: 1
Reviewer: 2

Output:
Basic reporting: The Introduction rambles and is not coherent. It also includes many extraneous sentences that should be removed.  Thus, the entire Introduction should be completely re-written so that it presents a coherent summary of the background on hedgehog genes in vertebrates and succinctly finishes with a sentence or two about what knowledge gap this paper attempts to fill.
Here are a couple specific examples of things to fix in the Introduction:
Lines 115-116: the authors should do more than merely state that “reptilian hedgehog signaling pathway has received little attention.”  The authors should cite these early papers on this subject and review what their key findings were.
Lines 116-118: again, the authors should cite some key papers here and briefly mention their contributions, shortcomings, etc.  This should represent a distinct paragraph that immediately precedes a paragraph describing what we know about reptilian hedgehog genes.
Experimental design: I am not an expert at detecting selection in genes but the bioinformatic methods employed by the authors appear appropriate to me.
Validity of the findings: I am not at all comfortable with the main Conclusion on lines 277-278:  "In particularly, it is likely that the degeneration of the snake’s limbs is due to the regulation of multiple genes."  I cannot find anything in their results that clearly shows this to be "likely."
Additional comments: This is a very interesting subject and the authors have a good bioinformatics-based approach to learn more about the evolution of vertebrate hedgehog genes.  However, the manuscript, as written, is not yet suitable for publication in Peerj.  The authors must try to improve the writing, especially the English, before it can be fairly evaluated by reviewers.


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: COMPARATIVE AND EVOLUTIONARY ANALYSIS OF THE REPTILIAN HEDGEHOG GENE FAMILY (SHH, DHH, AND IHH)
Review round: 2
Reviewer: 1

Output:
Basic reporting: The writing is improved from the first version, but still needs additional improvement in my opinion. I've highlighted some of the particular statements below that should be addressed:

Ln 60-61: No positive selection site was identified by the PAML site model or the three methods in the Data Monkey Server collectively.

Ln 82: The three hedgehog genes have different functions in their expression patterns

Ln 83-85: Namely, the Shh gene plays a core role in the growth and patterning of the skeletal and nervous systems (Ingham & Mcmahon 2001a), and all are structures that have undergone remarkable morphological changes in primates, especially humans

Ln 99-100 : Previous research on the adaptive evolution of the hedgehog gene family in invertebrates indicated positive evolution,

Ln 153-154: Reptiles were distributed into 3 different orders of Reptilia

Ln 179-180 In order to determine whether hedgehog genes have faced identity or discrepant evolutionary pressure

Ln 187: Amino acids with selection pressure for site model M8 were identified using a

Ln 237: Comparatively, the diverse clades of the Shh gene were not reached the significant level

Ln 288-229 We set different orders as independent lineages, which showing diverse development characteristics.

Ln 267-268: Site models performed in PAML found that each codon of the Shh, Dhh, and Ihh sequences was under diverse selective pressures

Table 1 should be moved to the supplement.

Table 2: If I am interpreting correctly this is the branch model test and not a test of positive selection. Should show both the background and foreground w values so the difference can be compared. You say "clade of". Are you highlighting the entire clade (using $1) or just the branch leading to the clade (#1). Both are valid ways of testing for differences in selection, but this needs to be clarified. What is serpentes+OG? Is this the test including Ophisaurus? These comments apply to the presentation of the results from the other models as well.

Table 3 w values should be reported.

The issues with the tree topology appear to be due to the trees not being appropriately rooted.
Experimental design: My main concerns with the experimental design appear to have been largely addressed. However the explanation of the methods is still difficult to follow. I would recommend the authors use previous studies that employ similar methods as a template for how to explain the methods and present the results.

The clade model test seems to have been implemented using only a model that contains 4 different clade partitions. These should be redone with smaller numbers of partitions as well, ideally to test specific hypotheses.
Validity of the findings: Some of the conclusions made are still too strong and don't reflect the findings. These are largely unnecessary for the scope of the paper and should just be removed or highly modified. The title needs to be changed as genomic evidence of adaptive evolution is much too strong of a statement. I've highlighted some other problematic statements below:

Ln 69-71: Overall, this study has provided significative information regarding the evolution of the hedgehog gene family in reptiles and has provided new insight that will contribute to the protection and conservation of reptiles.

Ln 311: Together, the findings of this study have provided extensive information regarding the evolutionary history of the hedgehog gene family in reptiles and new insight for the conservation of reptilian populations.

Some potentially interesting results tend to be glossed over in favor of making very broad (and unnecessary) statements. Some of the specific results that I think deserve more attention are the apparent loss of genes in different groups, the tests for differences in selective patterns in limbless squamates, and the evidence for positive selection in turtles.
Additional comments: I appreciate that the authors have made a substantial effort to improve the manuscript and that the language barrier makes effectively communicating the results more difficult. I think with some additional editing and minor modifications to some of the analyses the manuscript will be suitable for publication.


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

Input:
Title: COMPARATIVE AND EVOLUTIONARY ANALYSIS OF THE REPTILIAN HEDGEHOG GENE FAMILY (SHH, DHH, AND IHH)
Review round: 2
Reviewer: 2

Output:
Basic reporting: I am sympathetic to the authors because I know that English is not their first language--it is very challenging to write a scientific paper in a foreign language.  The authors have improved the English writing in this revision, but I still found many errors (words not spelled correctly or incorrectly used).  I will provide some concrete examples as well as my other specific comments below:
line 59:  what is "analogical topology"?
line 69:  do you mean "significant information"?
line 78:  this sentence needs to be re-written because it is misleading;  it was not the genomes that were duplicated, but the hedgehog genes themselves- according to Kumar et al. they were duplicated two times: the first duplication event gave rise to desert hh and the second produced Indian hh and Sonic hh.  The molecular mechanism for these tandem duplications was probably unequal crossing over.
lines 96-97:  I don't think it is appropriate to suggest that these genes possibly promoted the successful diversification of vertebrates without providing some kind of clear rationale or citations.
line 98: do you mean "positive selection"?  "positive evolution" does not make sense to me.
lines 112-113:  I think you can remove this sentence about the divergence of reptiles from amphibians - I don't see the relevance to the current study.
lines 115-118: same here: I don't see the relevance of this statement to the paper so I suggest taking it out.
lines 162-165: this needs to be written more clearly because it is confusing at present.  I understand that you used RAXML to construct a phylogenetic tree but the bootstraps are normally used to assess the statistical confidence of each node (or clade) in the tree.
lines 173-174:  which previous studies?  You need to cite them and provide more details on their key findings so that the reader can better understand the following sentence.
lines 176-178:  I had trouble understanding this sentence - what is "identity or discrepant evolutionary pressure"?  I suggest re-writing this sentence to improve its clarity.
lines 211-212:  I think you mean to say "hedgehog gene tree"
lines 223-224: this sentence needs to be re-written because it is not clear.
line 234:  this should be "Discussion"
line 253: I think you mean "species tree"
line 264:  I think you mean "positively selected site"
line 278:  I think you mean to say "because the mechanism of limb reduction in reptiles is..."
lines 299-301:  I am not sure I understand this conclusion.  I suggest re-writing this to improve the clarity.
I suggest increasing the size of the bootstrap values on the tree figures as they are too small to read.
Experimental design: The experimental design appears to be sound to me.  I think the authors greatly improved their study by including all the additional genomes.
Validity of the findings: The findings appear to be ok to me.
Additional comments: This is a very interesting study and I commend the authors for their excellent work overall.  I think if they further improve the writing to make everything more concise and clear, then their manuscript will be closer to being acceptable for publication in Peerj.


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: POSTURAL CONTROL IN GIRLS WITH ADOLESCENT IDIOPATHIC SCOLIOSIS WHILE WEARING A CHÊNEAU BRACE OR PERFORMING ACTIVE SELF-CORRECTION: A PILOT STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1.	The manuscript is well written and is clear. There are, however, a few typos that need to take care of:
a.	Line 72: “reallignemnt” should be” realignment”; also “patients autonomously performs” should be “patients autonomously perform”.
b.	Line 151, 170, Figure 3, 4, 5 and 6: “quite” should be “quiet”
c.	Line 251-2: “the respective changes in the AP plane hinted at the uncalled-for outcome” – do not quite understand. Suggest to rephrase it.
d.	Line 265:”shed light”. Would “shed light on” more appropriate?
e.	Figure 3: Some words missing after the phrase “post hoc dif….”
f.	Figure 4: “samle” should be “sample”
g.	Figure 5 Some words missing after the phrase “post hoc difference with respect …”
Experimental design: No Comment
Validity of the findings: No comment
Additional comments: The findings are valid, albeit the small size of the samples. The group is not a homogeneous group, with some having possibly Lenke 1 and others Lenke 3 curves. The authors are suggested to comment if there are differences between patients with the different types of curves and if the outcome measures vary with the size of the curves.


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: POSTURAL CONTROL IN GIRLS WITH ADOLESCENT IDIOPATHIC SCOLIOSIS WHILE WEARING A CHÊNEAU BRACE OR PERFORMING ACTIVE SELF-CORRECTION: A PILOT STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The intuition behind the design of the study is original and is interesting. However, there are some points that need to be clarified.
I would advise you on the manuscript revised by a native speaking, as there are several grammar mistakes in the text, and some sentences are hard to understand.
no other comment
Experimental design: A weakness of the work is certainly the small sample size limited to the female gender only.
1. Furthermore, going to look at the tables (table 1) with reference to the Cobb data, a non-uniformity of the sample would appear to emerge.
2. Moreover, in the exclusion criteria, no mention is made of how to consider Visus defects: did any of the subjects have visual defects with lens correction? This could represent a bias.
3. It is advisable to report the value of the P, especially where significant, in the Report of the Cop values in the three conditions indicated in material and methods  in Table 2: "(1) QST- standing upright with a neutral and comfortable stance with the arms relaxed at the sides, (2) ASC- standing upright with autocorrection where on the command “correction” the participant performed an active self-correction, and (3) BRA- standing upright wearing the Chêneau brace";this allows the reader to have a more immediate perception of how the data moves with respect to which subgroup directly from the table.
Validity of the findings: Considering the small sample number the conclusions should be softened.
Furthermore, had the patients been previously instructed on "how to correct the posture"? Because each of us can have different postural correction strategies and especially in scoliosis, self-correction may also depend on the presence, or not, of a bad alignment of the column on the sagittal plane.
Additional comments: Dear Authors
the idea is original but the paper has as its limit a too small sample size: keeping only nine female subjects, the description of the sample have to be more detailed (as previous prescriptions, other physiotherapy, sports activities etc ...), presence of  other postural associations with  scoliosis if present or not as the plantar foot support, the alignment of the column on the sagittal plane etc ...
There are some points to be clarified and explained better:
-I would advise you on the manuscript revised by a native speaking, as there are several grammar mistakes in the text, and some sentences are hard to understand.
- (table 1) with reference to the Cobb data, a non-uniformity of the sample would appear to emerge.
-in the exclusion criteria, no mention is made of how to consider Visus defects: did any of the subjects have visual defects with lens correction? This could represent a bias.
-report the value of the P, especially where significant, in the Report of the Cop values in the three conditions indicated in material and methods  in Table 2
-had the patients been previously instructed on "how to correct the posture"?
- Considering the data, the conclusions should be softened.


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: POSTURAL CONTROL IN GIRLS WITH ADOLESCENT IDIOPATHIC SCOLIOSIS WHILE WEARING A CHÊNEAU BRACE OR PERFORMING ACTIVE SELF-CORRECTION: A PILOT STUDY
Review round: 1
Reviewer: 3

Output:
Basic reporting: •	The title of your study is not consistent with objective and needs to reflect the content.

•	Bracing has been identified and discussed in the literature (lines 75 -76). However, you did not mention about Cheneau bracing.

•	English language needs improving throughout.
Experimental design: •	The aim of the study is not reflect the content.

•	You recruited 9 post-menarche female with AIS. However, you did not give details about sample size calculation. In addition, you did not mention why you recruited only post-menarche female (line 103). I am not clear why you recruit participants receiving brace treatment 2 months.

•	Could you provide the reason why you need recruit participants receiving brace treatment 2 months? (line 109)

•	Could you describe how participants know their ASC, please? and how long they practice ASC? And how to perform ASC (lines 113-114).
Validity of the findings: •	You have raised the point about the fundamental difference between the two therapeutic approaches: passive and active mode of operation (lines 186- 187).  However, you did not provide details in this 2 therapeutic approaches.

•	As your study compared the effects of Cheneau brace and Active self correction.  However, you have discussed effects of general bracing on postural balance. Could you discuss specific brace (Cheneau brace) on postural balance.

•	“First, the ASC resulted in a significant backward excursion of the COP mean position on hard surface in both visual conditions” In this sentence, could you explain more about increase or decrease backward excursion of the COP?

•	The limitation  of the study  ( lines 269 – 271) and further study (286-290) should be in discussion
Additional comments: No additional comments


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

Input:
Title: POSTURAL CONTROL IN GIRLS WITH ADOLESCENT IDIOPATHIC SCOLIOSIS WHILE WEARING A CHÊNEAU BRACE OR PERFORMING ACTIVE SELF-CORRECTION: A PILOT STUDY
Review round: 2
Reviewer: 1

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


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

Input:
Title: EFFECTS OF SHADING ON THE GROWTH AND LEAF PHOTOSYNTHETIC CHARACTERISTICS OF THREE FORAGES IN AN APPLE ORCHARD ON THE LOESS PLATEAU OF EASTERN GANSU, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Inclusion of forage crops into the orchard is advantageous to gain both ecological and economic goals. This work focused on the photosynthetic and morphological properties of three forages under apple tree. There were interesting results found. Each experiment was well designed. However, for more benefits of readers, a number of points need clarifying, and certain statements require further explanation.
How widely is the apple orchard established in the testing area and how about orchard-forage pattern? Do pay attention to the terms “forage”, “grass” in this part.
In the introduction, you mentioned the modulation of water and fertility of soils with forage sowing. How forage inclusion affected soil water? Under what condition the possible competition for water would no longer be a problem for both trees and forages?
In the materials and methods, the author should tell how the forage species were managed, by cutting? Grazing? Or they were commonly used in this region only as soil cover? Try explaining why there wasn’t P fertilization?
The results were mostly assigned to the different shading and potential effects with soil water and nutrient availability were not well considered. More information should be given on the soil water and nutrients which might have contributed to the findings. The information can be addressed in the discussion or introduction.
Why you stated to widen the distance between individual trees? Please clarify the reason to reduce the density of apple tree. If these forage species will be used just as soil cover, this density of trees may be good enough.
Line 41: Change “In the apple yard” into “In the apple orchard”.
Line 53: Delete “beneath”.
Line 148: “degrees” be replaced by ℃.
And other minor English 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: EFFECTS OF SHADING ON THE GROWTH AND LEAF PHOTOSYNTHETIC CHARACTERISTICS OF THREE FORAGES IN AN APPLE ORCHARD ON THE LOESS PLATEAU OF EASTERN GANSU, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Line 42, why reducing density of apple trees? In the apple yard, the goal is growing apple trees not grass, right? Planting grass is to help reduce soil erosion and enrich soil fertility for trees to grow.

Line 56, I suggested authors not introduce this issue/question, as this paper is not studying interactions between grass and trees or how grass impacts tree growth (competition).

Line 100, change this sentence "..they can be used.." to "..better being used?". I am sure all those species can be used.

Line 104, "under three shading treatments"

Line 106, change the second question to be more conservative, "which of the three species is more tolerant to shading in the orchard". The decision of which is more suitable involves more considerations (e.g. economy, diversity, etc). And usually we spell it out if count is less than 10, so use "three" instead of "3".

Table 2, it is better to add SE/SD to those values since authors had three replicates.

For Figure captions, use "Normal shading" would be better for "shading"
Experimental design: Line 112, "The mean annual precipitation is 543 mm with... The mean annual temperature.."

Line 147, would not 80 degrees too high for drying? I usually see people dry plant tissues around 55-60. Possible high drying temperature would cause loss of nitrogen

Line 170-176, put one sentence in the end "SPSS 17.0 was used for statistical analysis", so authors can delete the 3 extras.
Validity of the findings: Overall for Result section, 1. I suggested authors to put p values next to the sentences that describing the statistical results including differences between treatments and correlation test, so it would help readers to understand when authors said "hardly" or "barely". 2. Within each paragraph, please keep the subject consistent. Authors started with measured parameters such as "LDMC, LMA" as a subject in line 180, but used treatments such as "enhanced shading.." as a subject in line 183. 3. And for sentences describing insignificant results, use "did not influence.." or "was not changed/impacted" or "was similar" instead of "hardly affected it"

Line 215, the measurement of chlorophyll a and chlorophyll b was not mentioned in the Method section. And authors should add more details/explanations in the Data analysis part about why using chlorophyll a+b and a/b but not chlorophyll a or b alone?

I think in the Discussion section, authors should mention the soil nutrient status for the three forages if they had those data. Because some measurements here (e.g. biomass) is not only impacted by light but also soil carbon and nutrients. How the differences of soil nutrients between those plots bias the results of shading effects?
Additional comments: This paper studied the effects of three shading treatment on Leaf trait, photosynthesis, chlorophyll component and fluorescence for three grass species including lucerne (Medicago sativa), white clover (Trifolium repens) and cocksfoot (Dactylis glomerata). It reported that shading usually decreases leaf thickness, leaf dry matter content, leaf mass per unit area and net photosynthetic rate. Shading changed little to Chlorophyll contents. Among three species, cocksfoot had the least impacts compared to white clover and lucerne. I found this study is valuable but should be improved based on the above comments before 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: EFFECTS OF SHADING ON THE GROWTH AND LEAF PHOTOSYNTHETIC CHARACTERISTICS OF THREE FORAGES IN AN APPLE ORCHARD ON THE LOESS PLATEAU OF EASTERN GANSU, CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The revised paper is clear and readily understood. Sufficient references were cited. It is well structured and the figures and tables were of high quality. Raw data were shared. And the hypotheses were well tested.
Experimental design: The experiment is well designed and the methods are right.
Validity of the findings: The results were presented with good analyses. The conclusion is well stated.
Additional comments: The authors made a thorough revision and responded to the comments in a suitable way. In my opinion, it can be accepted at its present form.


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

Input:
Title: EFFECTS OF SHADING ON THE GROWTH AND LEAF PHOTOSYNTHETIC CHARACTERISTICS OF THREE FORAGES IN AN APPLE ORCHARD ON THE LOESS PLATEAU OF EASTERN GANSU, CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: None
Experimental design: None
Validity of the findings: None
Additional comments: I really appreciated authors' hardworking on revising this paper. I only have two minor question: 1."Why change all the subheading to Arial but not Times New Rome?" 2. Line 234, no need to mention those values are constant, omit "12.7, 2.59, 22.9, 4.67, 20.3 and 8.04 are the constants".


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

Input:
Title: EFFECTS OF SHADING ON THE GROWTH AND LEAF PHOTOSYNTHETIC CHARACTERISTICS OF THREE FORAGES IN AN APPLE ORCHARD ON THE LOESS PLATEAU OF EASTERN GANSU, CHINA
Review round: 3
Reviewer: 1

Output:
Basic reporting: None
Experimental design: None
Validity of the findings: None
Additional comments: I find this paper can be accepted as it is!


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: COMPARATIVE TRANSCRIPTOME ANALYSIS OF PANICLE DEVELOPMENT UNDER HEAT STRESS IN TWO RICE (ORYZA SATIVA L.) CULTIVARS DIFFERING IN HEAT TOLERANCE
Review round: 1
Reviewer: 1

Output:
Basic reporting: literature citation and background knowledge is enough, paper structure fits requirement. English in the manuscript need to improve. Writing skills need to improve, particularly the description of the results seems like the notes. Suggesting to use tables rather than just text description.
Experimental design: experimental design is pretty straightforward in this research, but the description is not clear. For example, authors indicated the rice plants were treated in high temperature for 9 d, but they didn't mention the stage of the plants they treated. For analysis methods of differential gene expression and GO, KEGG analysis, the description is too brief and thus is lack of sufficient information.
Validity of the findings: Findings in this research are pretty general and lacking of novelty. The pathways that were indicated to be related to heat response were also very general.
Additional comments: The manuscript need a major revision for accepting to publish.


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: COMPARATIVE TRANSCRIPTOME ANALYSIS OF PANICLE DEVELOPMENT UNDER HEAT STRESS IN TWO RICE (ORYZA SATIVA L.) CULTIVARS DIFFERING IN HEAT TOLERANCE
Review round: 1
Reviewer: 2

Output:
Basic reporting: In the submitted manuscript “Transcriptome comparison analysis of panicle development under heat stress in two rice cultivars differing in heat tolerance (Oryza sativa L.)” (#33492) by Wang et al. used high throughput method to identify differentially expressed genes (DEGs) in developing young panicles of heat-resistant (HHZ) and heat-susceptible (IR36) rice cultivars under heat stress. They identified 4070 heat stress-responsive genes including 1688 heat-resistant-cultivar-related genes (RHR), 707 heat-susceptible-cultivar-related genes (SHR) and 1675 common heat stress-responsive genes (CHR), and they validated 30 of them by qRT-PCR analysis and identified some DEGs and pathways involved in heat stress resistance through GO enrichment and KEGG analysis. Although the manuscript presents some interesting results, the novelty of the findings is not clear and some important deficiencies in the manuscript must be revised before publication. In addition, the manuscript writing requires a huge number of changes for both clarity and proper English usage such as in line 43-53, 61-62, 76-77, 122-123, 128, 155-159, 266-269, 297-299…
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Specific comments:
- In the INTRODUCTION section, what does IPCC stand for (line 44)? Authors must firstly descript the difference of heat stress in the HHZ and IR36 cultivar (lines 84-88), then start to why you need to carry out this study (lines 82-84).

- METHODS section, “high- temperature” need to remove one space (line 111). “Olympus DP70 digital camera system” (line 126) need to provide the information of company such as (Olympus Corp, Tokyo, Japan). For cDNA library construction by using TruSeq RNA Sample Preparation Kit, authors only followed the manufacturer's instructions, so authors don’t need to describe in detail the protocol (lines 134-146). The line space from 140 to 142 is larger than others. Need to provide the information resources of GO and KEGG enrichment analysis in line 162 and line 167. In addition, Line 109-110, 164-166 contain much information which must be moved to RESULTS section.

- RESULTS section, “Sequencing statistics” change to “Transcriptome analysis.” (line 194). “Go terms” change to “GO terms” (line 242). “Seventeen” change to “17” (line 250).

- DISCUSSION section, “GO enrichment analysis revealed that the DEGs were commonly enriched in response to heat, stress and temperature stimuli in the biological process category” descripted in Fig.3? “heat-tolerant” change to “heat-resistant” (line 336). “hsf” change to “HSF” (line 340). All “et al.” change to “et al.” (italicize) such as in line 343 and 348.

- REFERENCE section, all the references need to list full title of the Journal such as 438, 441, 444, 447…

- FIGURES, In Fig. 3, the position of texts (HHZ_32_vs_HHZ_40 and IR36_32_vs_HHZ_32) need to be modify. In Fig. 9 (a), two DEGs have same name (BGIOSGA015767).


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: COMPARATIVE TRANSCRIPTOME ANALYSIS OF PANICLE DEVELOPMENT UNDER HEAT STRESS IN TWO RICE (ORYZA SATIVA L.) CULTIVARS DIFFERING IN HEAT TOLERANCE
Review round: 1
Reviewer: 3

Output:
Basic reporting: Scientific quality and integrity of the manuscript is satisfactory.
Experimental design: Although the methodology opted to testify the said objectives is well equipped, but still some explanations need to be added, especially the heat stress treatments and the natural environmental variations. The statistical methods and data analyzing tools need to be mentioned (see attached files).
Validity of the findings: The results are valid as per mentioned methodology.
Additional comments: For detailed comments, please refer to the attached comments file.


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

Input:
Title: COMPARATIVE TRANSCRIPTOME ANALYSIS OF PANICLE DEVELOPMENT UNDER HEAT STRESS IN TWO RICE (ORYZA SATIVA L.) CULTIVARS DIFFERING IN HEAT TOLERANCE
Review round: 2
Reviewer: 1

Output:
Basic reporting: I noticed the improvement in the revision.
Experimental design: looks good in the revision.
Validity of the findings: conclusions seems fine though novelty not improved much.
Additional comments: Thanks for addressing all my comments in revision, and I think the manuscript is in good shape for accepting.


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: COMPARATIVE TRANSCRIPTOME ANALYSIS OF PANICLE DEVELOPMENT UNDER HEAT STRESS IN TWO RICE (ORYZA SATIVA L.) CULTIVARS DIFFERING IN HEAT TOLERANCE
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Comments to the Author
The revisions made in the current manuscript appropriately address all of my prior comments and it is more clear and concrete, and I am pleased to now recommend acceptance.

Minor comments:
Some sections are still not uniform in the manuscript such as line 66, 114-118, 153-157, I suggest you to go through the manuscript format again carefully and do changes following the guidelines.


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: COMPARATIVE TRANSCRIPTOME ANALYSIS OF PANICLE DEVELOPMENT UNDER HEAT STRESS IN TWO RICE (ORYZA SATIVA L.) CULTIVARS DIFFERING IN HEAT TOLERANCE
Review round: 2
Reviewer: 3

Output:
Basic reporting: Satisfactory.
Experimental design: Satisfactory.
Validity of the findings: Satisfactory.
Additional comments: Authors have revised well the manuscript and addressed the comments. However, authors have tried sometimes just to copy and paste the response to reviewer for certain comments from one reviewer response to other. Authors must be careful in typo errors in revised draft and it is recommended that authors must again need to get proofread their revised draft from the English experts, as it seems that revised draft has not been checked by native speaker. As authors have claimed in the response letter that revised changes are highlighted with red font color, however this was done nowhere. Be careful!


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: CYCLODIPEPTIDES FROM PSEUDOMONAS AERUGINOSA MODULATE THE MAIZE (ZEA MAYS L.) ROOT SYSTEM AND PROMOTE S6 RIBOSOMAL PROTEIN KINASE ACTIVATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The english language is generally good and the figures are well presented.

1.	Regarding the introduction, the authors mainly cite a review (Dobrenel et al 2016) for TOR pathway in plants. More recent reviews or original papers should be cited to reflect the most recent advances in the field  (for example, the sentence line 90-93 does not reflect the recent literature), particularly in relation to root development.

2.	Line 72, Deprost 2005 does not report TOR gene KO (but raptor KO) so it is not relevant for this sentence.

3.	Regarding the structure of the manuscript, the Results section is extremely short in comparison to other parts.

4.	MAJOR CONCERN: More data should be included as supplementary informations. The authors write in the legend of figures 5 and 6 that “experiment was repeated twice with similar results”.  As no statistical data is provided for these Western Blots, I recommend providing the second blots in supp data. Also, regarding Fig 5, a convincing rational for the selection of the cropped band with Phosphorylated S6K should be given as many bands of similar MW are observed on the full blot (Fig 5 raw in supp files). Idem for unphosphorylated SmS6K even if less bands are observed. These data and informations will help reviewers and readers analyzing the data.
Experimental design: This manuscript reports original primary research in the scope of PeerJ. Not ethical problems detected.

5.	Methods are well described, but the sentence line 121-123 is not clear. Did they use the same amount of DMSO for each condition or not?
Validity of the findings: 6.	MAJOR CONCERN: In Figure 2, the authors show the effect of 5 doses of CDPs on maize seedlings. That is nice to show such different doses, but surprisingly, no dose dependent effects were observed and CDPs affected root growth only at the concentration of 20 µM. This absence of a dose-dependence suggests that the effect observed might be an artefact. Testing other doses could help resolve this issue.

7.	MAJOR CONCERN: As written in the discussion (lines  283-286), this study reports a correlation between CDP effect of root growth and ZmS6K modification. The association between S6K modification and growth promotion is only suggested by this correlation.  Therefore, the title “by a mechanism involving S6 ribosomal protein kinase activation” is not supported by the data and must be changed. An alternative to modification of the title would be to provide experimental evidences supporting the claim of the title.

8.	Results line 207-208: “All the parameters showed increasing trends in CDP-treated plant (Fig 4)”. This in not correct for the parameter in Fig 4D that showed a slightly decreasing trend.
Additional comments: In sections 1 to 3, my most important comments are indicated by “MAJOR CONCERN”. They must be addressed prior to publication as they relate to the possibility to fully appreciate the data (4), the robustness of the findings (6) and the Title’s statement (7)