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: MORPHOLOGICAL AND MOLECULAR DATA CONFIRM THE TRANSFER OF HOMOSTYLOUS SPECIES IN THE TYPICALLY DISTYLOUS GENUS GALIANTHE (RUBIACEAE), AND THE DESCRIPTION OF THE NEW SPECIES GALIANTHE VASQUEZII FROM PERU AND COLOMBIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The writing is usually clear (but the discussion and part of the results should be rewritten) and there is strong evidences (molecular and morphological) supporting the taxonomical work. The literature is cited purposefully. However, the text sometimes overwhelmed the reader with useless details (see e.g. M&M section), while the figures have been rather sloppily prepared (see comments below).

Some subheadings should be modified to reflect their content and the result section should be rearranged (see details comments below).
Furthermore, the text can be simplified and shortened in several places (see some suggestions below).

Part of the results should be rewritten and I will suggest removing the chapter discussion that is unnecessary (as this MS is a taxonomical treatment).
Experimental design: This MS deals with the taxonomy of three plant species, there is no research questions or experimental design to evaluate.
Validity of the findings: no comment
Additional comments: Review of MS for PEERJ – Manuscript ID 18193 – Florentin et al., Morphological and molecular data confirm homostyly in the mainly distylous genus Galianther (Rubiaceae).

The 28th of June 2017

This manuscript deals with taxonomic changes among the “Spermacoce clade” of the tribe Spermacoceae (Rubiaceae). In particular the authors transfer two species Diodia spicata and D. palustris to the genus Galianthe and describe a new species Galianthe vasquezii R.M.Salas & E.L.Cabral from Peru.
The work is mainly based on results found in previous study (i.e. Dessein 2003 and Groeninckx et al. 2009). It provides four new DNA sequences for the species Diodia palustris and uses herbarium-based morphological observations.

The writing is usually clear (but the discussion and part of the results should be rewritten) and there is strong evidences (molecular and morphological) supporting the taxonomical work. The literature is cited purposefully. However, the text sometimes overwhelmed the reader with useless details (see e.g. M&M section), while the figures and part of the text have been rather sloppily prepared (see comments below).

As stated in the review guidelines, I will not comment on the impact and novelty of this study. As this is a MS dealing with the taxonomy of three plant species, there is no research questions or experimental design to evaluate.

It is yet unclear to me if taxonomical treatments are considered as “Research Article” by PEERJ. If yes, my impression is that this taxonomical note should be considered as worth to be published.

However, in my opinion, there are some issues to be addressed before publishing this study.
The authors emphasize, in the MS title, the presence of homostylous species within a mainly distylous genus. But do not discuss the evolutionary implications. They rather treat this biologically interesting phenomenon (see Darwin 1877 book on the different forms of flowers on plants of the same species or the Webb & Lolyd 1986 paper in New Zealand Journal of Botany 24: 163-178 and many others) as a character state.

Therefore, the title does not reflect the work done. I will suggest two options:
The first one: to adapt the title to reflect the work (e.g. Galianthe vasquezii, a new Rubiaceae species from Peru and the transfer of two Diodia species to Galianthe)
The second one: to use the current phylogenetical framework (i.e. the one published by Groeninckx et al. 2009 and the authors’ addition of D. palustre) to discuss the evolutionary implication of homostylous species within a distylous clade. In that case the author should be aware that with only 6 species (out-of the 50 of the genus) their discussion would remain highly speculative.

Additionally some subheadings should be modified to reflect their content and the result section should be rearranged (see comments below).
Furthermore, the text can be simplified and shortened in several places (see comments below).
Part of the results should be rewritten and I will suggest removing the chapter discussion that is unnecessary (as this MS is a taxonomical treatment).

Suggestions and minor issues:

P2, L15 “The remaining species described …” How many species of Dodia were transferred to the different genera.
P2, L18-20. The sentence is unclear. Do you mean that current species of Galianthe subgen Ebelia are all distylous?
P2, L21-28. I would suggest simplifying the whole paragraph, by acknowledging that you follow the work of Dessein (2003) and as a result move Diodia spicata, along with a recently sequenced species (i.e. D. plaustre) to Galianthe. By doing this you also describe a new species  G. vasquezii. (as stated in P2, L30).

P3, L11. Remove “Acronyms according to Index Herbarorium”, as this is obvious.
P3, L11. Change: “were analysed” by “were observed” or “were studied”
P3, L12-13. Are you sure PEERJ allow website citation within the main text? To be checked.
P3 L22-29. Is this necessary? It appears as obvious to me (following the last International Code of Nomenclature for algae, fungi and plants, art 29).

P4, L26-28. I believe you can spare some words here by saying that you “align your sequences with MAFFT and subsequent manual corrections in Geneious”.
P4, L24. change “Data analyses”, by “phylogenetic analyses”

P5, L13. Result section should be reorganized.
The “molecular study” at P15L18 (but I guess you mean “phylogenetic results”) should come first and the “Taxonomic Treatment” second (Because you based your taxonomic treatment on your phylogenetic analyses).
P5, L19. You may want to have the “Description-” subheading here, to be consistent with the following subheading (e.g. Distribution-, Ecology-, Conservation status-, etc.). I cannot recall if a Diagnosis is mandatory for a name to be validly published. You may want to check.
P5, L22. Replace “o” by “or”

P6, L2. What are P= 31 and E =29. You should state to what P and E refer.
P6, L3. “muri nanospinose”, what does this mean? It should be clarified for the readers.
P6, L3. “with notorious papillae” do you mean “conspicuous papillae”?
P6, L6. “caducous.; seed…” remove the “.” (i.e. “caducous; seed…”)
P6, L14. “21 Jul 1944” replace by “21 Jul. 1944”
P6, L15. “15 Dic 1933” replace by “15 Dec. 1933”

Throughout the text, when a month is abbreviated it should be followed by a point.

P6, L23. Change “nov. comb.” by “comb. nov.”

P7, L10-29. Same remarks than above for the subheadings, the P= and E = meanings.
P7, L28. What does “u” means?

P8, L5 to P10, L5. “Additional Specimens Examined” I did not review that part!

P10, L19. Add the subheading “description-”

P11, L5 what does P and E mean?

P11, L17 to P12, L 19. “Additional Specimens Examined” I did not review that part!

P15, L18 to P16, L23. “Molecular Study”: I guess you mean “phylogenetic results” needs to be rewritten in a clearer way. I am lost in your results, which sometimes contradict Figure 4.

A few none-exhaustive comments:
P15, L26. Are the genera unresolved or do you lack of statistical support?
P16, L2, remove the “s” or did you mean “statistical”?
P16, L3 what is a “low supported (40) to unsupported clade”. Is that statistically supported or not? The answer is “statistically not supported”.

I suggest removing the discussion, as this is a taxonomical treatment. Furthermore, It is unclear to me what you are discussing.

Figure 2:
Instead of presenting 2x6 pictures, you may want to present 4x3 pictures.
The caption should be rewritten as follow: Morphological characters distinguishing Galianthe vasquezii (pictures A-F from the Isotype in MO) and G. Palustris (Pictures G-L from A.-A. Cabana 19 in CTES). And then the details of each pictures

Figure 4:
In the caption, replace the “y” by “and”

Figure 5:
In the caption explain what are the numbers above the branches…
I suggest to collapse the branches statistically unsupported. (i.e. <51)


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: MORPHOLOGICAL AND MOLECULAR DATA CONFIRM THE TRANSFER OF HOMOSTYLOUS SPECIES IN THE TYPICALLY DISTYLOUS GENUS GALIANTHE (RUBIACEAE), AND THE DESCRIPTION OF THE NEW SPECIES GALIANTHE VASQUEZII FROM PERU AND COLOMBIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Authors analyzed the taxonomic position of two species that were before assigned to Diodia genus: Diodia spicata and D. palustris; but currently they have been translated to Galianthe genus. They use morphological and molecular data (ETS and ITS). The uncertainty position occurs due to some morphological differences exist between these two species and some Galianthe subgen. Ebelia species, mainly the homostylous flowers. Also authors describe a new species (Galianthe vazquezii) and provide a dichotomous key for taxa with indehiscent mericarps. They conclude that both analyzed species fall among Galianthe species subgen. Ebelia.

The English language of the manuscript is clear and correct. The Intro and background are well supported. Figures are in high quality and are well labeled and describe. However, references along the manuscript don’t seem to follow the PeerJ style (are in cursive font).  Some details in the Intro can help to improve the manuscript.

1.	In the abstract, and along the manuscript, authors mention the phrase: “generic concept” of Galianthe subgen. Ebelia, however in the introduction they never clarify which is this concept. They just mentioned some traits with taxonomic importance. It could be helpful to extend this concept.
2.	In the Intro (Page 2; Line 22-26) authors describe three different taxonomic proposals in order to relocate the taxonomic position of D. spicata and D. palustris. Finally, they decided “to verify the position of…. within Galianthe” genus. It is not clear why they decided to keep the Galianthe hypothesis over the Borreria subgen. Dasycephala hypothesis. Although they mention that species “share most affinities with Galianthe subgen. Ebelia” (Page 2; Line 27), is not clear if the decision is due to is the position currently accepted. They could clarify the point.
3.	Authors mention (Page 2; Line 27-28) that studied species have some differences with other species of the subgen. Ebelia, but they don´t mentioned these differences. It could be clarify with the point 1.
Experimental design: The method used was well defined and analyses are generally appropriate. The design of the morphological and molecular study was based on a good sampling of species of Spermacoce clade, however, it is noticeable that there is just one species of Galianthe subgen. Ebelia. (G. brasiliensis). Although this was correct due to this especies is the type of subgen. Ebelia, it is recommended the use of more species. Molecular markers in general showed well resolution. The methods and results are described with sufficient detail. Some suggestions:

1.	Page 4; Line 9. Authors mention three accession numbers added, but they just report four of them (Page 4; Line 22-23). Check.
2.	Why you don´t use Bayesian inference analyses instead of ML bootstrapping to obtain the posterior probability values as a measure of clade support?.
3.	Page 6; Line 3: be consistent with decimal separators (dots or commas).
4.	 Page 6; Line 6: caducous; (without dot)
5.	 Page 7; Line 27-28: be consistent with decimal separators (dots or commas).
6.	Page 11; Line 5: be consistent with decimal separators (dots or commas).
7.	Page 14; Line 6: x=15, (without dot)
8.	Page 14; Line 12: branch. Brazil. (space)
9.	Page 16; Line 2: an extra “s” Carajasia has moderate.
10.	Page 16; Line 7-9: write values of clade support by each minor clade mentioned.
11.	Page 16; Line 13-14: write values of clade support of Borreria species from the Americas.
12.	Page 16; Line 15-18: Mention values of clade support at least for the two subgroups of Spermacoce.
13.	Page 17; Line 15: “in” or “is”

Figure 5. Could be better if also highlight Borreria and Spermacoce clades.
Validity of the findings: The data and the results are robust and improve the knowledge of the Galianthe genus. The conclusions are well stated, linked to the main question and limited to supporting results.
Additional comments: I consider that the manuscript could potentially become acceptable for publication in PeerJ. Corrections could be considered as minor corrections but they can help to make it easier for the reader.


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: MORPHOLOGICAL AND MOLECULAR DATA CONFIRM THE TRANSFER OF HOMOSTYLOUS SPECIES IN THE TYPICALLY DISTYLOUS GENUS GALIANTHE (RUBIACEAE), AND THE DESCRIPTION OF THE NEW SPECIES GALIANTHE VASQUEZII FROM PERU AND COLOMBIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: This is the second review of this manuscript (previously submitted to PEERJ). This MS deals with taxonomic changes among the “Spermacoce clade” of the tribe Spermacoceae (Rubiaceae). In particular the authors transfer two species Diodia spicata and D. palustris to the genus Galianthe and describe a new species Galianthe vasquezii R.M.Salas & E.L.Cabral from Peru.

The writing is clear and the discussion and results section have been improved. I made some comments below.

Before being published, the MS need to be carefully checked by a native English speaker (I am not in a position to correctly assess this part – but my feeling is that there is room for improvement).

As mentioned in my previous review, the authors emphasize, in the MS title, the presence of homostylous species within a mainly distylous genus. It is a strategy that will attract readers and at the same disappoint some of them because of the absence of discussions regarding the evolutive implications of this finding. Nevertheless, as the authors consider distily/homostly as a morphological character state, it is acceptable.

The aims of the MS need some clarifications.

First, in an unclear sentence (P2L16-17; see suggestion below), the authors say “in this work we studied” … either the genus Diodia or the species with indehiscent mericarps (this is unclear to me). Then, to exemplify their focus, they list four species (P2L18 - namely:  D. bogotensis, D. brasiliensis, D. cymosa, D. hispidula).

Later in the introduction (P2L27-30), they discuss more specifically the position of two related species (D. spicata and D. palustris).

Then (P3L1-2): “As for Diodia spicata, Dessein (2003) proposed to transfer it to Galianthe based on molecular data, pollen grains (double reticulum), and fruit morphology”. Followed by “the aim of this work is to verify the position of D. palustris and D. spicata within Galianthe based on molecular and morphological data.”

The problem is that Dessein (2003) already did it. Thus (as mentioned in my previous review), I believe that the aim of the paper is rather the taxonomical transfer of D. spicata (along with its close relative D. palustris) to Galianthe. Which, by the way, is a honourable, perfectly publishable, aim.
Now, what about D. bogotensis, D. brasiliensis, D. cymosa, D. hispidula nothing is mention in the M&M or the Result sections about those four species?!?

Additionally, before publishing this MS, I recommend the authors to go through the text again and make clearer that they consider distyly (respectively homostyly) as a morphological character state (see e.g. comments below).
In some instance homostyly or distyly is presented e.g. like a syndrome (P1L28) but without explicitly mentioning a syndrome of what? Or as “scarcely manifested” (P18L22) - what does this mean?
Experimental design: Because this MS deals with the taxonomy of three plant species, there is no research questions or experimental design to evaluate.
Validity of the findings: the data support very well the taxonomical changes made by this paper.
Additional comments: Review of MS for PEERJ – Manuscript ID 18193 – Florentin et al., Morphological and molecular data confirm homostyly in the genus Galianthe (Rubiaceae), based on the new species G. vasquezii from Peru and the two new combinations of Dioda species.

The 9th of September 2017

This is the second review of this manuscript (that have been previously submitted to PEERJ). This MS deals with taxonomic changes among the “Spermacoce clade” of the tribe Spermacoceae (Rubiaceae). In particular the authors transfer two species Diodia spicata and D. palustris to the genus Galianthe and describe a new species Galianthe vasquezii R.M.Salas & E.L.Cabral from Peru.

The writing is clear and the discussion and results section have been improved. I made a few comments below.

The MS need to be carefully checked by a native English speaker (as I am not in a position to correctly assess this – but my feeling is that there is room for improvement)

I am not commenting on the impact and novelty of this study. Because this MS deals with the taxonomy of three plant species, there is no research questions or experimental design to evaluate.

As mentioned in my previous review, the authors emphasize, in the MS title, the presence of homostylous species within a mainly distylous genus. It is a strategy that will attract readers and at the same disappoint some of them because of the absence of discussions regarding the evolutive implications of this finding. Nevertheless, as the authors consider distily/homostly as a morphological character state, it could be acceptable.

The aims of the MS are not clearly presented.

First, in an unclear sentence (P2L16-17; see suggestion below), the authors say “in this work we studied” … either the genus Diodia or the species with indehiscent mericarps (this is unclear to me). Then, to exemplify their focus, they list four species (P2L18 - namely:  D. bogotensis, D. brasiliensis, D. cymosa, D. hispidula).

Later in the introduction (P2L27-30), they discuss more specifically the position of two related species (D. spicata and D. palustris).
Then (P3L1-2): “As for Diodia spicata, Dessein (2003) proposed to transfer it to Galianthe based on molecular data, pollen grains (double reticulum), and fruit morphology”. Followed by “the aim of this work is to verify the position of D. palustris and D. spicata within Galianthe based on molecular and morphological data.”
The problem is that Dessein (2003) already did it. Thus (as mentioned in my previous review), I believe that the aim of the paper is rather the taxonomical transfer of D. spicata (along with its close relative D. palustris) to Galianthe. Which, by the way, is a honourable, perfectly publishable, aim.
Now, what about D. bogotensis, D. brasiliensis, D. cymosa, D. hispidula nothing is mention in the M&M or the Result sections about those four species?!?

Furthermore, before publishing this MS, I recommend the authors to go through the text again and make clearer that they consider distyly (respectively homostyly) as a morphological character state (see e.g. comments below).
In some instance homostyly or distyly is presented e.g. like a syndrome (P1L28) but without explicitly mentioning a syndrome of what? Or as “scarcely manifested” (P18L22) what does this mean?

Further comments and suggestions:

Title:
P1L2: change “Peru and the two new…” with “Peru and two new….”

Abstract:
P1L18 and L27 are in contradictions - e.g. L27 mention, “bifid stigmas and indehiscent mericaprs” has morphological characters supporting the position of Dioda palustre and D. spicata within Galianthe. But those characters are not “diagnostic features” of the genus as listed on L18-21.
P1L28. Is homostyly a syndrome? If yes a syndrome of what? Has, within this paper, homostyly is considered soly as a combination of morphological character (because there is no references to its evolution implications – in particular the transition from outcrossing to selfing. I will suggest modifying this sentence to make it clearer.

Introduction:
P2L14. “Galianthe was linked to Diodia” how was it linked and by whom? Later you say: “due to certain morphological similarities”. I would avoid this imprecise phrasing and state immediately what “link” those two genera.
P2L16-17. It is not clear to me if the authors focus on the genus Diodia or on the indehiscent mericarps?
P2L17-18. What about all those species you mentioned? Where are they now? Should they be moved to Galianthe? This is very confusing. I though that you were focusing on only two species. Why then didn’t you add those species to your phylogeny?
P2L21. “numerous” please indicate how many are “numerous”
P2L25 “several”, please be more precise and indicate how many.
P3L1. Please indicate on what bases (which morphological or molecular data) Delprete transferred those species to Spermacoce.
P3L2-4. About the aims of the paper: you state, “The aim of this work is to verify the position of D. palustris and D. spicata based on molecular and morphological data”. But this has already been done by Dessein (2003) (at least for D. spicata). Thus what are your aims? I believe (as suggested in my previous review) that your aims are to do the taxonomical transfer of D. spicata along with its close relatives to Galianthe.

Key to Galianthe species:
P16L1. I would avoid mentionning chromosome numbers in the key. This character is not observable in the field.
Furthermore, very few is known about the karyology of this group and it might well be possible that a lot of variation (e.g. aneuploidy, dysploidy, along with polyploids) occurs. Too few material have been studied in this genus to provide reliable results.

Discussion:
P18L22 what does “scarcely manifested” means. Is it distylous or not? Please explain in more details what you mean. Is that an intermediate state (a transitional state?) from distyly to homostyly (or the inverse)?
P18L13. Change: “the transference of” by the “the transfer of”

I hope those comments may be useful to the authors.


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

Input:
Title: MORPHOLOGICAL AND MOLECULAR DATA CONFIRM THE TRANSFER OF HOMOSTYLOUS SPECIES IN THE TYPICALLY DISTYLOUS GENUS GALIANTHE (RUBIACEAE), AND THE DESCRIPTION OF THE NEW SPECIES GALIANTHE VASQUEZII FROM PERU AND COLOMBIA
Review round: 2
Reviewer: 2

Output:
Basic reporting: Authors have included most of suggestions made before. The manuscript has been improved significantly.
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: MODUS OPERANDI AND AFFECT IN SWEDEN: THE SWEDISH VERSION OF THE REGULATORY MODE QUESTIONNAIRE
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The article is well written, clear and respects the professional standards of structure, introduction and background, literature references, ethical issues. It is an article well-founded theoretically, with a clear and precise objective. It was intended to verify the independence of the two regulatory modes and the psychometric properties of RMQ in the Swedish context. These objectives have been achieved in an appropriate manner. No flaws were found in the experimental design, although the student-only sample could be improved. However, for the validation of the scale is a correct sample. The discussion section is very interesting and complete. The study will serve to improve the literature on this topic.The section Limitations and suggestions for future research is very extensive, even in some moments the wording is unclear. I suggest reviewing this section.


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: MODUS OPERANDI AND AFFECT IN SWEDEN: THE SWEDISH VERSION OF THE REGULATORY MODE QUESTIONNAIRE
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript investigated two regulatory modes using structural equation modeling. The manuscript is well-organized. However, the statistical analyses need improvement.
Experimental design: Structural equation models presented on Page 14 need to be further specified before any analysis. The model specification is usually guided by a combination of theory and empirical results from previous research.
Validity of the findings: It would be helpful to present a table of parameter estimates (i.e. standard deviation, test statistics) and equation models for the SEM.
Additional comments: Summary

This manuscript investigated two regulatory modes using structural equation modeling. The manuscript is well-organized. However, the statistical analyses need improvement.

Major comments
1.	Preliminary analysis
In the abstract, there were 5 participants did not report their gender. However, the percentage of male is much higher than female. That difference may lead to selection bias. Can the authors explain the data? In addition, preliminary descriptive statistical analysis such as collinearity issue and outlier detection need to be conducted carefully.

2.	Model
Structural equation models presented on Page 14 need to be further specified before any analysis. The model specification is usually guided by a combination of theory and empirical results from previous research.

3.	Results
It would be helpful to present a table of parameter estimates (i.e. standard deviation, test statistics) and equation models for the SEM.


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: MODUS OPERANDI AND AFFECT IN SWEDEN: THE SWEDISH VERSION OF THE REGULATORY MODE QUESTIONNAIRE
Review round: 1
Reviewer: 3

Output:
Basic reporting: No comment.
Experimental design: It seems that the analysis combines the university and high school students. I did not get any good sense as to why this was done. It is not clear whether separate analysis should be done for these two groups of students or not. Some clarification is needed.
Validity of the findings: No comment.
Additional comments: 1. Some sentences are repeated word by word: the sentence ``However, other values (the goodness of fit index and the root mean square error of approximation) indicated that the hypothesized model fits the data well.’’ appears in line 235-236 and again in lines 253-255.

2. Related to the previous point, what are these values (the goodness of fit index and the root mean square error of approximation)? Please report the numbers.


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: MODUS OPERANDI AND AFFECT IN SWEDEN: THE SWEDISH VERSION OF THE REGULATORY MODE QUESTIONNAIRE
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The authors have taken into account the suggestions and recommendations that the reviewers have indicated in their reports. The article may be published.


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: MORPHOLOGICAL CONVERGENCE IN ‘RIVER DOLPHIN’ SKULLS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Summary: Charlotte E Page and Natalie Cooper present a 2D geometric morphometric analysis of odontocete skulls with the aim of testing for convergence in river dolphins. The dataset contains 24 species with between 1 and 5 individuals of each species. The methods appear sound and thorough e.g. the checks of repeatability and multiple tests of convergence. I have a number of issues with the reporting that I think should be improved prior to publication.

Line edits:

Title: the sub title “a disparate grouping justified” generates a little confusion because the term “disparate” is often used to describe morphologically dissimilar species. Please consider rephrasing to a clearer title.

Line 6: I think the novelty of this study is overstated within the abstract. You state: “This has led many to using the ‘river dolphins’ as an example of convergent evolution. However, these morphological similarities have never been quantified.” McCurry et al. 2017a quantifies morphological similarities between a wide range of crocodilians and odontocetes, including each of the river dolphin species.
Please re-write the introduction as to clarify what the knowledge gap is, and how this study fills it.

Line 13: “The cause of this morphological convergence remains unclear, but our results support hypotheses of shared feeding mode or diet and thus provide the foundation for future work into convergence within the Odontoceti.”
Please state exactly how your results support hypotheses of the cause of convergence?

Line 24: Why is the “tree of life” written in Caps?

Line 42: “One iconic example of convergent evolution is in the ‘river dolphins’, a group of distantly related cetaceans that secondarily entered river systems from the ocean, evolving riverine lifestyles and similar morphological characteristics (Hamilton et al. 2001).”
The term “river dolphin” is more convoluted than this. Pontoporia is not a riverine species, inhabiting both estuaries and oceanic environments. Furthermore, some dolphins outside of the “river dolphin” grouping are found in riverine environments e.g. Sotalia fluviatilis. Please rewrite this section in a way that describes the complexity of habitat similarities/differences.

Line 62: “Here we present the first quantitative investigation of the morphological variation present in the skulls of river dolphins, and quantify whether the four river dolphin genera are convergent.”
This statement ignores past work, please fit Barroso et al. and McCurry et al.  into the introduction and explain what you do differently to these studies.

Line 75: What do you mean by “equally closely related to river dolphins”, this needs more clarification. Why did you include the species that you did?

Line 76: “we photographed specimens across all Odontoceti” please state the number of species sampled here, otherwise it sounds like you sampled all species within the group. You could even include an odontocete tree showing which species were sampled and the sample size for each species?

Line 78: “Sexual dimorphism varies among odontocete genera, being present in some species as differences in size, but with no differences in shape between sexes recorded (Amaral et al. 2009; Higa et al. 2002). We therefore chose males and females from different collection locations where possible to provide a representative sample of each species.”
This is confusing, do you mean that some species have sexual dimorphism in size and other have differences in morphology? Or that only differences in size exist? Some odontocetes do show variation in cranial morphology dependant on sex e.g. Mesoplodon (Besharse 1971), monodon etc..
Please rewrite to clarify.
Besharse, J. C. (1971). Maturity and sexual dimorphism in the skull, mandible, and teeth of the beaked whale, Mesoplodon densirostris. Journal of Mammalogy, 52(2), 297-315.

Line 106: Please state here that it was 2D GMM that was used.

Line 109: Which “putatively convergent features”? Please provide more detail.

Line 133 Is there a full stop missing after the reference?

Line 225: “Mandibular PC1 describes variation in the elongation of the mandible resulting in an elongation of the rostrum, symphysis and alveolar tooth row (Figure 4D)”.
The word use of the word “resulting” here inappropriately implies cause/effect.

Line 253: The four genera seem to have experienced evolution in the same direction.
Consider rephrasing to “evolved similar skull shapes”.

Line 296: What are the limitations/benefits of 2D vs 3D GMM? Please consider adding this to this paragraph.

Line 299: “Skeletals s” is a typo.

Line 313: “Here we have presented the first quantitative investigation into convergence in the river dolphins.”
As stated earlier, this is not the first study to use GMM on a sample including river dolphins, or to identify convergence.

Figure 2: Why used A and B for both the panels and the curves. Consider changing to lower case letters to identify curves or even C1, C2 etc.
Experimental design: Generally, the experimental design and use of methods is sound. However, in the introduction and conclusions the study makes several untrue claims about being the first to quantify variation in river dolphin skull shape (e.g. Line 7, Line 62, Line 313).

Several studies have quantified variation in odontocete skull shape, including river dolphins. For instance, Barroso, Cranford, and Berta (2012) identified a river dolphin morphotype in mandible shape. Also, McCurry et al. (2017a) identified a river dolphin morphotype, tested for convergence and discussed the cause of this convergence. Neither of these were cited in your introduction, but appear later in your discussion.

There are several differences in your approach and sampling that allow your study to fill a knowledge gap, but being the “first quantitative investigation of the morphological variation present in the skulls of river dolphins” is not one of them. Please rewrite your introduction and conclusions as to better identify a knowledge gap and alter your conclusions in relation to this.
Validity of the findings: Overall, I think that the conclusions are scientifically sound and supported with enough evidence.

As stated above, and in the line edits, I think that the rational, benefit to the literature and conclusions need to be re-written.

As stated in the line edits I think there needs to be more clarification of why the species sampled were sampled.
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: MORPHOLOGICAL CONVERGENCE IN ‘RIVER DOLPHIN’ SKULLS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper is generally clear and easy to follow. There is some detail lacking at times, but generally I see no issues with language or clarity of the text.

Figures 3 & 4 are hard to read. The dots are quite small, and don’t contrast from the other elements well enough. Correcting this would make the figures much clearer.

In Figure 2, I think it would be more helpful to show the placement of the semi-landmarks, as opposed to the outline only
Experimental design: The introduction is centred on the principle that morphological convergence in river dolphins as never been quantitatively assessed, however this has been done by other studies to some extent (Werth 2006; Barroso et al. 2012; Kelley and Motani 2015; McCurry et al. 2017a, b). In particular, the recent study by (McCurry et al. 2017a) was centred not only on the convergence between river dolphins, but also with crocodiles sharing a similar ecology. I suggest a better way to phrase this would be to state that although this has been done, a detailed analyses of the cranial features that converge (or not) in river dolphins is still lacking. This would also be more in line with the guidelines of the journal, of emphasising a gap in current knowledge rather than the novelty of a study per se.

Lines 98-99: there is usually more variation in the dorsal side of odontocete skulls than in the ventral, so the authors need to justify why this analyses focus only on the ventral side. I think I know why, but best to be explicit and clear so readers don’t have to guess.

References

Barroso C, Cranford TW, Berta A (2012) Shape analysis of odontocete mandibles: Functional and evolutionary implications. J Morphol 273:1021–1030. doi: 10.1002/jmor.20040

Kelley NP, Motani R (2015) Trophic convergence drives morphological convergence in marine tetrapods. Biol Lett 11:20140709. doi: 10.1098/rsbl.2014.0709

McCurry MR, Evans AR, Fitzgerald EMG, et al (2017a) The remarkable convergence of skull shape in crocodilians and toothed whales. Proc R Soc B Biol Sci 284:20162348. doi: 10.1098/rspb.2016.2348

McCurry MR, Fitzgerald EMG, Evans AR, et al (2017b) Skull shape reflects prey size niche in toothed whales. Biol J Linn Soc 121:936–946. doi: 10.1093/biolinnean/blx032

Werth AJ (2006) Mandibular and Dental Variation and the Evolution of Suction Feeding in Odontoceti. J Mammal 87:579–588. doi: 10.1644/05-mamm-a-279r1.1
Validity of the findings: I don’t think these results show independent convergence between all individual river dolphin lineages as implied, but rather convergence between Platanista and all other river dolphins. From the phylogenetic vs phenetic tree comparisons, only Platanista shifts its position relative to other river dolphins. These also group together in the molecular tree, so their placement is largely consistent in the phenetic tree.

The section where the possibility of plesiomorphy is discarded is not well justified. It’s not that the authors are not right in dismissing it necessarily, just that they don’t provide a convincing argument for it. I suggest the authors present more details to explain their position.

Lines 62-63: as per guidelines of PeerJ, statements like this highlighting the novelty of a study should be avoided. Also, please note my comments above as to why I feel this is not strictly true.
Additional comments: Overall, I think the manuscript is well written, and focus on an interesting scientific question regarding morphological evolution in cetaceans. The data analysis appears to be done competently, although I would like a bit more consideration of the phylogenetic uncertainty in molecular studies of river dolphins.

However, I think the narrative is slightly inconsistent as the paper states in the introduction this has never been done, and then cite in the discussion earlier papers that already suggested it. I think the paper would be much improved if the authors focused on the details of which aspects of the morphology change more, and how these fit with possible mechanisms driving the convergence. For this, I think it would be useful if the author could analyse the dorsal side of the skulls, where most of the variation is likely to be found.

Therefore I’m recommending the paper be rejected in its current form, but encourage a resubmission as the authors have the data to allow a more interesting analyses to be presented. In addition, please find below some minor comments on formatting and wording:

Lines 118-119: (McCurry et al. 2017a, b) also carried out GMM analyses on mandibles. This must be acknowledged

Lines 57-58: The authors probably mean cervical vertebrae, not caudal.  Also, references to Figure 1B are not entirely appropriate, as Figure 1B does not show the vertebrae.

Lines 75-77: the phrasing here is unclear. It suggests that all species were photographed, but this is clearly not the case from the list in the supplementary material. If the authors meant that the specimens analysed cover all the odontocete families, then they need to specify that the family Kogiidae is also not represented.

Lines 81-83: Please specify how individual specimens were determined as being full grown adults.

References

McCurry MR, Evans AR, Fitzgerald EMG, et al (2017a) The remarkable convergence of skull shape in crocodilians and toothed whales. Proc R Soc B Biol Sci 284:20162348. doi: 10.1098/rspb.2016.2348

McCurry MR, Fitzgerald EMG, Evans AR, et al (2017b) Skull shape reflects prey size niche in toothed whales. Biol J Linn Soc 121:936–946. doi: 10.1093/biolinnean/blx032


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: DEVELOPMENT OF MEDICAL INFORMATICS IN CHINA OVER THE PAST 30 YEARS FROM A CONFERENCE PERSPECTIVE AND A SINO-AMERICAN COMPARISON
Review round: 1
Reviewer: 1

Output:
Basic reporting: This paper is well structured and written.
Experimental design: The data used in this paper cover 30 years. The results are comprehensive and constructive.
Validity of the findings: Review the progress of medical informatics in China over the past 30 years to summarise the gains and losses even give constructive suggestions for future development is an important task for the whole country.
Additional comments: To show the development and do a comparison from a conference perspective, especially academic conferences, it would be better to show the impact of the precedings. An impact can be the number of citations or downloads of the publications of a conference.


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: DEVELOPMENT OF MEDICAL INFORMATICS IN CHINA OVER THE PAST 30 YEARS FROM A CONFERENCE PERSPECTIVE AND A SINO-AMERICAN COMPARISON
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English language in the manuscript should be improved. Others are fine.
Experimental design: No comment
Validity of the findings: Data is statistically sound and controlled. Conclusion are well stated.
Additional comments: In this manuscript, the authors compared four main Midical Informatics (MI) conferences held in China, and two main MI conferences held in USA from different perspectives. Some conferences are more industry-oriented, and some are academy-oriented. The authors concluded that, the conferences reflected that the Midical Informatics discpline in China is behind of that in USA, either in participants or topics involved. The content of the manuscript is informative, while the English language needs to be improved.

The followings are some specific points in the manuscript.

1) Something is wrong in the lines 88-90. The market was "23.7" billion US dollars. After 5 years, it will shrink to "14.5" billion US dollars.
In 2015, the market of hospital informatics alone reached 23.7 billion US dollars; by 2020, this market is projected to exceed 14.5 billion US dollars, at an annual compound growth rate of ≥ 24%

2) line 160: "choose" should be in the past tense "chose". Similar for many other verbs

3) lines 271-275: It is better to list "health administrative authorities" as a specific category for the comparison purpose. If it is treated as  "other", it is difficult for the readers to identify the difference from the Figures.

4) line 276: what's the meaning of SCMI?

5) The last Figure is Figure 7, while the figure legend is Figure 6(b). Need to be corrected.


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: DEVELOPMENT OF MEDICAL INFORMATICS IN CHINA OVER THE PAST 30 YEARS FROM A CONFERENCE PERSPECTIVE AND A SINO-AMERICAN COMPARISON
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: The 2020 estimate of the market volume (p.6) seems to be either miscalculated or mistyped.
I suggest to be more specific in Results and Conclusions of the Abstract.
Most of the figers and half of the tables don't touch USA MI therefore I suggest to exclude "the Sino-American comparison..." from the paper's title and to compare Chinese conferences in more detail.
P.12: The high variability in the paper's quality is intuitively acceptable but not proved. The low acception value may indicate the funding bias as well. Therefore I suggest to decrease the level of confidence when stating the conclusions about this.
Additional comments: I liked the paper: the authors managed to address an important issue by simple and transparent methods. The paper is written in excellent English and I've read the Appendix with special interest.


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: DEVELOPMENT OF MEDICAL INFORMATICS IN CHINA OVER THE PAST 30 YEARS FROM A CONFERENCE PERSPECTIVE AND A SINO-AMERICAN COMPARISON
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comments
Experimental design: no comments
Validity of the findings: no comments
Additional comments: In this revised version, the authors add a new part about preceding impact. The new finding from impact perspective is consistent with the conclusion of the whole paper. I feel this work meets the criteria as a research publication and suggest to accept this paper.


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

Input:
Title: DEVELOPMENT OF MEDICAL INFORMATICS IN CHINA OVER THE PAST 30 YEARS FROM A CONFERENCE PERSPECTIVE AND A SINO-AMERICAN COMPARISON
Review round: 2
Reviewer: 2

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: GENOME-WIDE SURVEY OF SINGLE-NUCLEOTIDE POLYMORPHISMS REVEALS FINE-SCALE POPULATION STRUCTURE AND SIGNS OF SELECTION IN THE THREATENED CARIBBEAN ELKHORN CORAL, ACROPORA PALMATA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Durante and Baums report on the genetic diversity and population genetic relationship of the coral Acropora palmata from a portion of this species' distribution in the Caribbean.  The overall presentation is clear and the tables and figures are of good quality.  The authors compare results from a small panel of microsatellite loci with genome-wide SNPs derived from genotype-by-sequencing.  The authors suggest these results are important for considerations regarding coral connectivity and management.  Overall, I found the description of the methods, thoroughness of the analysis and interpretation of the results to be quite limited.  The shortcomings of microsatellite analysis, particularly of small number of loci, are now generally known and likelihood of detecting selection with confidence (as opposed to genetic drift or demographic impacts) is even more limited with a relatively low sample size from each location.  The RAD-tag data could be utilized more effectively to address some of the authors hypotheses, particularly about relationships of individuals and populations with respect to geographic hypotheses related to the Mona Passage.
Experimental design: The experimental design is adequate by genotyping individual corals from a number of locations.  I detail major concerns below as well as indicate positions in the manuscript where additional clarification would be useful.

1. RAD-tag methodology.  The authors should provide additional details and support for their approach to RAD-tag.  It is unclear from the current text how the libraries were pooled and sequenced (Lines 132-135).  In Lines 163-166 it would be helpful for the authors to provide references and support for these filtering steps.  It is unclear how and why the authors came to the decision to only use loci present in at least 60% of individuals and a minor allele frequency of 0.05.  Similarly, I also found it surprising the authors only used STRUCTURE based approaches when addressing individual data.  Why did the authors not use phylogenetic based methods to look at relationships of individuals across the sites?  The 5X coverage is alarmingly low (which the authors acknowledge on Line 335) for interpreting their results and I would suggest the authors compare results using a data with lower and greater coverage (based on Figure 1).

2. Mantel tests and environmental data.  The authors correlate the FST values with geographic distance and a combination of environmental data.  The authors should provide a methodology for how the geographic distance was determined and support for their approach.  The environmental data comparison is an interesting comparison but the value of the confidence in these correlations appears suspect.  The authors note (Line 280-282) that these environmental data are coarse, which suggests to this reviewer they could be misleading when compared with the geographic distance as a potential explanation for the genetic differences between populations.
Validity of the findings: There are a few places in this manuscript where the findings could be described more clearly or in a more balanced way.

1.  Outlier analyses and results.  The identification of one microsatellite locus as under potential selection was interesting but given the low number of loci investigated it is difficult to interpret the confidence in this determination.  The authors used standard approaches for detecting potential SNPs under selection but the results from these are equivocal.  The different methods produced largely unique sets of potential SNPs and the authors should provide an explanation for this difference.  Detecting regions of the genome under selection is difficult and I think these results would suggest the possibility that they are false positives.  When combined with the data that these loci do not strongly match to any transcribed parts of the genome I would suggest these data and the corresponding Discussion section were removed from the manuscript.

2. Genetic diversity comparisons.  The authors invest a significant portion of the Discussion on comparisons of genetic diversity between animal species.   These comparisons should be prefaced with a number of caveats about where these numbers were derived (i.e., lab strain, population-averages, etc.).  More importantly, in Lines 372-375, the authors correctly state that their estimate from this species could simply be due to the small sample size.  This would be a more parsimonious explanation.  I think putting in this explanation (a technical one based on methodology) at the end of a more complex biological explanation is not a balanced discussion.
Additional comments: Small comments and suggestions

Table 3.  Fis should have capitalized "is"

Figure 2 and 3.  I would suggest the authors have a STRUCTURE analysis of with and without SNPs potentially under selection, similar to the microsatellites.  Also, the authors should include a STUCTURE analysis of the microsatellite data when comparing only the same sites and individuals as used for SNP analysis.

Figure 4.  Please check the figure legend for this figure.  I assume panel (b) is also microsatellite data but not clear from the legend.  Also, please label y-axis on panel (d).

Supplemental Table 3.  It is unclear why some of the sequences in this table have "Ns".  I am concerned that these positions were called as SNPs although they are apparently not identified base positions.


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: GENOME-WIDE SURVEY OF SINGLE-NUCLEOTIDE POLYMORPHISMS REVEALS FINE-SCALE POPULATION STRUCTURE AND SIGNS OF SELECTION IN THE THREATENED CARIBBEAN ELKHORN CORAL, ACROPORA PALMATA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The two data files in Supplementary Info that involve microsatellite calls "...STRUCTURE.txt" are unreadable, formatting problem.

In general the paper is well-written but there are a few ways in which it could be clarified.

1. the abstract mentions "an extended set of 12 microsatellite markers" but in Introduction authors refer to "...structure derived from ten and eleven microsatellite loci." First of all, address the mismatch between the 11 loci that were examined and the abstract. Second, to put this ambiguity at the end of the introduction was confusing and unnecessary. My understanding from the rest of the paper is that all of these samples were genotyped at 11 loci - and any dataset may have some missing data, after all - and then in the present analysis one of those loci was determined to be an outlier, so the analysis was repeated using only the 10 non-outlier loci. This is also quite typical, so it will make more sense if you say you used 11 loci, and then re-analyzed after the outlier analysis.

2. another confusing way this was written - Methods/Library Preparation you discuss concentrations without complete units, e.g. ng should be ng/µl, and then "Samples were pooled into four libraries..." please make it clearer that all libraries (individual coral colonies) are uniquely barcoded, to distinguish this from pooled-RAD-seq in which Fst can be determined but not individual-level statistics. This was confusing to me at several points in the manuscript.

otherwise the Intro/background writing is good and supports this paper well. There are places in the Results, e.g. lines 280-285, that are probably more appropriate for the Discussion section of the paper.

Table 1 explain the distinction between A (SNPs) and B (microsatellites) in the legend. Also explain the missing latitude/longitude data?
Experimental design: Experimental design and question are straightforward. A large dataset of individuals with 10 microsatellites are analyzed in the context of a RAD-seq study on a subset of these individuals from 4 primary geographic regions. This analysis allows the determination of any outlier (perhaps locally adapted) diversity, and re-assessing hypotheses of spatial variation in Acropora palmata. For some readers who are less familiar with this region/system, a map may be helpful to distinguish between the competing hypotheses. Genotyping, sequencing, and bioinformatic approaches are typical and appropriate.
Validity of the findings: The overall result - concordance of SNP and microsatellite data once outlier loci are removed and considered separately - is a useful contribution to understanding spatial distribution of diversity in Acropora palmata and other species in the region. Clarifying some of the reporting/writing as mentioned earlier will make these results make better sense to the reader; again I think a map contrasting the hypotheses and the results in this paper may be of value.

Make clear where the Supplementary Figure fits into the general story - that is the IBD analysis when all 11 loci are used, not referred to in manuscript. All the IBD tests are relatively weak with only 6 data points (pairwise contrasts) but with the Structure analyses this is a working hypothesis for the pattern of diversity until more data come along. The argument in lines 280-285 should move to Discussion, but I also don't agree that the spatial scales are so distinct - if the environmental data have spatial resolution of 0.25-1° latitude, that is about 28-111km, not so disparate from the spatial separation of reefs within the 4 regions? So please clarify that argument perhaps with more information on those spatial separation distributions.

I would also consider Meirman 2012 when evaluating the approach to IBD, the consideration of outlier loci under an island model, and so on for interpreting these results at this scale.

The second paragraph under "Genetic diversity indices in A. palmata" is confusing. You are mixing diverse summary statistics, and it isn't clear until late in the paragraph why the specific examples are being chosen - there are many 1000s of estimates of nucleotide diversity in metazoans, and even synthetic analysis across multiple cnidarian species. The contrast with the Romiguier paper starts to clear up what your goal was with those paragraphs, ostensibly to tie observed diversity with known life history to suggest that diversity is quite low in this particular species, which may be an effect of recent devastating losses in A. palmata among other things. I would clarify these paragraphs tremendously, recognize that this type of comparison is common especially in the plant literature (e.g. older work by Hamrick and Godt), but that of course every species has idiosyncratic issues driving their diversity. So just make it more apparent up front what this paragraph/section is attempting to communicate.
Additional comments: Overall a nice contribution that will be a useful resource for Caribbean biogeography and coral diversity projects in the future once it is improved and clarified.


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

Input:
Title: GENOME-WIDE SURVEY OF SINGLE-NUCLEOTIDE POLYMORPHISMS REVEALS FINE-SCALE POPULATION STRUCTURE AND SIGNS OF SELECTION IN THE THREATENED CARIBBEAN ELKHORN CORAL, ACROPORA PALMATA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article is mostly written in clear professional english. There are some parts where grammar needs to be corrected to improve clarity:

- Line 22. Suggest substituting the word 'place' for 'infer'.
- Lines 37-39. Should be split into two separate sentences.
- Line 52. 'permitting agencies'? should it be 'managers' instead?
- Lines 62-63. Not clear meaning
- Lines 91-94. Statements are redundant
- Line 163. 'More' than what?
- Line 172. Replace 'within' with 'in'
- Lines 251-253. This sentence is awkward, suggest splitting in two to make more clear.
- Lines 330 - 334. Sentences are contradictory, not sure what the overall message here is.

The literature references are appropriate, however, given the emphasis on the authors place on the novel use of RAD markers in corals, these results should be placed in a broader context of studies that have used this technic in other animals, particularly invertebrates and non-scleractinian anthozoans.

The results are relevant to test the population structuring hypothesis presented (Mona Passage as a location of major genetic discontinuity)

The article is wells structured. Figures and tables are appropriate, however, Figure 1 should be supplementary as it does not contain critical information to deliver the main message of the paper.

Specific comments:

- Tables 1 and 4. Define in legend what A) and B) indicate

-Figure 3. Is not clear what each pane represents. There are references to (a-c), (d-f) and (D-E). Please make sure it is clear how they are grouped
Experimental design: The article constitutes an original contribution to our understanding of the mechanisms that structure the genetic diversity of species in the ocean. It also provides a nice example where a previous result is reevaluated and updated through the use of newer methods that increase resolution and accuracy. As such, this manuscript nicely fills a knowledge gap in marine biology with conservation implications.

The research was conducted to an acceptable technical (see comments below) and high ethical standard. The methods are described in detail, however it would be useful to see the actual commands run as supplementary material to ensure its reproducibility.

Specific comments:

- Are the samples utilized for RAD-seq the same as the ones used for microsatellites? If so, details of individual samples should be presented as supplementary information.

- Additional methods to select K should be explored (see Janes et al 2017 Molecular Ecology). How were the tested values of K selected? (they differ between RAD-seq and microsatellite analyses).

- Was there a check for clones performed? The authors mention that samples belonged to different genets, but there is no mention of how this was determined. It would be good to show these results.

- The authors present point estimates of population statistic values, such as Fis. With hundreds/thousands of markers these statistics are more informative when shown and discussed as distributions

- The logic behind considering Read 1 and Read 2 of the paired end as replicates is not clear. How are they replicates? This needs to be better justified/explained.

- Lines 327-329. Numbers of fragments are discussed. Please provide the actual numbers (expected vs. observed). Postulate an explanation for discrepancy (see Herrera et al 2015 GBE).

- Genetic diversity is presented in values of pi and also in terms of SNPs/bp. Please present in consistent units.

- Paragraph lines 350-367. What is the main message of this paragraph? It ends without a tying end or conclusion.

- Line 371. What is the predicted nucleotide diversity of A. palmata? Please specify. Also see Arnold et al 2013 Molecular Ecology for a discussion of genetic diversity estimation from RAD-seq data.
Validity of the findings: The data is seemingly robust and the statistical analyses performed are appropriate. However, a greater exploration of the parameters used in the populations analysis in STACKS should be performed. The authors selected conservative parameters regarding the number of individuals per population and the number of populations for a particular locus to be included in the analyses. These parameters have great influence in the number of SNPs that are included in the analyses. The authors correctly identified the relatively low number of SNPs as a weakness in some of their analyses. Performing the population structure and selection analyses in SNPs datasets produced with a variety of parameters is necessary to understand the robustness of the conclusions. Furthermore, the authors should explore additional methods to evaluate population structuring such as PCA, which does not necessarily  bins populations into discrete K categories.
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: GENOME-WIDE SURVEY OF SINGLE-NUCLEOTIDE POLYMORPHISMS REVEALS FINE-SCALE POPULATION STRUCTURE AND SIGNS OF SELECTION IN THE THREATENED CARIBBEAN ELKHORN CORAL, ACROPORA PALMATA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have done a fine job in their revision of this manuscript.  The revision clarified the ambiguous methods and results in the originally submitted manuscript.  The addition of the supplemental figures for analyses exploring impact of cut-offs for inclusion of loci is useful.  I have no further comments for this section.
Experimental design: The experimental design is good and the authors have clarified questions I had with the analysis of the data.  I have no further comments for this section.
Validity of the findings: The authors have done what they can do in their revision to address my concerns with the RAD data.  Frankly, I am not entirely convinced that the sequence-based data are robust because of the low coverage.  I understand that sometimes projects do not go as planned.  The authors now include some statements in the manuscript to explain these shortcomings.  I have no further comments for this section.
Additional comments: The authors have done a good job with this revision, overall.  The section in the Discussion that summarizes the genetic diversity is various animals (beginning on Line 390) still seems unnecessary because these are different types of comparisons (e.g. whole genome compared, small regions of the genome, transcriptomes), thus difficult to compare with any degree of confidence.  The authors acknowledge their estimates are potentially not representative for this species (Lines 426-429).  I would suggest again that the section "Genes under positive selection" adds little to the manuscript and the manuscript would present better if this were removed.  There are few hits to a potential protein and the function would be even further removed.


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

Input:
Title: GENOME-WIDE SURVEY OF SINGLE-NUCLEOTIDE POLYMORPHISMS REVEALS FINE-SCALE POPULATION STRUCTURE AND SIGNS OF SELECTION IN THE THREATENED CARIBBEAN ELKHORN CORAL, ACROPORA PALMATA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have satisfactorily addressed the review points.
Experimental design: The authors have satisfactorily addressed the review points.
Validity of the findings: The authors have satisfactorily addressed the review points.
Additional comments: The authors have satisfactorily addressed the review points.


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 ABILITY OF LAYING PULLETS TO NEGOTIATE TWO RAMP DESIGNS AS MEASURED BY BIRD PREFERENCE AND BEHAVIOUR
Review round: 1
Reviewer: 1

Output:
Basic reporting: This article is very well-written and clear to read, the level of English is satisfactory.
The introduction is well-referenced and provides a clear background for the need for the study.
The raw data file is supplied and is clear to read.
Figures are relevant and clear although I found the direction of the x-axis labels difficult to read in Figure 4, I think they should be flipped around if possible. I think Figure 1 is extremely valuable and good to see it included.
Minor comments:
Comments on the abstract are first impressions, some information becomes clear when you read the entire manuscript but these were things that were identified when reading the summary.
Lines 29-30: Definition of attempts?
Line 33: Is there any other way to navigate a LR than jumping it?
Lines 35-36: The LR is a clear potential perching apparatus, therefore it would be expected that birds may rest on it more than the GR.
Line 73: ‘ramps’ not ‘rams’
Line 83: comma after ramp
Experimental design: This experiment is original research that is needed for understanding how birds use ramps that are increasingly used in alternative housing systems yet there is currently little scientific literature on the best ramp designs. The controlled individual testing allows for detailed observations of individual bird responses. The experiment was well-designed with a high standard of habituation/training regimes and controls in place but I had a few queries throughout the methods section for additional clarification (see comments below).
However, my biggest query is why the effects of rearing were not included in the current manuscript (written they are to be included in a separate manuscript). As the current manuscript is not that long, it seems like the effects of rearing would be a great addition to this paper rather than being included separately. Particularly as the birds were tested during the rearing age as 12-14 week pullets.

Comments:
Line 97: More information on why this particular design of the ladder ramp was chosen.
Line 104: I assume birds were divided evenly between rooms/groups. Could birds see/hear each other? It is not clear how the rooms/groups are divided? Mesh? Solid walls?
Line 111: comma after ‘room’
Lines 111-112: Clarify here that all birds were used in the current study despite being reared differently.
Line 131: Company details for the camera system?
Line 149: Clarify if any food deprivation prior to testing and how hunger/lack of hunger was potentially controlled for as a motivation factor.
Line 150: Age of birds during habituation stated here would be useful.
Lines 150-152: Did this occur within the home pen?
Lines: 152-154: Were all birds given the same amount of habituation or did habituation depend on individual bird responses. I imagine some birds were quicker to habituate than others?
Lines 154-157: It is not entirely clear to me the difference between test room and test pen. Where precisely were the birds placed for each of these habituation periods?
Line 160: Delete the word ‘because’
Lines 164-165: Was this pencil-tapping also done during habituation or just started during training?
Lines 165-166: Was training always in the same direction first?
Lines 173-174: I am not clear on what is the difference between the 2 groups. From my understanding, birds were reared in two rooms, with 2 groups per room. Therefore, are you only testing birds from 2 groups within 1 room?  Or are you referring to 2 rooms (2 groups per room) here?
Line 180: change to ‘testing order per ramp type’
Lines 231-232: Were these the only behaviours used as indication of hesitation? If so, I think the sentence should read ‘including head orientations, crouches…..etc’. Right now it reads as there were also several other behaviours included as indicative of hesitation and I think all should be listed here as this is a novel approach for behavioural observations.
Lines 242-243: Further clarification as why were these not counted? Were these interpreted failed attempts or birds just using the ramps for resting? Based on your observations, if a bird did not complete a transition within 1 min, it was likely the bird was not using the ramp for transition purposes but was just perching on it (if you can make that assumption from the observations).
Thus is this why the 5-min scan samples were included to look at ramp use for resting/perching?
Line 251: ‘included’ not ‘analysed’
Lines 255-256: Would be useful for the reader to state how many birds these exceptions applied to. Particularly for the 2 or 3 min test if this was only a small number of birds.
Lines 269-270: Further details on how interactions were assessed using t-tests.
Lines 271-272: I don’t understand what two variables are being combined. Further clarification for this sentence.
Line 273: ‘some of the data’
Validity of the findings: I think the data are thoroughly analysed with statistical analyses presented where possible. The group tests just provide visual data due to the low sample size but the visual presentations are still valuable.
The discussion is well written and conclusions drawn from the findings are valid. I have a few comments on the results and discussion as detailed below.

Lines 303-306: Perhaps I missed somewhere earlier any statement about measuring/analysing attempts.
Line 307: But sometimes 3 mins? For how many birds? Any effect of ramp type on whether 3 mins was required?
Lines 317-320: Can you comment on pauses with the LR. It almost seems by design, there are pause breaks inserted as there are rungs compared to the continuous nature of the GR. Would you therefore expect birds to pause on the LR compared to the GR, regardless of whether one is more difficult than the other or not?
Line 357: in individual bird behaviour
Line 359: Lambe et al.
Lines 419-425: I think here it would be more valuable to include some discussion of using the LR as a perch and whether this will have impact on bird movement in the system compared to a GR that is typically not used as a perch. Since the LR appears to have a dual purpose, in a commercial system this may impact bird movement in different areas of the house if it is consistently blocked by birds using it for perching rather than transitioning. Discussing diurnal patterns of perching seems a bit out of place here, but perhaps could be included in relation to what is discussed above and any interplay between perching patterns and transition patterns within a housing system. The LR is potentially confounded by its dual purpose and this may then be affected by available perch space within the system, perhaps this could be discussed.
Lines 426-429: For clarification, could birds in the group testing room go from the slats to the litter without using a ramp? Or did the ramp placement eliminate this possibility (I think by your figure the two ramps had no gaps inbetween)? If birds could bypass the ramp completely, did you look at the numbers of birds that did this? Whether the perching on the LR meant more birds were jumping down to the litter and not using a ramp at all? Would be valuable to discuss whether just ladder ramps in a commercial setting that could be consistently blocked may mean more birds execute jumps that could injure them.

Lines 441-443: another reason why the effects of rearing might be valuable to include in this current manuscript rather than as a separate manuscript.
Lines 448-454: I think the confound of the LR being used a perching space needs to be mentioned here as this is likely to have impact in a commercial system as to what the birds use the ladder for.
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: THE ABILITY OF LAYING PULLETS TO NEGOTIATE TWO RAMP DESIGNS AS MEASURED BY BIRD PREFERENCE AND BEHAVIOUR
Review round: 1
Reviewer: 2

Output:
Basic reporting: Line 33:  Collisions with the food reward bowl were “greater.”  Specify more frequent instead of greater, as greater collisions implies more significant impact, the forces of which were not measured in this study.

Line 54:  define “pop-hole” and/or, if possible, provide a citation.

Line 58:  define “end of lay” for the non-specialist in poultry rearing.  How long does this interval last, or how old are the birds at the end of lay?

Line 73:  typo “ram” should be “ramps”

Line 96:  spell out MDF

Line 131:  Spell out CCTV.  Add sampling rate (frame rate) and video pixel resolution.
Line 180:  “Systematically balanced” give slightly more detail.  Presumably this means non-random, that every other bird was treated to a different order, or was it a different order for a given group of birds (tested individually within a group).  This is relevant to interpreting the confidence intervals for individual performance criteria.

Lines 261-266:  It seems that only Z statistics are reported.  If that is the case, it would be better to state that non-parametric tests were used because assumptions of parametric tests could not be met, then delete the specific reference to paired t-tests and repeated measures ANOVAs.

Line 266 (and figures):  95% CI’s are reported in the figures.  Why not use standard deviations instead?  Otherwise, clarify how you calculated the 95% CI’s.  It would seem that an N of 4 groups would lead to unnecessarily large CI’s.

Line 286:  Add percentages here to the numbers, as percenages are more broadly relevant than the exact numbers

Line 323:  I suggest starting with sentence two and putting (“Fig. 4”) at the end of the sentence instead of using the present opening sentence (to eliminate redundancy).

Line 343:  As previous, start with second sentence and then direct the reader by putting (“Fig. 5”) as the end of the sentence (delete current topic sentence).

Line 351:  Here it is not clear what you mean by “fully accounted for”  Expand slightly on detail.

Discussion, General:  Two issues would be useful to explore, even if briefly, in the discussion (for example, perhaps near lines 391-394, or 426-427).  You do not describe whether the birds ever fell or appeared to lose locomotor control, and you do not mention whether they ever used their wings to assist during climbing or to outright fly.  For the research into keel-bone damage, it is worth mentioning if they birds never fell due to loss of control.  Likewise, even in general terms, it would be helpful to understand whether wing flapping and flight increases or decreases in relation to ramp design.

Lines 437-438:  this is somewhat confusing because you earlier wrote that you could not analyze the data according to a repeated-measures ANOVA.  Clarify with additional detail what you mean by “accounted for”.

Figure 1 (legend).  It seems that the A figure is a ladder and the B is a grid, but these are reversed in the legend.
Experimental design: Nothing to add.
Validity of the findings: Nothing to add.
Additional comments: Your research is interesting and worthwhile for improving our understanding of ways to design housing systems for layer hens that will lead to reduced frequency of keel bone damage.  Your experimental design and analyses are well conceived and rigorous, and I have no major criticisms.  I offer minor comments to help improve clarity in selected instances (basicreporting section).


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 ABILITY OF LAYING PULLETS TO NEGOTIATE TWO RAMP DESIGNS AS MEASURED BY BIRD PREFERENCE AND BEHAVIOUR
Review round: 2
Reviewer: 1

Output:
Basic reporting: Article is well written and the authors have made all suggested changes.
Experimental design: The methods section has been clarified as suggested by both reviewers and is now much clearer to read.
Validity of the findings: The discussion is much improved and reads very well.
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: UNCOVERING THE RELATIONSHIP AND MECHANISMS OF TARTARY BUCKWHEAT (FAGOPYRUM TATARICUM) AND TYPE II DIABETES, HYPERTENSION, AND HYPERLIPIDEMIA USING A NETWORK PHARMACOLOGY APPROACH
Review round: 1
Reviewer: 1

Output:
Basic reporting: Nice and highly relevant paper. It is a report on important results of the investigation, based on a comprehensive systemic approach integrating drug target prediction, network analysis, and molecular docking simulation, developed to reveal the relationships and mechanisms between the putative targets in Tartary buckwheat and Type II diabetes, hypertension, and hyperlipidemia.

Authors are reporting that some pathways discovered in the study, such as the insulin resistance pathway, AGE-RAGE (Advanced glycation end products) signaling pathway, and insulin signaling pathway, have a direct relationship with the three studied diseases.

They revealed the relationship of Tartary buckwheat and the three diseases to provide more information on the clinical applications of Tartary buckwheat and to further research on Tartary buckwheat properties and quality.

Mainly clear professional English is used. Paper with nice novel results.  Title of the manuscript is suitable, abstract is enough informative. Literature references are sufficient. Conclusions are of broad  interest and based on the results. Abstract, Introduction, Results and Discussion are clearly presented. Professional structure of manuscript is well performed. Figures are clear, but the reviewer has a specific suggestion to Fig. 1.
Results are self-contained with the results relevant to hypotheses.
Experimental design: Research questions are well defined and within the aims and the scope of the journal. Materials are accordingly defined. Methods are suitable, properly described and used, in a way that is possible to replicate experiments. The investigation is performed to high technical standards. It is no ethical problem involved.
Validity of the findings: Data are obtained in a sound way, they are statistically evaluated in a proper way.
Conclusions are very well stated and  based on the results. Discussion and conclusions are sound and relevant.
Additional comments: Specific suggestions:

Line 1 and elsewhere in the manuscript: Instead of  »tartary buckwheat« correct to »Tartary buckwheat«, where applicable. In difference to »common buckwheat« (with lower-case first letter), »Tartary buckwheat« should be in English always written by upper-case first letter; this way of writing was internationally accepted, among others in the discussion on International Buckwheat Research Association (IBRA) Assembly in 2013, as word »Tartary« comes from the name of the Tartar people.

Line 51, delete: amount of

Line 67, instead of: shell, better: husk

Figure 1, Nice and illustrative figure, however »PT« letters should be better placed outside the »T2D« area, to be more clear, including to be clear on black/white prints.


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: UNCOVERING THE RELATIONSHIP AND MECHANISMS OF TARTARY BUCKWHEAT (FAGOPYRUM TATARICUM) AND TYPE II DIABETES, HYPERTENSION, AND HYPERLIPIDEMIA USING A NETWORK PHARMACOLOGY APPROACH
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript reported new and relevant results on systemic approach integrating drug target prediction with the network analysis, and molecular docking simulation. Results are important for understanding  relationships and mechanisms between the putative targets in Tartary buckwheat and Type II diabetes, hypertension, and hyperlipidemia.

Professional English of the manuscript  should be improved
Experimental design: Experimental design is well performed and within the aims and the scope of the journal. Materials and methods are well defined and used. It is thus possible to replicate experiments. The investigation is performed according to high technical standards. There seems that no ethical issues are involved.
Validity of the findings: Data are obtained in a suitable  way,and correctly evaluated.
Conclusions are properly based on the experimental results.
Additional comments: Reviewer suggests improvement of English  style.

In the title and manuscript Tartary buckwheat should be written with the capital first letter.

Text in lines 44-47 is not clear enough, needs rewriting.
Line 54: correct »which have«
Line 54, punctuations are not correct.
Line 132. punctuations are not correct.
Line 263, the reference  should be inserted.

Conclusions are not clear enough, they should more clearly pointed out the purpose, results and focus of the paper.


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

Input:
Title: THE REANALYSIS OF BIOGEOGRAPHY OF THE ASIAN TREE FROG, RHACOPHORUS (ANURA: RHACOPHORIDAE): GEOGRAPHIC SHIFTS AND CLIMATIC CHANGE INFLUENCED THE DISPERSAL PROCESS AND DIVERSIFICATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: Orlov, Poyarkov, Vassilieva, Ananjeva, Nguyen, Sang, and Geissler, 2012, Russ. J. Herpetol., 19: 23-64 noted extensive confusion with Rhacophorus robertingeri in the literature and mentioned R. chuyangsinesis considered as a junior synonym of R. calcaneus. Thus, the authors need to correct data.
Additional comments: Because computer programs change over time and the default parameters are not necessarily rigid, it would help to specify what the default parameters are. This also helps the reader to know that you judged particular parameters and associated assumptions to be the best ones for your data.


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 REANALYSIS OF BIOGEOGRAPHY OF THE ASIAN TREE FROG, RHACOPHORUS (ANURA: RHACOPHORIDAE): GEOGRAPHIC SHIFTS AND CLIMATIC CHANGE INFLUENCED THE DISPERSAL PROCESS AND DIVERSIFICATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Excellent manuscript by the authors. Since the manuscript talks about geological phenomenon, I felt Two important papers from Indian sub-continent were mission from the manuscript. I would be good if the following papers are cited in the revised manuscript.
1. Taxonomic revisions of Rhacophorus genus in Indian sub-continent was given in Biju et al 2013. This paper did not find a place in the manuscript.
2. Similarly, Vijayakumar et al 2016 provided insights on glaciation, gradient and geography of Western Ghats, that perhaps shaped diversification in Raorchestes genus. This can be cited in 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 REANALYSIS OF BIOGEOGRAPHY OF THE ASIAN TREE FROG, RHACOPHORUS (ANURA: RHACOPHORIDAE): GEOGRAPHIC SHIFTS AND CLIMATIC CHANGE INFLUENCED THE DISPERSAL PROCESS AND DIVERSIFICATION
Review round: 1
Reviewer: 3

Output:
Basic reporting: Format of text is not consistent throughout the manuscript. For example, "et al." are italicized in some case, but not, in normal, in other case. Correct such basic formatting throughout the manuscript before submission.
Experimental design: The results of the present study and the former one (Li et al., 2013) were very different. Especially, the estimated ancestral area is quite different. The present authors must clarify any difference in samples, analysis, and interpretation on the results between them.
Validity of the findings: As shown on Fig.S1, 1) a lot of nodes lacked a significant supports. Further, 2) the topology is not consistent between Fig. S1 and Fig. 2. Need to improve or explain on these two major concerns.
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: THE REANALYSIS OF BIOGEOGRAPHY OF THE ASIAN TREE FROG, RHACOPHORUS (ANURA: RHACOPHORIDAE): GEOGRAPHIC SHIFTS AND CLIMATIC CHANGE INFLUENCED THE DISPERSAL PROCESS AND DIVERSIFICATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Excellent work by the authors. Congrats!


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 REANALYSIS OF BIOGEOGRAPHY OF THE ASIAN TREE FROG, RHACOPHORUS (ANURA: RHACOPHORIDAE): GEOGRAPHIC SHIFTS AND CLIMATIC CHANGE INFLUENCED THE DISPERSAL PROCESS AND DIVERSIFICATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Thanks for addressing the 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: THE REANALYSIS OF BIOGEOGRAPHY OF THE ASIAN TREE FROG, RHACOPHORUS (ANURA: RHACOPHORIDAE): GEOGRAPHIC SHIFTS AND CLIMATIC CHANGE INFLUENCED THE DISPERSAL PROCESS AND DIVERSIFICATION
Review round: 2
Reviewer: 3

Output:
Basic reporting: I confirmed the improved MS.
Experimental design: No problem.
Validity of the findings: OK.
Additional comments: I am looking forward for seeing this 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: PBXPLORE: A TOOL TO ANALYZE LOCAL PROTEIN STRUCTURE AND DEFORMABILITY WITH PROTEIN BLOCKS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: Some conclusion and discussion need more clarification (see below in general comments).
Additional comments: The manuscript entitled ‘PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks’ by Barnoud et al presents the implementation and development of a python tool based on Protein Blocks definition to characterize local structures in a protein.  The protein blocks (PBs) used in this work have been previously published and have been shown to be useful in many applications such as peptide design, local protein conformation predictions etc. The suit of tools presented by the authors can be used either for a single structure or for a trajectory. The work presented is technically sound, however a few points could be clarified when comparing the results of PBxplore and RMSF calculations for instance.
Even though more details about the RMSF calculation are present in the cited paper (Jallu et al 2012), the authors could specify that it was calculated on Calpha atoms. Since RMSF values are obtained when aligning each frame of the simulation on a selection of atoms, what would be the values if the authors align their trajectory on the loop 33 to 35? It should be clarified that indeed RMSF values if performed on all the structure including the loops for instance will give a more global view of flexibility, but if calculated with respect to a subset of atoms of interest it could give a more local picture. It is not very clear what the authors imply when stating the residues 32 and 36-37 around the loop of interest are acting as hinges. From the Neq plot it seems that indeed residue 32 has an elevated value, but it is not as striking for residues 36 and 37. Also, the sentence on page 6 ‘These results question the relationship between MD simulations and allostery and the role of long range effects on protein structure’ is a bit of an over-statement in this context, as long range effects have not been explored thoroughly in this work. It is rather the difficulty to extract from MD simulations meaningful information on structural changes which play a role in allosteric signaling.
Notwithstanding the above, it is interesting to see that regions displaying elevated global RMSF values can easily be pinpointed in a straightforward fashion using PBxplore for further analysis regarding local vs global flexibility. Therefore this tool should be a valuable tool for analysis in computational structural biology.


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: PBXPLORE: A TOOL TO ANALYZE LOCAL PROTEIN STRUCTURE AND DEFORMABILITY WITH PROTEIN BLOCKS
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: It will be good to develop a statistical measure to identify the residues which are not deformable and flexible, yet their RMSFs are high (example of beta-3 integrin). It will help PB analysis on the top of RMSF. On the other hand it will also help to highlight regions in an analysis, if any, for which the RMSFs are low yet deformabilty and flexibilty are high (as around residue 20).
It will also help users if a web based server could be setup for PBxplore (should not be difficult).
Small suggestion: Name of the tool should be "PBxplorer" and not "PBxplore".


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: DETECTION OF BACTERIAL CONTAMINANTS AND HYBRID SEQUENCES IN THE GENOME OF THE KELP SACCHARINA JAPONICA USING TAXOBLAST
Review round: 1
Reviewer: 1

Output:
Basic reporting: Unclear, ambiguous writing and need some language editing

Scientific writing need significant effort. e.g. no references, poor hypothesis and synthesis
Experimental design: No sufficient evidence/detail to highlight that this tool is anywhere near the state of the art in this category
Validity of the findings: Zero Novelty

Data is not robust, e.g. used only one genome, no benchmarking
Additional comments: Thanks for your efforts. According to me this paper/tool is not publication ready in its current form and needs a significant effort (especially in benchmarking and scientific writing)

Major

Where is the benchmarking? You should compare the tool with the existing mainstream tools and provide some comp. Stats.

Why using only one genome? Why not Bacterial Genomes?

Since authors have mentioned that this tool can be used for “other genomes” let me give some bacterial genome scenarios. (a) If I have multiple genomes from diff. strains of single species, do you think this tool can distinguish the intra-species contamination? Here the strain means whole genome based ANI >99%? I don't think its possible. (b) How can we use this tool to identify the contamination in genomes assembled across shotgun microbiome denovo assemblies? where we have very few ref. Genomes?

You have used word “matched” all across the text, mentioning the blast hits. Honestly the word “matched” is very unclear to me, what is the cutoff that makes you decide that its a match?

Overall, its not a well written paper and need some significant effort.

Line 79 “but if such searches are carried out with the
entire scaffolds, they may be biased by highly conserved regions, which frequently have very little
discriminatory power (transposons, virus insertions etc.)”

This statement need ref.

Line 81 “ Alternatively, protein-based searches may be
performed with all predicted proteins of a genome against a reference database (frequently NCBI nr or
uniref90).”

where is the ref.? Who created these two categories?

Line 83 “Based on these results,”

what results? Please re-frame

Line 84 “The advantage of this approach”

what approach? Please write the text clearly.

Line 141 “also detected via a 16S sequence in a different scaffold, see above”

According to me the above line makes no sense, what is “via a 16S sequence” do you mean a blast hit? If yes, what is the aignment parameters? e.g. length, e-value?

Line 142 “large regions that were homologous”

what is the defination of large here?

Line 147 “This clearly supports the hypothesis of diverse phylogenetic origins of
the scaffolds classified as bacterial.”

The above statement needs ref.

Line 150 “the 90% threshold”

what is that threshold

Line 151 “These scaffolds
may comprise assembly artifacts the have merged contaminating sequences with sequences of the
target species as well as recent horizontal gene transfers.”

The above sentence is very confusing, poorly written and has no evidence mentioned in this paper.

Line 152 “It is not the aim of this publication to re-
analyze the S. japonica genome, but for the purpose of illustration we have selected the two scaffolds
with the highest numbers of blast hits from this category, and manually examined them.”

If its not the aim why to do this illustration at the first place?

Line 155 “The first, scaffold159, is approximately 500 kbp long and has 557 blast hits for different 500 bp-
segments, 26% of which (towards the beginning of the sequence) are with bacteria.”

above senetence needs formatting and reframing

Line 157 “GC profile server”

I think its GC-Profile server


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: DETECTION OF BACTERIAL CONTAMINANTS AND HYBRID SEQUENCES IN THE GENOME OF THE KELP SACCHARINA JAPONICA USING TAXOBLAST
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript and the provided software-tool Taxoblast addresses the need of molecular biology scientists to analyse scaffolds from genome assemblies for possible contamination or lateral gene transfer. It describes the tools functioning and features and explains the utility based on an example assembly from the brown alga Saccharina japonica. Advantages of the method in relation to screening reads before assembly are shown. Overall the writing is good instructure, language and well understandable in expression.
The provided tool is described as helpful for biologists that do not have capacity to perform similar analyses as effectively as with the tool (abstact: "usable also by researchers with little background in informatics"). This is an important added value of bioinformatics tools in general, thus not worth mentioning for publishing of this specific tool.
Experimental design: Validating the tool by an example data set was done carefully and has led to new insight, useful for improving the publication of the chosen genome data.
Validity of the findings: The findings are well documented, and the summary given in statistics data is complete.
Additional comments: I recommend the paper for publication after minor revision indicated above.