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

Input:
Title: A REVIEW OF THE OPPORTUNITIES TO SUPPORT POLLINATOR POPULATIONS IN SOUTH AFRICAN CITIES
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a well-written and detailed review around the topic of urban pollinators and their conservation, management and appreciation.

The review brings together global literature and connects the different aspects of the current state of the science with a more focused analysis of the context of urban areas in South Africa.
Experimental design: The study design is adequate.

A bit more effort could be made to access some of the literature and evidence about urban pollinator programs and conservation more widely in Africa. While some of this is in what would be considered 'grey literature' it provides an important context on what the current state of things are - which is what the review intends to do.
Validity of the findings: Overall the findings are valid and well-presented.

One aspect that is lacking is the bias towards both western urban areas and a lack of detail about the different urban cultures in South Africa. Given the history of South Africa, it would be prudent to present this context, as it has serious impacts for human settlements and thus where biodiversity is conserved, or not, within urban areas. For example, segregation of cities historically has major impacts for current patterns of green space and who can access them. While this is not a focus of the review, it does have very real impacts in the present day situation in urban areas.
Additional comments: This is a well-written and detailed review around the topic of urban pollinators and their conservation, management and appreciation.

The review brings together global literature and connects the different aspects of the current state of the science with a more focused analysis of the context of urban areas in South Africa.

A few minor points to consider:

There is a vast and rich literature on urban agriculture in Sub Saharan Africa and other developing countries. I suggest adding this as it provides a wider context and also noting that the perceived boundaries between urban-rural or protected-developed are blurry in many areas:

Lee-Smith, D., 2010. Cities feeding people: an update on urban agriculture in equatorial Africa. Environment and urbanization, 22(2), pp.483-499.

Foeken, D.W.J., Owuor, S., de Bruijn, M.E. and Dijk, R.A., 2001. Multi-spatial livelihoods in sub-Saharan Africa: rural farming by urban households-the case of Nakuru town, Kenya. African dynamics, pp.125-139.

Speybroeck, N., Berkvens, D., Mfoukou-Ntsakala, A., Aerts, M., Hens, N., Van Huylenbroeck, G. and Thys, E., 2004. Classification trees versus multinomial models in the analysis of urban farming systems in Central Africa. Agricultural Systems, 80(2), pp.133-149.

Across many parts of West and East Africa, there are increasing efforts to have public green spaces that are multi-functional and many local conservation or citizen organisations are engaged in developing these. While much of this is outside the core scientific literature, it would be worth a mention in the paper as it provides a more nuanced and comprehensive picture of what is currently happening:

https://friendsofcitypark.org/pollinator-garden-gets-a-jump-start-with-a-boscowen-makeover/

There are a number of more recent reviews that provide a wider context of pollinator conservation, management and the many complex issues that intersect with their wider understanding and appreciation. I suggest that these references be added to the the ms:

Hall, D.M. and Martins, D.J., 2020. Human dimensions of insect pollinator conservation. Current opinion in insect science, 38, pp.107-114.

Potts, Simon G., et al. The assessment report on pollinators, pollination and food production: summary for policymakers. Secretariat of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services, 2016.

There is a growing appreceation of the potential impacts of more dense urban beekeeping efforts on wild or non-managed pollinator species in urban landscapes. Given the wider issue that there is still limited understanding of biodiversity and its’ connection with human life and livelihoods in many areas, this is subject that might be worth a bit more of a discussion in this review.


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

Input:
Title: A REVIEW OF THE OPPORTUNITIES TO SUPPORT POLLINATOR POPULATIONS IN SOUTH AFRICAN CITIES
Review round: 1
Reviewer: 3

Output:
Basic reporting: The present research reviews the international literature about opportunities to support pollinator population and compare with the few studies realized in South Africa in the agricultural landscape. With the lack of studies about this subject in South Africa, authors tried to do some parallels with the urban landscape.

While the main part of the article is very interesting to read with a good English used throughout, the introduction appears a little bit disconnected. The introduction is difficult to follow, and I suggest to the authors to maybe merge their actual introduction with the first part of their review entitled “A CONCEPTUAL MODEL FOR ANALYSING THE INTERACTIONS OF MOBILE AGENTS (POLLINATORS) » mainly based on the work of Kremen et al. 2007.

I have some concerns about the title and the lack of presentation or description of South African cities. Maybe it could be interesting to highlight some specificities of the South African context in introduction or develop more within each part of the review.
Regarding the introduction, I think it could contain more information about the decline of pollinators, why urban landscape could be favorable for some taxa. Please detail for which taxa it is favorable or not, and add some precision of the work of Wenzel 2020 which is described L51-54 (see miner comments). The third paragraph of the introduction is not easy to follow as a reader and I did not completely understand why there is a switch for urban to agricultural landscape. I understand that some factor could act similarly in urban and agricultural landscape but I think it is risky to do the parallel. It could be better to reformulate this paragraph.

I don’t see what is the input of the figure 1 which is the same figure as Kremen et al. 2007.
Experimental design: The survey methodology is well described. Maybe authors could provide the total number of papers they included in their review (158 papers).

The review is organized as follows :
1.	A CONCEPTUAL MODEL FOR ANALYSING THE INTERACTIONS OF MOBILE AGENTS(POLLINATORS)
2.	POLLINATOR COMMUNITY STRUCTURE: THE IMPORTANCE OF WILD BEES AND NON-BEE POLLINATORS IN DIFFERENT LANDSCAPE SYSTEMS.
2.1.	LANDSCAPE STRUCTURE: POLLINATORS RESPOND DIFFERENTLY TO URBAN AND AGRICULTURAL LANDSCAPES
2.2.	LOCAL HABITAT: OPPORTUNITIES TO IMPROVE CONNECTIVITY AND QUALITY FOR URBAN POLLINATORS
2.3.	FLOWER COMMUNITY STRUCTURE: ITS EFFECTS ON POLLINATOR DIVERSITY
2.4.	HUMANS AS FACILITATION AGENTS

I suggested merging the first part of the review with the introduction of the review as the authors were based only on the work of Kremen et al 2007.
Validity of the findings: The review highlight the lack of knowledge about the effect of urbanization on pollinators in South Africa. Authors only provide information in some bee taxa and insects taxa at the end of the manuscript whereas they could mentionned some studies in the main text.

Development and Future of Insect Conservation in South Africa https://link.springer.com/chapter/10.1007/978-94-007-2963-6_12
Lepidopterology in Southern Africa: Past, Present and Future
https://link.springer.com/chapter/10.1007/978-94-007-2963-6_12

Some studies on plant diversity across urban-rural gradient could also be mentionned in the FLOWER COMMUNITY STRUCTURE part.

Impacts of urbanization in a biodiversity hotspot: Conservation challenges in Metropolitan Cape Town https://www.sciencedirect.com/science/article/pii/S0254629910001390

Post-apartheid ecologies in the City of Cape Town: An examination of plant functional traits in relation to urban gradients
https://www.sciencedirect.com/science/article/abs/pii/S0169204619301197

Ecological outcomes of civic and expert-led urban greening projects using indigenous plant species in Cape Town, South Africa
https://www.sciencedirect.com/science/article/abs/pii/S0169204614000802

Even it is not the main subject here, maybe you can do some hypothesis about these previous works.
Additional comments: Minor comments :

Abstract

L21-22. What do you mean by regions and taxa ? This sentence is not clear for me.
L27. Which taxa ? Please precise and reformulate the sentence by avoiding “do well”.
L33-34. Why do you finish by some precise advice only for honeybees ? Please stay wide for the conclusion sentence.

Introduction

L38-41. Please merge the 2 sentences, I suggest, “In the context of global decline of insect species and biomass (references), there is growing evidence that …. (References).”
L43. Remove « indicating that”.
L51-54. How many studies have been referenced in the work of Wenzel 2020 in total ?
L63. Replace “this” by “there”.

Review parts
L181. Please use Apis mellifera instead Apis melifera all along the manuscript.
L390. Remove "for"
L396-397. Please reformulate.


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

Input:
Title: A REVIEW OF THE OPPORTUNITIES TO SUPPORT POLLINATOR POPULATIONS IN SOUTH AFRICAN CITIES
Review round: 2
Reviewer: 1

Output:
Basic reporting: I suggest to remove the dotted line in figure 1b, since you did not report on any stats, nor any descriptive information (like slope) the line is not useful at all and even with stats & slope I am not sure that it would add value.
Experimental design: I think the authors addressed the critical points raised
Validity of the findings: The authors refocused the MS significantly and I think they make a convincing case for a South African focus
Additional comments: Without the line in figure 1b I would have said "accepted as 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: EVOLUTION ANALYSIS OF FRIZZY PANICLE (FZP) ORTHOLOGS EXPLORED THE MUTATIONS IN DNA CODING SEQUENCES IN THE GRASS FAMILY (POACEAE)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is written in professional English and follows a logical structure. I have one point of criticism where changes would strongly improve the paper.

Figure 1 would be more useful if it would show an alignment between at least one candidate of each of the three subgroups with the logo shown alongside (an example would be Figure 4 in the follwoing paper: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034231). The alignment should be extended outside of the domain and the domains clearly highlighted. It would further improve the paper if you would then mark the positive selection sites identified in section 3.4. Or even highlight the previous identified mutations which caused phenotypes in maize, rice and wheat.

The authors switch in the results over to discussion from lines 138 to 147 which is also picked up again in the discussion from line 240 to 249. In addition, the location of the genes on different chromosomes in the respective species make sense when one looks at syntenic regions between the grasses. It might be worth checking up on the synteny between grasses in the literature.
Experimental design: The methods should be further extended. Which versions of the databases were used? What was the p-value cut-off and the length identity cut-off to identify potential orthologs?
For the phylogeny it is not clear if you used the protein sequence or the CDS.

Your hypotheses from line 149 about not being able to identify genes in some of the grasses should also be moved to the discussion. I would also advise you to have another look at the data. You should be able to find out if the genomes are incomplete in the databases. Also, based on the method descriptions you seem to identify the genes based on searches against the transcriptome (which you should state in the methods), but not the genome. Incomplete transcriptomes are very common, and you might be able to find the genes with a search against the genome itself.
Validity of the findings: The last sentence of the conclusion is in no way supported by the paper and should be removed. An evolutionary analysis of one gene family is not enough to conclude anything about domestication. In general, the conclusion needs a bit more work.
Additional comments: The authors need to check their use of the word significant. Everything underpinned by a statistic analysis as for the positive selection is correct. But a mutation would only be classified as significant if an obvious phenotype could be associated with it. This is not the case for line 159, 194, 237. To estimate the effect the variance differences might have on the resulting protein, the authors could calculate PROVEAN scores to underpin their hypothesis (http://provean.jcvi.org/index.php) that those amino acid changes have an effect.

170 I assume you mean monocot species?

218 Should be “maize genome duplication”

Table 1 – why is one "NCBI" highlighted in red?

Odd changes in text size in the conclusions.


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: EVOLUTION ANALYSIS OF FRIZZY PANICLE (FZP) ORTHOLOGS EXPLORED THE MUTATIONS IN DNA CODING SEQUENCES IN THE GRASS FAMILY (POACEAE)
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comments
Experimental design: No comments
Validity of the findings: No comments
Additional comments: In this manuscript, authors have used bioinformatics methods for evolutionary analysis of 35 FZP orthologs identified in 29 species of the grass family. Authors have shown that phylogenetic analysis classified these FZP orthologs into three groups (Triticeae, Oryza, and C4 plants). Also, authors have found significant difference in the acidic C-terminal regions of these three groups. Moreover, authors performed selection pressure analysis and found significant positive selection sites in species of the Triticeae and Oryza groups. This manuscript provide theoretical aspect for understanding the functional divergence of the FZP orthologs among different grass species. Overall, the manuscript is fine, and I have few comments:

1. Details about MEME is missing. For example, maximum and minimum motif length, maximum number of motifs and motif sites to be distributed in sequences.
2. Details about phylogenetic reconstruction are completely lacking for Mrbayes. What model was used to construct phylogeny?? What was the sampling frequency?? What percentage of burn-in generation was taken??
3. Line 91 & 92 Using the protein sequence of the FZP gene from rice as the seed sequence, searches were performed in the PlantGDB and other databases using what??? blastp/blastx/tblastx?? authors should mention this and what cutoff was taken to search FZP orthologs??
4. Line 130: which -> , which???
5. Line 169-170: "Using MEGA X, the optimum tree construction model T92+G was identified to generate the ML tree for the FZP gene in dicot species". I did not find any dicot species in fig2. Authors should correct it. Moreover, in method section, authors have mentioned that they have used MEGA X and Mrbayes. But there is only one phylogenetic tree in manuscript. Phylogeny present in fig2 generated by MEGA X or Mrbayes?? authors should write it in the figure2 legend. Also, authors should add another phylogenetic tree as supplementary figure.
6. I think authors should include multiple sequence alignment (MSA) as supplementary figure so that positive selection sites and other important residues that authors have mentioned could easily seen in MSA. It would be great if authors could mark those important residues in MSA with protein residues numbers.
7. For the sake of consistency, Sorghum bicolor should be referred to as S. bicolor after its first occurrence in the text. Authors should check this for all 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: EVOLUTION ANALYSIS OF FRIZZY PANICLE (FZP) ORTHOLOGS EXPLORED THE MUTATIONS IN DNA CODING SEQUENCES IN THE GRASS FAMILY (POACEAE)
Review round: 1
Reviewer: 3

Output:
Basic reporting: This manuscript contains mostly clear and unambiguous, professional English throughout, but there are many grammatical and contextual issues in places. Examples include,
	Line 58-59: “Maize bd1 mutants are characterized by indeterminate branches in place of female spikelets, the production of indeterminate branches, and a series of lateral spikelets in tassels.“

	Line 94-96: “The retrieved orthologs were identified as sequence-wise for the elimination of incomplete and redundant sequences.”

Line 236-238: “However, the rich evolutionary information of the various species has been retained through significant mutations in the acidic C-terminal region of the gene in species of the tribe Triticeae, genus Oryza, and C4 plants, which can be used for phylogenetic analyses.“

Revision for grammatical errors and more detail to slightly vague statements will bolster the quality of the manuscript.

Literature references are used in sections of the manuscript to various degrees, but are missing through as a whole, particularly with information in the results that are not from the data of this study (i.e. Line 238-240: “Previous research has indicated that foxtail millet and rice diverged approximately 50 million years ago, but the two species' genomic structures remained highly collinear.”).

The article structure, figures and tables are professional, but no raw data are provided and many other materials are missing. Only one phylogenetic tree image is used in a figure, but the underlying tree file and sequence alignment to generate tree are not provided.

The results of the study are relevant to the hypothesis presented and is self-contained.
Experimental design: The research presented in the manuscript is original, within the aims and scope of the journal, and consists of a well-defined question, relevant and meaningful to provide an understanding of the evolutionary history of FZP orthologs and the consequence on inflorescences development across grasses.
However, the study and manuscript are underdeveloped and lacking several important components.
Line 91: “Using the protein sequence of the FZP gene from rice as the seed sequence,”
•	Which rice species? Two rice species included in study, Table1.
Line 91-94: “searches were performed in the PlantGDB (http://www.plantgdb.org/), Phytozome (https://phytozome.jgi.doe.gov), and NCBI (http://www.ncbi.nlm.nih.gov/) databases for orthologs contained in grass species (the corresponding CDSs were also saved).”
•	Several versions of Phytzome and other databases exist, version information is missing from this study.
•	It is unclear if searches were performed in only grass species or only homologs from grass species were used downstream after search. Search parameters are not provided or described.
Line 98: Dicots are mentioned, as well as in Line 128+170 and Figure 2 title, but dicots are not included in study.
Line 124-125: “we evaluated which of four codon substitution models (Model A, Model B, Model C, Model D)”
•	Only Model A results reported
•	Branch-Site model tests for positive selection typically involve testing different initial omega(w) to test the robustness of the analyses. The authors do not indicate if this was done in their study.
Line 155: “with mutations only occurring at positions 4 and 30.”
•	It is unclear if these mutation sites are present in a single or multiple homolog sequence.
Line 170-172: “Results indicate that the grass species could be classified into groups I, II, and III. The bootstrap values of the three groups were 89%, 93%, and 68%, respectively, which were >50% and indicative of high reliability.”
•	It is unclear if the groups being classified are in reference to FZP homologs or the grass species themselves.
•	The bootstrap values described do not match the phylogenic tree in Figure 2
•	Is the Figure 2 phylogeny based on protein or nucleotide sequence? The whole sequence or portion of alignment?
•	The interpretation of bootstrap support values is inaccurate. Bootstrap values less than 95% can still provide some confidence in a branching pattern but anything below 75% is not considered reliable or “good”. (Hillis and Bull (1993) Systemic Biolgy)
Line 178-180: “Group Ⅱ was comprised entirely of species of the genus Oryza and had a bootstrap value of 93%, which indicates the extremely high reliability of the group.”
•	Group II as described in Figure 2 is a paraphyletic group of Oryza and Leersia homologs, and the support value described in the manuscript for this group do not match the figure.
Line 216-218: “This indicates that the BD1B gene maybe a tandem repeat of BD1 generated during the maize genome's replication.”
•	The authors have the resources to determine if the maize BD1A and BD1B are located in tandem.
•	The maize homologs are not sister in the phylogenetic tree in Figure 2, suggesting a more complex evolutionary history than simple tandem duplication through replication or extensive evolution between possible tandem homologs.
Line 231: “FZP ortholog that only existed in plants”
•	Were grasses he only species analyzed in this study? It would be expected that only plant homologs would be present if this is true.

The materials and methods are insufficient in information and detail to replicate the study confidently. Only one phylogenetic tree is provided, which displays data inconsistent with statements made the manuscript. This phylogenetic tree, as well as any others produced during this study, should be provide or made accessible through a public repository, such as TreeBase (https://www.treebase.org/treebase-web/home.html). Additionally, the alignments generated and used to construct the phylogenetic tree(s) should be treated similarly. Homolog searches and PAML analyses described are lacking detail in terms of the parameters used during those processes.
Validity of the findings: The finds of this study appear to be valid based on the limited data provided. The data sources used are publicly available, therefore someone could obtain the sequences used and repeat the study. However, without the parameter information for programs used and the lack of raw data corresponding sequence alignments and phylogenetic trees, it would be impossible to confidently replicate the study and results. As long as the results and finds are consistent with the underlying raw data, providing the underlying raw data will strongly bolster the quality and transparency of the manuscript. The brief conclusions drawn are supported by the data and relate to the question originally proposed.
Additional comments: This investigation into the study of FZP evolution and possible functional roles in reproductive development provides critical information as to the evolutionary role FZP has played. The results description and conclusions are basically statements of the data described in the tables. More thoughtful interpretation of the results will strengthen the impact of the study and manuscript.


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

Input:
Title: EVOLUTION ANALYSIS OF FRIZZY PANICLE (FZP) ORTHOLOGS EXPLORED THE MUTATIONS IN DNA CODING SEQUENCES IN THE GRASS FAMILY (POACEAE)
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have made suggested changes and I accept the manuscript with very few minor changes. these changes are below:
line 52- Oryzasativa -> Oryza sativa??
line 60- spikeletsand -> spikelets and??
Line 257: In a specific Poaceae species category, the acidic domainofC -> domain of C (space missing). These kinds of missing spaces are a lot in the manuscript. The authors should correct it.
Line 131- Then use PyMOL v2.5.0 software(Schrodinger 2015) -> Then we did use???
Line 145: Do not start a sentence with a numeral
Line 256: The amino acids of position -> The amino acids of positions??
Line 370: Use PROVEAN online server -> We used PROVEAN online server or PROVEAN online server was used ???
Line 390-391: Use I-TASSER online server -> We did use I-TASSER or I-TASSER online server was used ??
Line 398: red area in 3D structure -> what is the red area in 3D structure. is it alpha-helix, beta-sheet, or loop region??
Line 399-401: I can not see C-terminus in 3D structure as the authors have mentioned: "The 3D structure of Arabidopsis AtERF96 gene does not have an acidic domain at the C-terminus, and gramineous plants all have an acidic domain (the orange region in the 3D structure)at C-terminus". The authors should show C-terminal in figure 3.
Line 400: the orange region in the 3D - > Authors should mention clearly what orange region is alpha-helix/beta-sheet or loop. It is good to call how these regions are called in the 3D protein structure terms.
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: EVOLUTION ANALYSIS OF FRIZZY PANICLE (FZP) ORTHOLOGS EXPLORED THE MUTATIONS IN DNA CODING SEQUENCES IN THE GRASS FAMILY (POACEAE)
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The author's have addressed and corrected most of the comments and concerns presented following the initial review of this manuscript. However, typographical errors, primarily the lack of appropriate spaces between words, are found throughout the manuscript. The Materials and Methods section has been updated and corrected based on comments from the reviewers. However, section 2.4 and 2.7 address the same program and tests of evolutionary selective pressure, and should be combined and consolidated. Lastly, I strongly encourage the author's to review the underlying assumptions of their process. The author's state that FZP "only existed in plants", but only grass (Poaceae) species were included in this study. They have not demonstrated that other plants or organisms lack FZP orthologs. Additionally, the interpretation of phylogenetic results are slightly inaccurate. As mentioned in the initial review of this manuscript, bootstrap values less than 95 can still provide some confidence in a branching pattern but values between 95 and 75 are not typically considered "indicative of high reliability", and a softer stance on values in this range should be incorporated. Bootstrap values >75 but less than 95 are "good" but not highly reliable.


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 EVOLUTION OF REPRODUCTIVE STRATEGIES IN TURTLES
Review round: 1
Reviewer: 1

Output:
Basic reporting: First of all, there is a lack of literature up to date and most of the manuscript rely upon old bibliography. Despite important, such old literature (1980 decade) were overlapped by new theories. For instance, there are several bibliography on turtles geographical distribution X climate or phylogenetic associated to body size and/or behavior (for instance: de la Fuente, M. et al. 2014. Origin, Evolution and Biogeographic History of South American Turtles; Angielczyk, K.D., Burroughs, R.W. & Feldman, C.R. 2015. Do turtles follow the rules? Latitudinal gradients in species richness, body size, and geographic range area of the world's turtles. J. Exp. Zool. B Mol Dev Evol. 2015 May;324(3):270-94. doi: 10.1002/jez.b.22602; Rodrigues, J.F.M. & Diniz-Filho, J.A.F. 2016. Ecological opportunities, habitat, and past climatic fluctuations influenced the diversification of modern turtles. Mol. Phyl. Evol. 101: 352-358). Also, authors must search for literature reviews on the theme to have a more robust theoretical approach. Otherwise, it remains most speculative (for instance: Janzen, F.J. & Warner, D.A. 2009. Parent-offspring conflict and selection on egg size in turtles. J Evol Biol. 2009 Nov;22(11):2222-30. doi: 10.1111/j.1420-9101.2009.01838.x. Epub 2009 Sep 29. PMID: 19796084; Iverson, J. B., Lindeman, P. V., & Lovich, J. E. (2019). Understanding reproductive allometry in turtles: A slippery "slope". Ecology and evolution, 9(20), 11891–11903. https://doi.org/10.1002/ece3.5697).
Figure 2 must be improved. Points from Figure 4 must be related to solid lines. Figure 1 is not informative at all (please, delete).
Experimental design: It lacks a more detailed hypothesis explanation as well as its premises.
Even the supplementary material must be reviewed to introduce and/or change mistake information on turtles reproductive biology.
Validity of the findings: The discussion section must be improved by explaining what really your results tell us about your idea. For instance, what means those phylogenetic trees for each variable throughout evolutionary history?
Additional comments: The manuscript "The evolution of reproductive strategies in turtles" address simple but interesting points and aim to verify which factors shape an important issue on turtles evolutionary history. Despite such approach has been investigated in the last years, the authors fail to go deep in the theme.


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 EVOLUTION OF REPRODUCTIVE STRATEGIES IN TURTLES
Review round: 2
Reviewer: 1

Output:
Basic reporting: I complete the review of the manuscript (MS) “The evolution of reproductive strategies in turtles” submitted by Jorgewich-Cohen et al. The MS try to test the hypothesis of convergence of reproductive traits using a wide data base covering all turtle genera. Authors approached the data analysis using comparative methods and at least two evolutionary models (OU and Brownian motion). The data set is interesting, and they used relevant variables, they compared between elongated eggs vs. spherical eggs, climate zones, and diet as categorical variables, using clutch size, fecundity, and egg size as continuous variables. I also reviewed the response letter to the comments made on their first round of revision. In my opinion, this version improves a lot of sections of the MS and focus the analysis on the evolution of reproductive strategies in an evolutionary convergence context. Nevertheless, I consider the MS still confusing and I´m not sure if they really test evolutionary convergence in reproductive strategies. I fund several inconsistencies along the MS and I consider authors avoid important references on the evolution of life history of turtles.
Experimental design: The idea of the paper is very interesting; however, their analysis and interpretation is confusing. I think authors are not familiarized with the methods to test convergence. I suggest pertinent literature directly in the MS. One of the important flaws of this paper is there is a lack of seminal papers in their literature review. Authors omit other studies trying to explain the life-history evolution in turtles such those of Wilbur and Morin (1988), and Smith and Fretwell (1974) on optimal egg size theory, among others. Otherwise, authors omit important approaches on the study of convergence such those of McGhee (2011), among others.
Validity of the findings: I fund the following issues concerning and I think authors should resolve these comments before the MS has been consider for a new review:

Authors claim that the independent evolution of a trait or a character indicate convergence, this is not necessarily true, it could be parallelism. Authors should review McGhee, G.R. 2011. Convergent Evolution: Limited forms most beautiful. MIT Press, for a detailed and modern explanation of convergence and how approach it.

Authors motion the used Pereira’s et al. phylogeny, but they did not mention how the resolve the missing species in the phylogeny or their data set? Did they prune the phylogeny?

The results section is very brief. Authors make a lot of tests and used complex analytical tools; I think authors should expand their results report. At least not only refer the reader to the tables and figures. Figure 2 is ok, but it needs a color code inside the figure because it´s very hard to follow.

Authors mention the optimal egg size theory as theoretical guide of their work. Their entire framework is based on this theory, however, they didn´t mention the possibility of pelvic constraint as an alternative hypothesis. Both hypotheses have been proved in the past and there is evidence supporting both. Authors should acknowledge the evidence of pelvic constraint hypothesis, at least in small body size species or individuals within a single population.

I´m not sure authors provide proofs of convergent evolution. Perhaps they have a clue, or their data suggest a potential convergence, but they didn´t proof these turtles’ lineages were affected by similar environmental or more precisely, similar selection pressures to derive in convergent life history traits. Other thing, authors transform continuous variables to interval variables, which they map on the phylogeny. Since reproductive traits such clutch size, egg size, and fecundity vary yearly, seasonally, and even between females of the same population. A more important approach should include a variation measure such standard error or coefficient variation. Even if their data suggest or point to a possible convergence, authors should conduct other studies to really document this phenomenon.

Discussion has some flaws. Authors quoted other studies several times to contrast their results and to support his data, I think they should contrast their data with the framework they develop. Discussion didn’t support their claim of convergent evolution, also they mention several other factors could be driven the evolution of life history in turtles. Authors cited Johnathan Losos work on Anolis convergence, but authors didn´t follow the same methods and framework suggested by Losos (2011) and in other work conducted by Professor Losos.

Finally, I consider this paper still interesting, however the MS is not fully developed and still needs work and authors should integrate a more compete framework.
Additional comments: I complete the review of the manuscript (MS) “The evolution of reproductive strategies in turtles” submitted by Jorgewich-Cohen et al. The MS try to test the hypothesis of convergence of reproductive traits using a wide data base covering all turtle genera. Authors approached the data analysis using comparative methods and at least two evolutionary models (OU and Brownian motion). The data set is interesting, and they used relevant variables, they compared between elongated eggs vs. spherical eggs, climate zones, and diet as categorical variables, using clutch size, fecundity, and egg size as continuous variables. I also reviewed the response letter to the comments made on their first round of revision. In my opinion, this version improves a lot of sections of the MS and focus the analysis on the evolution of reproductive strategies in an evolutionary convergence context. Nevertheless, I consider the MS still confusing and I´m not sure if they really test evolutionary convergence in reproductive strategies. I fund several inconsistencies along the MS and I consider authors avoid important references on the evolution of life history of turtles.

The idea of the paper is very interesting; however, their analysis and interpretation is confusing. I think authors are not familiarized with the methods to test convergence. I suggest pertinent literature directly in the MS. One of the important flaws of this paper is there is a lack of seminal papers in their literature review. Authors omit other studies trying to explain the life-history evolution in turtles such those of Wilbur and Morin (1988), and Smith and Fretwell (1974) on optimal egg size theory, among others. Otherwise, authors omit important approaches on the study of convergence such those of McGhee (2011), among others.

I fund the following issues concerning and I think authors should resolve these comments before the MS has been consider for a new review:

Authors claim that the independent evolution of a trait or a character indicate convergence, this is not necessarily true, it could be parallelism. Authors should review McGhee, G.R. 2011. Convergent Evolution: Limited forms most beautiful. MIT Press, for a detailed and modern explanation of convergence and how approach it.

Authors motion the used Pereira’s et al. phylogeny, but they did not mention how the resolve the missing species in the phylogeny or their data set? Did they prune the phylogeny?

The results section is very brief. Authors make a lot of tests and used complex analytical tools; I think authors should expand their results report. At least not only refer the reader to the tables and figures. Figure 2 is ok, but it needs a color code inside the figure because it´s very hard to follow.

Authors mention the optimal egg size theory as theoretical guide of their work. Their entire framework is based on this theory, however, they didn´t mention the possibility of pelvic constraint as an alternative hypothesis. Both hypotheses have been proved in the past and there is evidence supporting both. Authors should acknowledge the evidence of pelvic constraint hypothesis, at least in small body size species or individuals within a single population.

I´m not sure authors provide proofs of convergent evolution. Perhaps they have a clue, or their data suggest a potential convergence, but they didn´t proof these turtles’ lineages were affected by similar environmental or more precisely, similar selection pressures to derive in convergent life history traits. Other thing, authors transform continuous variables to interval variables, which they map on the phylogeny. Since reproductive traits such clutch size, egg size, and fecundity vary yearly, seasonally, and even between females of the same population. A more important approach should include a variation measure such standard error or coefficient variation. Even if their data suggest or point to a possible convergence, authors should conduct other studies to really document this phenomenon.

Discussion has some flaws. Authors quoted other studies several times to contrast their results and to support his data, I think they should contrast their data with the framework they develop. Discussion didn’t support their claim of convergent evolution, also they mention several other factors could be driven the evolution of life history in turtles. Authors cited Johnathan Losos work on Anolis convergence, but authors didn´t follow the same methods and framework suggested by Losos (2011) and in other work conducted by Professor Losos.

Finally, I consider this paper still interesting, however the MS is not fully developed and still needs work and authors should integrate a more compete framework.

I made several comments along the MS and made direct suggestion to the authors.

Literature cited

Smith, C.C. and S.D. Fretwell. 1974. The Optimal Balance between Size and Number of Offspring. The American Naturalist 108:499–506.

Wilbur H.M. and P.J. Morin. 1988. Life history evolution in turtle. P. 387-439. In: Gans, C. and Huey, R.B. (Eds.). Biology of the Reptilia Volume 16 Ecology B. Defense and Life History. Alan R. Liss, New York.

McGhee, G.R. 2011. Convergent Evolution: Limited forms most beautiful. MIT Press. Boston.

Losos, J. 2011. Lizards in an Evolutionary Tree: Ecology and Adaptive Radiation of Anoles. University of California Press, Berkeley.


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 EVOLUTION OF REPRODUCTIVE STRATEGIES IN TURTLES
Review round: 2
Reviewer: 2

Output:
Basic reporting: This study approaches an interesting and important evolutionary question about turtles’ “optimal egg strategy”, whereas egg and clutch size evolves by an energetic trade-off, influencing their egg shapes. The authors studied the “optimal egg strategy” by applying established and modern phylogenetic comparative methods on a dataset comprehending all turtle genus. The paper has professional English, structure, figures, and tables. The raw data and analytical scripts were shared. I do not have the expertise to judge the literature references about "optimal egg strategy" in turtles, but it seems well represented. The introduction needs to explore and provide more information about how and which environmental and ecological variables (e.g. climatic zone, diet, habitat, and zoogeographical regions) determine egg and clutch sizes, as these variables are evaluated further in the methods. The reference misses articles about convergent evolution such as Ingram & Mahler (2013), Bastide et al. (2018), Castiglione et al. (2019), and Mahler et al. (2017). The paper is self-contained, but the statistical methods need to be better linked to which hypothesis they are evaluating. The manuscript has the potential to be published in PeerJ, but the authors need to improve some writing and methodological issues to have more robust statistical analyses and fluid writing, mainly in the methods and results.
Experimental design: This manuscript has ethical, well-defined, and relevant questions, within the aims and scope of the journal. The materials and methods section needs to be more straightforward in linking the statistical methods to the tested hypotheses. Also, the methods section requires more details about how data were collected, why the author chose the phylogenies they used, there are other published phylogenies comprehending 300 species (Rodrigues & Diniz-Filho, 2016) that may be useful. The fitting of multivariate evolutionary models requires details about the different regimes evaluated. For instance, there are regimes defined in Table 1 as control, diet, Clima, Zoogeography, but there is no explanation about these variables, how they were collected, how ancestral states were estimated, and which evolutionary models were used. Furthermore, some regimes were defined based on body size reconstruction, but the authors did not present it was done splitting body size into 2, 3, and 4 categories. These multivariate evolutionary models may describe how some variables evolved correlated to other variables (regimes), but it is not clear how it answers the question about convergent evolution (Mahler et al., 2017). Perhaps the use of methods developed for testing convergent evolution such as Bastide et al. (2018), Ingram & Mahler (2013), and Castiglione et al. (2019) may be better alternatives. MANOVA analysis also requires better explanations about what it is evaluating. Looking at the script, in supplementary material, it seems to test the effects of diet on reproductive traits, but the methods section says nothing about it.
	The PGLS models included as independent variables climatic zone, diet, clutch size, and egg size, but in the introduction, body size is described as a well-known variable in determining both egg size and clutch size. Why body size was not included in the PGLS to control its effects on both response variables? Additionally, PGLS was evaluated by a Full-Null Model Comparison approach. It is not explained how this method works, there are no citations enabling the reader to understand the methodology. Furthermore, it is not clear why the authors excluded two species from the PGLS analyses, these species have wrong data, or the models used were not adequate to describe trait distribution? How these species' exclusion impacted ancestral state reconstruction and evolutionary model inferences? How the exclusion of these species impacted the analyses and conclusions of the manuscript?
       A possible approach to improve this manuscript's understanding is fitting multivariate models to body size, egg size, egg shape, and clutch size to evaluate their correlations, thus answering the first paper’s question. Testing reproductive traits convergence with Bastide et al. (2018), Ingram & Mahler (2013), or Castiglione et al. (2019) methods. To answer the main question of the paper, optimal egg strategy, use PGLS models with lambda parameter to control phylogenetic signal (Revell, 2010).

References

Bastide, P., Ané, C., Robin, S., & Mariadassou, M. (2018). Inference of adaptive shifts for multivariate correlated traits. Systematic Biology, 67(4), 662–680. https://doi.org/10.1093/sysbio/syy005.

Castiglione, S., Serio, C., Tamagnini, D., Melchionna, M., Mondanaro, A., Di Febbraro, M., Profico, A., Piras, P., Barattolo, F., & Raia, P. (2019). A new, fast method to search for morphological convergence with shape data. PLoS ONE, 14(12), 1–20. https://doi.org/10.1371/journal.pone.0226949.

Ingram, T., & Mahler, D. L. (2013). SURFACE: Detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise Akaike Information Criterion. Methods in Ecology and Evolution, 4(5), 416–425. https://doi.org/10.1111/2041-210X.12034.

Mahler, D. L., Weber, M. G., Wagner, C. E., & Ingram, T. (2017). Pattern and process in the comparative study of convergent evolution. American Naturalist, 190, S13–S28. https://doi.org/10.1086/692648.

Revell, L. J. (2010). Phylogenetic signal and linear regression on species data. Methods in Ecology and Evolution, 1, 319–329. https://doi.org/10.1111/j.2041-210X.2010.00044.x

Rodrigues, J. F. M., & Diniz-Filho, J. A. F. (2016). Ecological opportunities, habitat, and past climatic fluctuations influenced the diversification of modern turtles. Molecular Phylogenetics and Evolution, 101, 352–358. https://doi.org/10.1016/j.ympev.2016.05.025.
Validity of the findings: All data and scripts were shared to guarantee reproducibility. Statistical methods to evaluate convergent evolution need to be clear and more robust. The methodology implemented to evaluate Phylogenetic Linear Generalized Models (PGLS) needs more details to understand how variables were selected and how confidence intervals and coefficient of determination were calculated. Also, PGLS needs to control the effect of body size to estimate the partial effects of egg size and clutch size on each other.
The results of explanatory analyses are not clear, there is methodological information that appeared, for the first time, in the results. For example, Table 1 has information (e.g. control, zoogeography, body size, habitat) that did not appear before in the manuscript. It is not clear how MANOVA and the multivariate evolutionary models are complementary analyses. It is written MANOVA results are different from multivariate evolutionary models results, but they have different proposals, MANOVA tests the effect of diet on reproductive traits considering only tip data, multivariate models fit the models considering the ancestral reconstruction of other variables.
Conclusions are well stated, but as methodology and results are not robust and clear, it is not well supported by the results.
Additional comments: Some minor comments:

Line 34-43 Information about ecological and environmental variables may be included along lines 34 and 43.

Line 41 In this line it is written “These hypotheses, largely based on studies of trait correlations (Gibbons, 1982), can be tested by methods that consider phylogeny, as they reduce the variance of estimated regressions (Rohle, 2006).” This sentence seems out of context here.

Line 59-60 The second question is not clear enough. Rephrase this question to better represent what will be tested.

Line 62-63 The hypothesis is too vague. Define which ecological factors may impact egg and clutch size.

Line 67-72 Explain how PRISMA guidelines were conducted. Likely, it is better to write Appendix 2 here. However, even Appendix 2 requires more details about inclusion criteria.

Lines 74-92 Perhaps the exploratory analyses may be sent to supplementary materials in order to enhance readability.

Line 87-89 Create a paragraph describing the data collection and cleaning, synonym standardization, transformation of variables (ESI, ESH, FEC). Make clear that these variables are those modeled by the evolutionary models.

Line 108-113 Describe which variables had their ancestral state reconstructed to define evolutionary regimes, how reconstructions were done. Explain how body size was categorized to define its regimes.

Line 112  Instead "model fitness", use model selection.

Line 114-116 MANOVA is not testing regimes here, but the effect of diet on reproductive traits.

Line 131 Habitat and zoogeographic zones did not appear before in the manuscript.

Line 132-133 How variables collinearity was evaluated?

Line 135-138 Full-Null Model Comparison approach needs to be explained in detail and referenced. It is not clear how the coefficient of determination, statistical significance, and confidence interval were calculated.

Line 154 Diet means here an OUM model fitted over an ancestral state reconstruction of diet, as it was not described before in the methods section, it is causing confusion.

Line 182 Exclude the extra parenthesis.

Figure 1 change adult? to adult in the legend.

Figure 3 Make clear what are the types of climatic zones in the legend.

Table 1 Describe what column System means in the legend. Make clear that diet OUM is a diet regime and explain the other regimes.


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 EVOLUTION OF REPRODUCTIVE STRATEGIES IN TURTLES
Review round: 3
Reviewer: 1

Output:
Basic reporting: The MS to test the hypothesis of convergence of reproductive traits using a comparative approach with a wide data base covering all turtle genera. This second version has been shortened and methods were reformulated. This version is improved and succinct, author did find the same conclusions overall.
Experimental design: Analitical approach is correct and did achieve the objectives and test the hypothesis of the study, how ever I consider the following points should be covered before acceptance:

1.	I understand authors choose Pereira et al. (2017) phylogeny, but what about use the recent published phylogeny of Thomson et al (2021)? You could use both phylogenies and compare both results and see if you find any concordance between both phylogenies.
2.	The average clutch size also could be used as a continuous variable, it could be transformed to log. I'm not sure if the categories of clutch size are valid. I understand they are arbitrarily chosen, but doesn´t make any sense the category A, why use a larger interval than A? Authors should try to analyze or re-think what you understand or consider of a "reduced clutch" or "large clutch".
3.	Authors didn’t analyze the medium clutch size; they focus in large (>30 eggs) vs. small clutch size (<4 eggs), but what about the “middle” cutch mass? I think author should dig deep in the results on strategies on the middle spectrum of reproductive strategies.
4.	I would like to see a clearer explanation or interpretation on the selection pressures inducing convergence in the reproductive strategies in turtles.
Validity of the findings: I think this paper is very interesting and find this version suitable for publication in PeerJ. However, I have some small concerns that authors should address before acceptance. I consider this concerns as minor changes.

In this new version of the manuscript authors really explain how they test the convergence in reproductive strategies in all genera of turtles.
Additional comments: I provide additional comments directly on the manuscript.


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

Input:
Title: THE EVOLUTION OF REPRODUCTIVE STRATEGIES IN TURTLES
Review round: 3
Reviewer: 2

Output:
Basic reporting: This study (“The evolution of reproductive strategies in turtles”) approaches an interesting and important evolutionary question about turtles’ “optimal egg strategy”, whereas egg and clutch size evolves by an energetic trade-off, influencing their egg shapes. The authors studied the “optimal egg strategy” by applying established and modern phylogenetic comparative methods on a dataset comprehending all turtle genus. The paper has professional English, structure, figures, and tables. The authors shared the raw data and analytical scripts. I do not have the expertise to judge the literature references about "optimal egg strategy" in turtles, but it seems well represented. This paper is not self-contained as many methodological explanations are not described in the manuscript and need further searches in the literature.

The introduction is well-written and contextualizes the theory, but there is still lacking a better theoretical introduction about how the climatic zone and diet may affect “optimal egg strategy”. The authors cite that these variables may affect egg and clutch size, but they do not explain the process. It is missing in the methodological section important information about how methods were performed, such as convergence testing does not present the null model and how many times it was replicated. Basic information to guarantee reproducibility, even if the code to run the analyses is provided, should be included in the main manuscript.
Experimental design: This manuscript follows a high technical and ethical standard and is within the aims and scope of the journal. Like the previous version of the manuscript, there is yet a lack of methodological information. The implemented methodology can answer the questions that the authors intended to evaluate, but the description of statistical analyses and the presentation of the results are still confusing, lacking important information. For instance, the authors evaluated the correlation among some variables and tested if there are shifts in these correlations across the phylogeny, but they did not show the correlation, that is the main result to evaluate if clutch size and egg shape followed “the optimal egg strategy” expectation. Furthermore, the analyses tested correlation shifts based on categories of fecundity, it is not clear how it is related to the theory being evaluated. Also, the section describing the search of the literature is still vague, the authors did not present how many papers were found, where papers were searched, how papers were selected. It is not enough to say the literature search followed PRISMA guidelines, it must be described how it was done. The supplementary material shows more details about the literature search, and the inclusion of that description in the main manuscript would improve the paper.
The description of the methodology to evaluate convergent evolution is superficial, the readers may not understand how the methodology works. Also, they tested convergence between cryptodirans and pleurodirans, but it is also not clear how it is related to the “optimal egg strategy”. In other words, the methodology section needs to guide better the reader into how the methodology answers the questions and how they are related to the “optimal egg strategy”.

In PGLS test, two species were excluded from the analyses to achieve homoscedastic and normality of the residuals. The authors can perform a sensibility test to evaluate how the exclusion of the two species may affect the results and conclusions. It is a fast analysis and requires only re-run the function with the complete data. These two species are not wrong data, and may show a piece of important information about egg size and fecundity in turtles. For instance, these lineages may have a different evolutionary process than in the whole clade.

The authors mixed model selection and test of significance to evaluate the PGLS models, maybe it is better to exclude model selection as the results and variable’s importance were evaluated by significance tests. The model selection seems meaningless in these regressions.
Validity of the findings: The conclusion needs to be better sustained by the results. It is not clear enough how the results corroborate the “optimal egg size strategy”. The result shows that clutch size is inversely related to egg size, but there is no information about egg shape. Also, the authors evaluated and found convergence on clutch size evolution, but it cannot be extrapolated to “reproductive traits in Testudines evolved independently several times across non-directly related clades”. The answer to “optimal egg strategy” is on the correlation test that should be better explored. The authors only show that the correlations and rates of reproductive traits are constant across the phylogeny, the correlations among these variables should be presented. Perhaps, the shifts included in the correlation test may follow the shifts of the regimes found in the convergent evolution analysis, instead of the arbitrary categories that were used. Firstly, detect the shifts in clutch size evolution, then evaluate if there are correlations among the variables following the “optimal egg strategy”.
Additional comments: Line 41 – explain how environmental factors (climate zone), diet and biogeography affect clutch and egg size.

Line 89-90 - what is Model hierarchy selection, cite the paper describing the method and also cite AIC.

Line 124 – It is not Pagel correlation, it is known as Pagel’s lambda model. Make clear that is was done to control phylogenetic signal among species.

Line 188-189 – How niche should be taken into account, explain better it.

Line 191-197 – This paragraph needs a better link to the other paragraphs.

Line 219 – Where is the fact that reproductive strategies are correlated to colonization of new environments?

Line 221-225 – It is not clear the point in this sentence.


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 EVOLUTION OF REPRODUCTIVE STRATEGIES IN TURTLES
Review round: 4
Reviewer: 1

Output:
Basic reporting: This study (“The evolution of reproductive strategies in turtles”) approaches an interesting and important evolutionary question about turtles’ “optimal egg strategy”, whereas egg and clutch size evolves by an energetic trade-off, influencing their egg shapes. The authors studied the “optimal egg strategy” by applying established and modern phylogenetic comparative methods on a dataset comprehending all turtle genus. The paper has professional English, structure, figures, and tables, but requires more attention on typos. The authors shared the raw data and analysis scripts. I do not have the expertise to judge the literature references about "optimal egg strategy" in turtles, but it seems well represented.

The introduction is well written and contextualizes the theory.  The lack of information in the methods section has been solved, but there are still unclear sentences.
Experimental design: This manuscript follows a high technical and ethical standard and is within the aims and scope of the journal. The authors improved the previous versions of the manuscript solving the lack of methodological information. The implemented methodology can answer the questions that the authors intended to evaluate, but the description of the convergence and trait correlation analyses is still confusing. For instance, the author wrote they performed a likelihood ratio test and Akaike information criterion to select the best model of traits correlation, but only presented the AIC table. Also, it is unusual selecting a model based on two different inferential philosophies (frequentist and model selection).
Validity of the findings: The conclusion needs to be better sustained by the results. Convergence analyses are still unclear and hard to interpret and achieve a clear conclusion.
Additional comments: 133 – states instead of estates.

line 153- The null model should describe the null model used to test the statistical significance of the convergence test instead of the theoretical expectation.

Lines 175-178 – The description of variable’s selection is confusing.

Line 211-214 – This paragraph is too vague and hard to understand its importance to the discussion.


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 SIGNIFICANCE OF THE PREOPERATIVE LACTATE DEHYDROGENASE/ALBUMIN RATIO IN THE PROGNOSIS OF COLON CANCER: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment.
Experimental design: I think it is quite a small number, only 126 cases in 3.5 years of case accumulation. Is this the number of consecutive cases that were included in the study?

Lines 84, 85
I suggest you add "before."
Serum biochemical examination was performed within 1 week before surgery and the data were complete.

All eligible cases are assumed to have undergone radical resection, but can even M1 cases be considered radical surgery?

Are there any errors in the PNI formula?　I think this is a very serious error.
Validity of the findings: Lines 127
CONUT's scoring criteria and groupings are in Table 1.

Where are the multivariate results for PFS in N stage and M stage?　And what are the multivariate results for OS in N stage?

Does the value of lactate dehydrogenase alone not show a significant difference in PFS or OS?　I would like to know.

In other reports, what is the cut-off value for LAR that makes a difference in the prognosis of malignancy?  Is there an increase or decrease compared to this study?　And why?

Is there a difference between predicting prognosis with LAR and the currently widely used stage? What is the usefulness of preoperative LAR in predicting prognosis?　Isn't the stage alone sufficient?
Additional comments: I thought it was very interesting to read that the preoperative lactate dehydrogenase/albumin ratio is useful in predicting the prognosis of colorectal cancer. However, I think some alterations are necessary.


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 SIGNIFICANCE OF THE PREOPERATIVE LACTATE DEHYDROGENASE/ALBUMIN RATIO IN THE PROGNOSIS OF COLON CANCER: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: see attached PDF


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 SIGNIFICANCE OF THE PREOPERATIVE LACTATE DEHYDROGENASE/ALBUMIN RATIO IN THE PROGNOSIS OF COLON CANCER: A RETROSPECTIVE STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: nothing
Experimental design: nothing
Validity of the findings: Thank you for your sincere answer to my question. I have a further question for your answer.

1.	In general, factors that show significant differences in univariate analysis are examined in multivariate analysis and the results are presented. Even if there is no significant difference, the results of multivariate analysis for PFS in stage N and M , and the results of multivariate analysis for OS in stage N should be presented.
2.	If lactate dehydrogenase alone is significantly correlated with OS and PFS in colorectal cancer patients, I think it should be included as a factor to be evaluated. Lactate dehydrogenase alone is not significant compared to LAR?
Additional comments: nothing


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 SIGNIFICANCE OF THE PREOPERATIVE LACTATE DEHYDROGENASE/ALBUMIN RATIO IN THE PROGNOSIS OF COLON CANCER: A RETROSPECTIVE STUDY
Review round: 2
Reviewer: 2

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


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

Input:
Title: COMPARISON AND CORRELATION OF CERVICAL PROPRIOCEPTION AND MUSCLE ENDURANCE IN GENERAL JOINT HYPERMOBILITY PARTICIPANTS WITH AND WITHOUT NON-SPECIFIC NECK PAIN—A CROSS-SECTIONAL STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is an interesting topic worthy of further investigation. However, the statistical approach it’s not well aborded. For the first aim, the authors compared the cervical joint position error and muscle endurance in two groups of people with general hypermobility with and without neck pain. For the second aim, the general joint hypermobility was correlated with the principal outcomes (i.e., cervical joint position error and muscle endurance. The correlation analysis applied separately for each group may not respond to the second aim. ). The correct way is using a General Linear Model (GLM). Using the GLM, the authors can check the interaction between group x Beighton scores for each outcome (i.e proprioception, and endurance).
Furthermore, the authors need to check the gender effect in the model (e.g., group x Beighton x gender). To apply the GLM, the author needs to check first the potential assumption violations. Please consider these recommendations and recheck your results.
Experimental design: Line 98. The exclusion criteria need to be expanded. What about the neurological disease and Ehlers-Danlos Syndrome?
Line 112. Beighton score. It’s unclear whether the authors analyzed the dominant or both sides. Please clarify.
Line 114 and 133. Does the same operator make all assessments? Was the operator blinded to the group condition? Please clarify.
Line 135. Would you please give the error of the digital inclinometer used related to a gold standard
(e.g., 3D kinematic analysis).
Line 173. It`s unclear how the post-hoc analysis was made. They are only two groups (with and without neck pain), therefore only one comparison. Did the authors correct the p-value for multi-correlation analysis?
Validity of the findings: Results:
Please consider including figures to show the individual data and a 95 % confidence interval to illustrate the differences observed between groups.
Limitations:
The limitation needs to be expanded. The ideal would have been to have three groups. The lack of a healthy control group makes it difficult to conclude the effects of hypermobility combined with pain on proprioception and muscle endurance.
The association is not causation. Therefore, the authors need to have cautious about the interpretation and extrapolation of the results.
Additional comments: Abstract
Line 23. It does not clear the link between the first and the second sentences. The authors need to give the relevance to study the cervical joint position error and muscle endurance in people with general hypermobility with and without neck pain.
Introduction
Line 63-69. Please consider giving references to each sentence.
Line 68. Please consider using “therefore or consequently” instead of “so.”
Line 153. 2kg need to be separated (2 kg)


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: COMPARISON AND CORRELATION OF CERVICAL PROPRIOCEPTION AND MUSCLE ENDURANCE IN GENERAL JOINT HYPERMOBILITY PARTICIPANTS WITH AND WITHOUT NON-SPECIFIC NECK PAIN—A CROSS-SECTIONAL STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: Clear, with some minor noun-verb agreement and definite/indefinite article problems.
These are listed below by their line number.
Experimental design: Solid and appropriate
Validity of the findings: Findings here are novel and of scientific importance, but a more developed attempt at an explanatory account is needed. This account does not have to be right, just consistent with the current and previous findings, and generative of future research.
Additional comments: The findings in this study on cervical proprioception and muscle endurance in GJH patients with and without neck pain are novel and interesting, combining significant differences between groups and correlational findings regarding the Beighton score. However, the findings have scientific significance beyond the clinical significance that is emphasised in the conclusion, and deserve a more concerted explanatory effort from the researchers here. This additional explanation should also involve consideration of the findings on cervical endurance, proprioception, range of motion and subclinical neck pain reported in the papers by Lee et al [Lee, H., Nicholson, L. L., & Adams, R. D. (2004). Cervical range of motion associations with subclinical neck pain. Spine, 29(1), 33-40.     Lee, H., Nicholson, L. L., & Adams, R. D. (2005). Neck muscle endurance, self-report, and range of motion data from subjects with treated and untreated neck pain. Journal of manipulative and physiological therapeutics, 28(1), 25-32.   Lee, H., Nicholson, L. L., Adams, R. D., & Bae, S. S. (2005). Proprioception and rotation range sensitization associated with subclinical neck pain. Spine, 30(3), E60-E67.]  While this work did not involve GJH participants, it involves similar findings with respect to exactly the same test of cervical endurance, but different findings regarding proprioception, where pain was associated with greater proprioceptive sensitivity.
By including a review of this work, plus some account of the findings here with GJH participants, a more integrated view of the cervical system under stress from hypermobility and pain could be developed.

Specific edits needed:
l.26 to assess (rather than ‘see’)
l.42 Also, a moderate negative correlation …….was found. (currently, there is no verb in the sentence)
l.46 More explanation of this finding is needed
l.57 with women being five times
l.61 more mobility than stability
l.66-68 Previous research? Please cite some at the end of the sentence
l.78 In the literature, researchers have shown that
l.80 These findings suggest that
l.85 2) to assess the strength of the relationship
l.97 Participants were included
l.101 physical therapist’s directions.
l.109 has been used globally
l.112 was the most common
l.118 had to reposition to.
l.127 reaches what he or she thinks
l.130 A single examiner
l.159 2) omit ‘when’, as there is an ‘if’ before 1)
l.296 Pearson’s correlation analysis
 l.217 Table 3
l.221 and to correlate
l.289 may be
l. 304-306 This finding is novel, and deserves more explanation


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: COMPARISON AND CORRELATION OF CERVICAL PROPRIOCEPTION AND MUSCLE ENDURANCE IN GENERAL JOINT HYPERMOBILITY PARTICIPANTS WITH AND WITHOUT NON-SPECIFIC NECK PAIN—A CROSS-SECTIONAL STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: Unfortunately, the authors do not respond to all requirements.
My major issue is about the statistical approach to respond if there is a relationship between GJH Beighton score and cervical JPS scores, neck muscle endurance capabilities in participants with and without NSNP. The authors need to check the interaction between conditions, as well as the interaction between gender. Again, my suggestion is to check if the conclusion of the study is still the same if the author makes a statistical analysis using another approach as General Linear Model. The authors should verify if there is an interaction between group x Beighton scores for each outcome (proprioception and endurance). Furthermore, the authors need to verify if gender influences the result in an interaction between group x Beighton x gender. Finally, the authors need to be sure that there is no statistical error type I in their conclusions.

Minor comments:
Same comment by the first revision. “It`s unclear how the post-hoc analysis was made. They are only two groups (with and without neck pain), therefore only one comparison. Did the authors correct the p-value for multi-correlation analysis?”. Please verify the accuracy of the sentence.
“Post-hoc analysis using the Bonferroni analysis was done for the variables which showed a statistically significant difference”
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: No comment.


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

Input:
Title: COMPARISON AND CORRELATION OF CERVICAL PROPRIOCEPTION AND MUSCLE ENDURANCE IN GENERAL JOINT HYPERMOBILITY PARTICIPANTS WITH AND WITHOUT NON-SPECIFIC NECK PAIN—A CROSS-SECTIONAL STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: The English definite article is used inappropriately on several occasions. I have detailed these.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: In my original review, I asked the authors to look at some work by Haejung Lee and colleagues, on neck extensor endurance and cervical proprioception, to integrate into the current manuscript.
No mention was made of this work, so I thought that the authors could not find it, until I found a paper by Reddy et al (Journal of Bodywork and Movement Therapies, 2021), where, in their section 2.4.2, they stated that the endurance testing protocol that they followed came from Lee et al (2005). So, in the present paper in Line 205 I would ask that the authors acknowledge that the actual source of the testing protocol was Lee et al (2005), as is done in Reddy et al (2021).
Reddy, R. S., Meziat-Filho, N., Ferreira, A. S., Tedla, J. S., Kandakurti, P. K., & Kakaraparthi, V. N. (2021). Comparison of neck extensor muscle endurance and cervical proprioception between asymptomatic individuals and patients with chronic neck pain. Journal of Bodywork and Movement Therapies, 26, 180-186.

In addition, the following specific edits are needed.
Specific Edits:
L.67 No English definite article needed
L.111 to evaluate the relationship
L.150 has been utilized
L.178 No English definite article needed
L.179 No English definite article needed
L.205 test was adapted from Lee et al (2005)
L.265 No English definite article needed
L.279 correlation [not connection]
L.298 no significant correlations
L.311 No English definite article needed
L.325 reflexively
L.326 omit ‘vicious’
L.382 From the results of this study


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: COMPARISON AND CORRELATION OF CERVICAL PROPRIOCEPTION AND MUSCLE ENDURANCE IN GENERAL JOINT HYPERMOBILITY PARTICIPANTS WITH AND WITHOUT NON-SPECIFIC NECK PAIN—A CROSS-SECTIONAL STUDY
Review round: 3
Reviewer: 1

Output:
Basic reporting: The authors have made all suggested changes.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: No comment


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

Input:
Title: COMPARISON AND CORRELATION OF CERVICAL PROPRIOCEPTION AND MUSCLE ENDURANCE IN GENERAL JOINT HYPERMOBILITY PARTICIPANTS WITH AND WITHOUT NON-SPECIFIC NECK PAIN—A CROSS-SECTIONAL STUDY
Review round: 3
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: In line 38 of the revised text, please use the plural noun 'times' and not 'timings''


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: STAGE 2 REGISTERED REPORT: INVESTIGATING A PREFERENCE FOR CERTAINTY IN CONVERSATION AMONG AUTISTIC ADULTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is an excellent and original study, which abides by the standards of pre-registration and data transparency. The topic is timely and the planned analyses are adequate.

I do have some minor suggestions, but most of them are rather optional.

First, there is no particular reason to focus the introduction on Relevance theory. Uncertainty is inherent in any model of pragmatic inferencing; on any notion of pragmatic inference or implicature, the inference at hand is non-monotonic. As far as I can see, the authors' study does not test any hypothesis which would be specific to Relevance theory as opposed to other pragmatic theories. The focus on Relevance theory may also render the introduction less friendly to people in the field of autism or clinical linguistics, who are not necessarily familiar with the details of pragmatic theorising.

Second, since the authors' hypothesis mainly bears on (un)certainty as a source of pragmatic performance in autistic individuals, they may want to test, as an additional analysis, the potential effect of trial (ideally, trial by participant random slopes should included within the models).  (Un)certainty may increase during the task, and group differences could be more visible towards the end of the experiment. In the same vein, it is possible that some autistic individuals use compensatory, more explicit but also more cognitively costly, processing routes, which may, again, have an effect on response along the experiment. (In a traditional experimental setting, such an effect might show up in RTs; my guess is that owing to the online nature of this study, the RTs are rather unreliable. Is this so?)

Third, I'd use violin plots of per-participant average confidence, with superimposed fitted CIs; this would make the individual variation clearer.

Fourth, why not testing accuracy on Grammar and Implicatures tasks using logistic multilevel regressions? This would make the results much more homogeneous and easier to process.

Fourth, in testing Hypothesis 1, the authors should explain explicitly how Group, Task and Response are coded (I assume that they all are dummy coded, but this should be stated). Also, it could be worth running a stepwise, forward or backward model comparison, to clearly determine the contribution of each factor and their interactions to the model fit. Also, I'm not sure I understood why Group in this model is a binomial variable, and does not include participants with reading difficulties.

Fifth, why not including by item random intercepts?
Experimental design: The experimental design is sound. One limitation, but one that is also present in the near totality of the experimental literature on pragmatics in autism, is that the task is meta-linguistic. That is, the authors test how participants understand an exchange as a third party, not whether and how they process an implicature directed at them. This point may be worth discussing in generalising the results to communication difficulties autistic individuals may face in real life.
Validity of the findings: Findings are valid and valuable. See the comment above on result generalisation.
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: STAGE 2 REGISTERED REPORT: INVESTIGATING A PREFERENCE FOR CERTAINTY IN CONVERSATION AMONG AUTISTIC ADULTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The level of presenting the study is overall clear throughout the text. There are, however, a few exceptions. For instance, the abstract fails to convey the findings in a clear and unambiguous way. References to the literature are insufficient and quite limited. There has been a wealth of recent studies (including experimental studies, reviews and meta-analyses) of figurative/non-literal language skills in autism and the evidence is still controversial regarding exactly what might be the main contributing factor in the well-observed problems with non-literal language comprehension on the spectrum, in particular, to what extent structural language skills explain the variance. in this respect, two recent reviews and meta-analyses by Morsanyi & colleagues are worth reviewing for a more balanced picture. The early review by Loukusa & Moilanen (2009) is misrepresented as providing evidence in support of the language problem account. in that study "pragmatic inference weaknesses, but not inabilities, were found throughout the studies. However, researchers did not wholly agree on the reasons and the extent of processing difficulties. The most commonly suggested explanations for pragmatic inference deficits were theory of mind and central coherence."
Recent research on inferencing ability in highly-verbal individuals with autism (Micai & colleagues) suggests also problems with meta-cognitive skills and not clearly differentiating between goals in individuals with autism in comparison to age- and language-matched controls. This may be an additional source of variance for the communication problems. As reflected in these studies, and many other recent studies, the problems for language-matched individuals on the spectrum do not reside as much in lower accuracy. Rather, they are reflected in processing speed and employing different/compensatory strategies.
The structure of the paper is appropriate and the figures and tables are informative.
Experimental design: The paper reports original primary research and is well within the scope and aims of the journal. The research question is well defined, relevant and original and clearly deserves empirical support (as planned for the study). The study is marked by overall rigorous design and consistent with the research question and hypotheses.
Even though the measures collected for the analyses are well described, their role in the analyses is not sufficiently well identified. For instance, results from the ICAR are not reported and not taken into account in the analyses. The same applies to autistic traits/symptomatology as measured on the AQ-10. Often in studies of autism, the latter are included as predictors of performance.
The use of a grammaticality judgement test may be problematic when assessing structural language competence, simply because it is a meta-linguistic task. This deserves being addressed.
What was the role of the 16 explicit response items? How were they analysed? This is probably an overall issue with the design, namely that it did not include an equal number of stimuli requiring explicit, literal interpretation.
Validity of the findings: The results are adequately reported and addressed in the discussion. It also deserves merit reporting and discussing results which do not support the original hypotheses. More in-depth discussion is in order, especially given the gaps identified in introducing the background and context of the study.
Additional comments: This is an interesting and important paper which deserves publication after the critical issues have been addressed.


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

Input:
Title: DISSECTION OF GENETIC ARCHITECTURE FOR TILLER ANGLE IN RICE (ORYZA SATIVA. L) BY MULTIPLE GENOME-WIDE ASSOCIATION ANALYSES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors provided an exhaustive list of references in the place. but lack of recent literature. For example: TIG1 gene，Weifeng Zhang, Lubin Tan (2019), Molecular Plant, 12(8): 1075-1089.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: 1、	Your introduction needs more detail. I suggest that you improve the description at lines 26-28 to provide more justification for your study (specifically, you should expand upon the knowledge gap being filled).
Tiller angle is one of the most important factors affecting rice plant architecture.
	Plant architecture, a collection of the important agronomic traits that determine grain production in rice, is mainly affected by factors including tillering, plant height, leaf shape and arrangement, and panicle morphology. (Yonghong Wang, Jiayang Li. (2005) Plant Mol Biol. Sep;59(1):75-84.)
	Plant architecture, usually referred to as the three-dimensional organization of the aerial part of a plant, is mainly determined by factors including branching (tillering) pattern, plant height, leaf shape and arrangement, and inflorescence morphology (Reinhardt, D. and Kuhlemeier, C. (2002) Plant architecture. EMBO Rep. 3, 846–851. Wang, Y. and Li, J. (2006) Genes controlling plant architecture. Curr. Opin. Biotechnol. 17, 123–129.
2、	lines 60-73: The authors provided an exhaustive list of references in the place. but lack of recent literature. For example: TIG1 gene，Weifeng Zhang, Lubin Tan (2019), Molecular Plant, 12(8): 1075-1089.
3、	There are many errors in the manuscript, such as, Lines 146-147: “positively semi-skewed frequency”, Figure 1. No normal distribution curves, Table 1. “skewness”. Lines 170-171: “Among these QTLs, 13 and 10 QTLs were specifically identified in indica and japonica subpopulations while 14 non-common QTLs were observed in whole population.” Table 3, japonica:9, 15 non-common QTLs. Please check the manuscript carefully.


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: DISSECTION OF GENETIC ARCHITECTURE FOR TILLER ANGLE IN RICE (ORYZA SATIVA. L) BY MULTIPLE GENOME-WIDE ASSOCIATION ANALYSES
Review round: 1
Reviewer: 2

Output:
Basic reporting: Rice is one of the most important crops in the world. Tiller angle is an important factor affecting yield. In this work, Muhammad Abdul Rehman Rashid et al. performed genome wide association analysis by GLM and cMLM for three populations. Thirty-seven QTLs with 93 annotated loci were identified. Among the loci, a known tiller angle controlling locus TAC1 was also identified. The introduction of sequence pooling technique was observed fruitful to screen the 12 significant QTLs with 22 annotated loci. The research method is reasonable and good research results are obtained.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Q1: The paper should analysis protein domain of candidate gene Os10g0412700 and Os01g0621600. And the genes function should be analysis.
Q2. In discussion, the candidate genes Os10g0412700 and Os01g0621600 should be discussed with relevant literature.
Q3. The language and writing of the paper still need to be polished.  For example, there are too many similar sentences between Abstract and Conclusions.


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: DISSECTION OF GENETIC ARCHITECTURE FOR TILLER ANGLE IN RICE (ORYZA SATIVA. L) BY MULTIPLE GENOME-WIDE ASSOCIATION ANALYSES
Review round: 1
Reviewer: 3

Output:
Basic reporting: The research is on QTLs and genes mapping for tiller angle in rice. The manuscript is clear and well-drafted to understand.
The overall structure of the manuscript and raw material provided is unambiguous. The defined problem and hypothesis of the research are well addressed in the results and discussion.
However, some most recent studies on tiller angle genes and QTLs are not cited in the literature review. I suggest to cite the important genes/QTLs including, LAZY2, qTAC-8, TAC-3, TAC-4, TIG1, OsHOX28 etc in this regards
Experimental design: the research belongs to the tiller angle in rice as a model plant that is directly related to the scope of the journal. The research purpose and problem are clearly defined.  the methodology is well explained and the statistical models the clearly explained.
Validity of the findings: The research is replicated multiple times and findings are reproducible. the genetic and phenotypic information is clearly provided.
the conclusion part is well stated.
Additional comments: Additionally, it's observable that there was no recent research of this tiller angle has been cited.
It's highly recommended to add some newer investigations to identify the gap between previous and present studies.


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

Input:
Title: DISSECTION OF GENETIC ARCHITECTURE FOR TILLER ANGLE IN RICE (ORYZA SATIVA. L) BY MULTIPLE GENOME-WIDE ASSOCIATION ANALYSES
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: DISSECTION OF GENETIC ARCHITECTURE FOR TILLER ANGLE IN RICE (ORYZA SATIVA. L) BY MULTIPLE GENOME-WIDE ASSOCIATION ANALYSES
Review round: 2
Reviewer: 2

Output:
Basic reporting: In the first round of review, the authors have made significant changes. Now the draft is much clear and acceptable to publish.
Experimental design: Good enough
Validity of the findings: Experiments are well designed and results are clear and repeatable. Shortly, results are valide.
Additional comments: the authors have made the linguist and technical corrections as suggested.


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: DISSECTION OF GENETIC ARCHITECTURE FOR TILLER ANGLE IN RICE (ORYZA SATIVA. L) BY MULTIPLE GENOME-WIDE ASSOCIATION ANALYSES
Review round: 2
Reviewer: 3

Output:
Basic reporting: The version2 is satisfactor and authors have addressed all my comments.
Experimental design: Well written in v2
Validity of the findings: Valid and statistically robust
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: EXPRESSION OF IER3 IN HEPATOCELLULAR CARCINOMA: CLINICOPATHOLOGY, PROGNOSIS, AND POTENTIAL REGULATORY PATHWAYS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article presents clear, fluid, and technically correct English, with only a few incorrect verb forms that are necessary to be corrected by authors (p.e., -- in the abstract section, line 36 “were used to explored the molecular mechanisms of IER3” explored instead of explore.)
The article includes sufficient references to contextualize the introduction section and to substantiate the discussion of the work.
The Figures and tables are relevant to the work. However, some of there have enough resolution and/or incorrect information necessary to be corrected by authors:
 -- In Figure 1 legend (Figure 1 IER3 protein expression levels in HCC) should be replanted this legend, in this figure is not presented an “expression level” analysis is shown the expression of IER3 in tissue samples of normal liver and HCC by IHC, the analysis of the data of the intensity of the expression is not presented in this caption.
-- In Figure 5, it is necessary to improve the image quality to a major dpi.
-- The 242 line (Fig.3B) must be corrected in the figure caption B and C are in an incorrect order.
The raw data were available.
Experimental design: It is an original investigation under the aims and scope of the journal.
It was Performed with an actual and novel experimental design that interrelates in-silica analysis of gene databases with data obtained from a cohort of patients that allowed obtaining good approximations and answering the questions posed in the design.
Validity of the findings: The approximations obtained from the data analysis are good, the approximations obtained from the data analysis are reasonable, it allows establishing a possible relationship between the RFX5 factor and the IER3 in the context of the HCC.

In the conclusion section line 393 to 395 “RFX5 may bind the IER3 promoter domains and regulate the p53 signaling pathway to promote the incidence and development of HCC” there is not enough experimental data in this work to claim this, is necessary to replant this idea002E
Additional comments: Once the authors have addressed the observations and recommendations described here, I recommend it 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: EXPRESSION OF IER3 IN HEPATOCELLULAR CARCINOMA: CLINICOPATHOLOGY, PROGNOSIS, AND POTENTIAL REGULATORY PATHWAYS
Review round: 1
Reviewer: 2

Output:
Basic reporting: (1) Please check the whole stupid mistakes, such as “Figure 3 (B) sensitivity analysis. (C) Egger’s test.”;
“Figure 1, Fig. 2A.”
(2) The language should be modified. Commercial service or the help of a native English speaker is recommended.
(3) It's a little bit distorted for some figures, such as Figure 3B, 3C. Some of the images have different font sizes, e.g., Figure 5, 6.
Experimental design: (1) For the prognostic analysis, only Kaplan–Meier was performed. Uni-/Multi-factor Cox analyses adjusting other factor are needed for the survival analysis using TCGA, GEO.
Apart from the OS, other types of prognostic status, such as DSS, PFI, should be considered. Only this way, on objective prognostic conclusions can be drawn.
(2) The DEGs and CEGs were obtained from the TCGA? The DEGs from the different datasets of TCGA and GSE may give more reliable information. Additionally, the GSEA should conducted.
(3) Just as stated in discussion, the correlation between IER3 and RFX5 should be analyzed in cellular experiments. The expression pattern of the two proteins can be analyzed in different datasets.
(4) The IHC data of HPA can be considered.
(5) The expression feature of IER3 in different datasets should be analyzed and pooled as well.
Validity of the findings: (1) The detailed P value was not provided in some meta-analysis (such as Figure 3A), Egger’s test (Figure 3B).
(2) After simple check, I did not observe the relatively high expression level in the HCC tissues, compared with paired paracancer tissue. Also, the IHC data of paired cancer and paracancer was not shown. Only two HCC and control data were provided. Since 127 samples were enrolled, the statistical analysis should be performed.
Additional comments: The authors explored the potential correlation between IER3 expression and the clinicopathology, prognosis, and potential regulatory of HCC, based on the collected 94 paraffin masses of HCC and adjacent tissues and 33 cases of normal liver tissues, and the TCGA, GEO public available datasets. The above issues should be concerned.