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: NON-LINEAR GENETIC DIVERSITY AND NOTABLE POPULATION DIFFERENTIATION CAUSED BY LOW GENE FLOW OF BERMUDAGRASS [CYNODON DACTYLON (L.) PERS.] ALONG LONGITUDE GRADIENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. This paper is difficult to read due to its many errors (grammar, verb tense, word choice, and incomplete/run-on sentences). I would classify the extent of these errors as severe, but with sufficient proof-reading and revision, they could be fixed. I mainly regret that I was unable to understand some key sentences, as their meaning was unclear. In some cases, I was unsure whether I was having difficulty with a sentence due to an error or because the authors were making a conceptually challenging point. There are too many mistakes to note, but I will draw attention to a small selection:
	88: This sentence is incomprehensible.
	234: I don't know if they mean "low temperature" or "low temperature variability."
	243: The "because" doesn't seem to follow logically.
	260: The phrase "no need" seems out of place here.

2. Several important concepts were not adequately discussed in the Introduction and Materials & Methods.
	Crucially, the justification for their interest in longitude as a meaningful environmental gradient is not addressed in the introduction. Though many environmental variables predictably co-vary with latitude, covariance with longitude is case-specific, not general. Further, they do not justify their choice of environmental variables, though mean annual temperature and mean annual precipitation are frequently default selections. On line 226 in the Discussion, they begin to talk about the other environmental complexities that may account for the non-linear patterns of genetic diversity. In the next paragraph, starting at 244, the authors begin to discuss aridity, flooding, mountain ranges that hinder gene flow, and much later, they mention glaciation history. All of this information is greatly beneficial, and should be moved to the introduction (and expanded) as justification for this question. Even after this revision, the question would remain: Why structure your research question around longitude? The plant experiences myriad environmental variables, but longitude is a human construct of no direct biological importance (as far as I know, though if I am wrong, the authors should explain why). It seems that these same analyses could be re-contextualized in reference to temperature, precipitation, elevation, soil type, habitat fragmentation, or any combination of environmental variables, for a more intuitive and direct discussion of the association of genetic diversity, population structure, and environment in these sampled populations.
	The role of demography in shaping geographic patterns of genetic diversity is neglected. Throughout the manuscript, I found myself wondering about the demographic history of these populations, their population sizes, and the direction and timing of dispersal. The paragraph beginning at 280 comes close to discussing these ideas, and with some revision, may provide some valuable insight for the paper.
	They do not explain why their model system is suitable for their study questions. In particular, I wonder why you would choose a weedy, invasive species for investigations of local adaptation, a process which involves multiple generations of directional selection within an environment and which produces organisms particularly suited for their home environment. They could also be more clear on their criteria for population selection and specimen harvesting.

3. In general, sufficient literature seems to be referenced when discussing ideas. See below for some exceptions:
	125: The three statistics for genetic diversity should be referenced with their corresponding citations.
	268: This sentence is written as if the numbers are applicable across many systems, but in fact these numbers were from an experiment on mosquitoes and should not be generalized. As written, this sentence is highly misleading.
	290: Generally accepted according to who, or in what circles?
	291: It has been hypothesized by whom?
Experimental design: 1. This manuscript meets the criteria for inclusion in this journal (original primary research within the scope of the journal). The research questions are defined, relevant, and meaningful, though they would be more impactful if the Introduction better explained their relevance, and they fill an identified knowledge gap.

2. However, this experiment has considerable statistical and conceptual flaws:
	They utilized a simple Pearson correlation to establish a causal relationship between environmental conditions and genetic diversity. This approach disregards neutral effects due to demography (shared ancestry, gene flow). Numerous methods (BayEnv, Sambada, LFMM) have arisen to account for neutral effects when investigating gene/environment associations, and this principle should be applied here. A Pearson correlation is too weak a tool for addressing this research question.
	They provide no way for the reader to know which populations are which ploidy level. I suspect that they considered and investigated this angle but failed to report it. This is an unfortunate oversight, as patternation of ploidy level across the longitudinal transect or composition of different ploidy levels within a population could explain (at least in part) the nonlinear patterns of population structure and/or genetic diversity. Not accounting for ploidy level when running a Pearson correlation between genetic diversity and environment would almost certainly confound results. Perhaps the effect of environment on levels of genetic diversity is present and significant, but is masked by the greater effect of ploidy differences.

3. At times, the authors apply analytical tools without justification.
	They do not distinguish their three statistics of genetic diversity, nor do they explain why they used all three.
	They cluster populations using both UPGMA and PCoA (Figures 3 and 4). Both provide the same clustering results. Why use both?

4. The authors provide a fair amount of detail in methodology, except for the few cases I have pointed out previously. I would have preferred to be able to see the scripts that were used in data analysis, but these were not provided.
Validity of the findings: 1. I am suspicious of some of the conclusions at which the authors arrive:
	Throughout the manuscript, demographic effects are either mentioned in passing or just ignored. These effects are important for understanding the population structure and genetic diversity of populations. Their environment/genetic diversity analysis is therefore flawed.
	In the Conclusions, at line 349, the authors write, "The level of variation among populations is highly dependent on different environments." Perhaps they were speaking generally, but in the context of this experiment, the results do not indicate that genetic variation is highly determined by environmental conditions.

2. The strongest conclusion they arrive at is in relation to the lead author's 2019 paper. Starting on line 352, they state that north-south gene flow is greater than east-west gene flow. This is an unexpected result that deserves a more thorough discussion than it was given.

3. They also find that genetic diversity increases with elevated ploidy level, and that genetic distance is positively correlated with geographic distance. These are expected results, and the authors do a fair job of discussing them (excepting the fact that I was unable to discern which populations were which ploidy level).

4. The Supplementary Materials provided little in the way of underlying data. The raw microsatellite data was present with suitable metadata, but nothing else.
Additional comments: There are interesting angles in this manuscript that can be played up during revisions. The nuances of environmental variation across this longitudinal transect could be explored, along with better treatments of environment/diversity and/or environment/ploidy associations. Finding stronger population structure across longitude than latitude is an unexpected result that could be made exciting by tighter writing clearer statistical underpinnings. With a more careful and thorough look at the data and some additional analyses, this can be a very interesting and valuable 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: NON-LINEAR GENETIC DIVERSITY AND NOTABLE POPULATION DIFFERENTIATION CAUSED BY LOW GENE FLOW OF BERMUDAGRASS [CYNODON DACTYLON (L.) PERS.] ALONG LONGITUDE GRADIENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Listed in order of importance:
1. The flow cytometry data should be reported for each individual. This should include the genome size and inferred ploidy.
2. The English language should be improved to ensure that your international audience can clearly understand your text. Some examples of where the language could be improved include lines 61-64, 227-230, and 275-279. The current phrasing of these sections makes comprehension difficult.
3. I appreciate the inclusion of the genetic diversity values in tables 2 and 4, however the significance lettering in Table 4 is confusing. I recommend either describing the lettering in more detail in the table caption or not including the lettering and instead describing the significance in the text.
4. I thank you for providing figures that thoroughly describe your results, however figures 5 and 6 could be reduced and move to the supplementary material. STRUCTURE is a well-known algorithm therefore Figure 5 can be moved to the supplement. Additionally, Figure 6 can be reduced to only include the panels K=4 and K=8. All other panels in Figure 6 could be moved to the supplementary material.
Experimental design: no comment
Validity of the findings: Listed in order of importance:
1. In your analysis of genetic diversity in relation to polyploidy, individuals of the same ploidy level are treated as a population in order to compare genetic diversity among different ploidy levels (lines 128-129). In the discussion, you hypothesize “each chromosome replication process increased genetic diversity” (lines 303-304). This is a possibility, but it’s also possible that pentaploids and hexaploids have increased genetic diversity because their diploids and tetraploid progenitors were from C. dactylon populations with higher genetic diversity. This concept is discussed in Monnahan et al (2019) (https://doi.org/10.1101/411041). I recommend you either discuss this alternative hypothesis in your discussion or investigate this hypothesis in your data. You could test this alternative hypothesis by evaluating how the polyploids are distributed across the populations in relation to genetic diversity. For example, are pentaploids and hexaploids primarily found in populations with high diversity, such as Population 12?
2. Lines 268-272: You cite a study by Edillo et al. (2009) which found FST increases by 0.035  by for every 100-km. It is unclear whether you are suggesting their species also increases by 0.035 FST for every 100-km or whether they are using Edillo et al. as an example of isolation-by-distance. As Edillo et al. evaluates a different species, Culex pipiens, their FST calculations are not transmittable to your paper on Cynodon dactylon. These lines should be improved for clarity.
3. Lines 290-293: It is unclear if you are stating a new hypothesis or if this hypothesis has been supported in other studies. If this hypothesis has been previously acknowledged, please provide citations. If it is a new hypothesis, you should restate this sentence as a hypothesis.
4. Lines 232-233: Please consider exchanging “was beneficial to” with “was associated with”.
Additional comments: The methods and results of this study are well described, however portions of the introduction and discussion could be improved for clarity. I have noted these sections in my review. Additionally, I highly recommend the authors provide their flow cytometry data and investigate the relationship between ploidy distribution and genetic diversity.

Strengths of the paper:
-The EST-SSR data is very well documented and should serve as a good resource for future studies on this species.
-The study has a good sample size and marker density that is sufficient for a landscape genetics study.
-I commend the authors for the detailed description of their methods, particularly the genotyping methods. I feel the methods can be easily replicated if the flow cytometry data is included with the final manuscript.
-The research question is well defined (lines 84-85 and 91-95) and the authors have clearly answered each objective.
-The data on which the conclusions are based is statistically sound. I thank the authors for providing their results in well-formatted tables.
-I appreciate the discussion of the results of this study in relation to your previous study on C. dactylon across a latitudinal cline as it is highly relevant and contributes to the overall goal of your study.


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

Input:
Title: NON-LINEAR GENETIC DIVERSITY AND NOTABLE POPULATION DIFFERENTIATION CAUSED BY LOW GENE FLOW OF BERMUDAGRASS [CYNODON DACTYLON (L.) PERS.] ALONG LONGITUDE GRADIENTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: This article does not exhibit clear, unambiguous use of English. Though some grammatical, spelling, and punctuation errors have been fixed from the first version, many remain. Most of these errors are minor, but at times, ambiguous language prevented me from understanding parts of the experiment and the results. I will include below some of the errors and confusing/unclear segments I spotted:

50: "Gene" need not be capitalized.
57: These phrases are lifted from Zhang 2016. The changes the original authors' sentence are muddying; "mainly" has the wrong meaning for this context, and "populations" should be singular (the original sentence used the word "species," which can be singular or plural, but was singular in this case).
100: "include" should be "includes".
103: What "biological characteristics" are you referring to here?
104: What "obvious genetic pattern" are you referring to here? Genetic structure?
105: These Objectives have no verb, consider something like "quantify genetic diversity", "test the relationship", etc.
109: This sentence is confusing. You just finished laying out the objectives of the study, and you more directly into stating what the results do. Also, what does "broaden the genetic base" mean? Shouldn't "understand" be "understanding"? More generally, by this point in the introduction, you shouldn't still be explaining the design of the experiment ("by tapping into the gene pools of the wild C. dactylon along longitudinal gradients"); that should be sufficiently covered prior to stating the objectives.
143: "Calculating" seems like the wrong word here.
144: "The variation degree" seems wrong. Maybe "the degree of variation"?
147: The referencing of the method of Zhang 2020 is not proper. Should be something like, "based on the method outlined by Zhang et al (2020).".
151: "test Mantel test" seems wrong. Also, some clarification would be helpful here. What matrices are being compared, and how are they computed?
188: The words "significant" and "significance" are misspelled throughout the manuscript.
192: "had the higher" should be "had higher".
194: "was", not "were".
212: Sentence is missing a word or two. "was identified", not "were identified".
214, 223: "Populations", not "Population".
222: Sentence is incomplete.
229: "clusters", not "cluster".
231-241: You now mention populations with "No.", but in the previous paragraph you did not. Be consistent with your naming conventions. Also, see note from 214.
234: "Each of the other", not "Each of other".
244: "Those prediction was" is improper.
283: "exist", not "exit".
285. Where is the "on the other hand"? Also, "genotypes", not "genotype". Also, missing parenthesis.
334: This sentence is confusing. How does this grass directly emerge from sites of low and high longitude?

The structure of the article is appropriate. The figures and tables that were included were relevant, and easy to read. I did note several places were the text unclear for reasons related to narrative flow or lack of explanation:

166: K value selection should be discussed after introduction of STRUCTURE and the permutation test.
238: This sentence may be better placed in the Discussion.
267-270: These sentences seem to be placed here randomly.  What is the logical narrative flow?
275: Where does this come from?
281-305: This paragraph is difficult to follow. The first sentence should do a better job of setting up the main idea of the paragraph, and the following sentences need to support that idea. Cutting down on the number of referenced sources here may help.
335-360: Would you expect that the mid-longitude populations, rising from complex hybridizations, might have elevated ploidy levels? Was this investigated or tested?
364: From where are you inferring that one is beneficial to the other, rather than a simple correlation?
369: I recommend a new paragraph here.

Though a good amount of literature is cited, in my opinion, it is not properly used. In numerous instances, the authors' wording is similar enough to the reference material that it makes me uncomfortable. Though it is clear that efforts were made to adapt the words of others into new phrases, in my opinion, a greater effort must yet be made.

I feel that this is a coherent body of work, but based on the authors' response to my first review, I also suspect that the authors are holding back some data and analysis (the spatial patterns of ploidy levels) for a later publication. I don't know if I am right, and if I am, I do not speculate as to their motives. I do think that that data would contribute meaningfully to this article, were they to have included it.
Experimental design: This article qualifies as primary research which falls within the aims and scope of this journal. The research questions are defined and relevant, though I am still unsure why so much focus is placed on longitude. On lines 61-66, longitude is shown to be an important variable because of the other things (MAT, MAR, altitude, migration barriers) that vary across it. Once again, I am led to ask, why does longitude itself matter, other than as a proxy for other biologically-relevant variables or for distance in general? Either important elements of the environment vary across longitude, in which case those elements can be discussed more directly, or longitude is a benign measure with no discernable biologically meaningful factors that vary across it, in which case it can be replaced with geographic distance, especially in the case of this experiment, in which almost all geographic distance between samples is across longitude.

The methods were mostly thorough, though there were sections that were not detailed enough, and others that were absent. I could not deduce the methods by which the authors arrived at a number of their results, and there was a time or two that I wished there were an additional figure or table. See below:

155: Mantel test is mentioned here again. On line 151, this test is between genetic diversity (genetic distance?) and environmental factors (environmental distance?). On line 155, this test is between genetic distance and geographical distance. Why not combine the descriptions of these Mantel tests into the same paragraph, or at least in the same section of the Methods?
166: Consider mention of Delta K, to which you dedicate one of your supplementary figures.
177: What is the value of g that you used? Also, my understanding is that Cynodon dactylon is primarily rhizomatous, reproducing asexually. If I'm right, how does that affect the use of this statistic, if at all?
194: What test is this referring to? In this paragraph, you have been plotting genetic diversity (He and I) across longitude, as in Figure 2 and Table 2. Have you also plotted these diversity metrics across MAF and MAT, or run a simple Pearson correlation? Why not include a table or figure, or reference to methods? Also, did you hypothesize that higher/lower MAF and/or MAT would increase/decrease the level of genetic diversity in these populations (for example, higher temperature and rainfall result in higher genetic diversity)?
205: I cannot find the methods that outline how you calculated gene flow. If you used FST to estimate it, then your estimate may be inaccurate, as your longitudinal sampling likely violates the island biogeographic model (Whitlock, Michael C., and David E. Mccauley. "Indirect measures of gene flow and migration: FST≠ 1/(4Nm+ 1)." Heredity 82.2 (1999): 117-125.).
Validity of the findings: Since the first version, efforts have been made to discuss the demographic history of these populations. Their use of the mismatch distribution and neutrality tests is an improvement.

Another improvement is their incorporation of the Mantel test. However, the authors may note that a Mantel test is still another application of a correlation statistic (between pairwise distances rather than between the values themselves). Furthermore, this analysis still does not account for the effects of demography. Had demographic effects been accounted for, stronger relationships between genetic and environmental distances may have been uncovered, while other noted correlations may be explained by neutral processes.

The Mantel test analysis can be improved. Looking specifically at 200-204: Mantel finds positive correlations between genetic, geographic, and precipitation distance. It is unclear whether geographic or precipitation distance is the stronger determinant of genetic distance. It is clear from the language of the sentence at 202 that the authors believe geographic distance is the determinant, and precipitation is strongly correlated with genetic distance only because precipitation distance is also strongly correlated with geographic distance. This hypothesis could be tested by way of a partial Mantel test: Test the correlation between genetic distance and geographic distance, while controlling for precipitation distance. This could also be reversed, testing the correlation between genetic and precipitation distance while controlling for geographic distance. This would disentangle these relationships and allow clearer interpretation, greatly improving this analysis.

In the cases where methods were insufficiently detailed, I am uncertain whether those results are valid or not. This mostly applies to their estimation of gene flow.

The final paragraphs of the paper attempt to rationalize unexpected results by speculating human interference. The authors properly identify this speculation when doing so, and do not engage in much speculation beyond this context.
Additional comments: The writing in the Discussion (and to a lesser degree, the Introduction) comes across as disjointed and lacking in narrative direction. I suspect that many of the sentences that the authors use in these sections are taken from their referenced sources with only minor modifications. The end result of writing in this way is that each sentence feels like a discrete idea in a long chain, isolated by conceptual distance from the others. Investing effort into greater synthesis of these ideas will improve the clarity of the story you are presenting in this article.


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: NON-LINEAR GENETIC DIVERSITY AND NOTABLE POPULATION DIFFERENTIATION CAUSED BY LOW GENE FLOW OF BERMUDAGRASS [CYNODON DACTYLON (L.) PERS.] ALONG LONGITUDE GRADIENTS
Review round: 2
Reviewer: 2

Output:
Basic reporting: 1. Genome size and inferred ploidy has not been provided. Without this information, analyses investigating the relationship between ploidy and genetic diversity cannot be replicate. The submission of this raw data is necessary.

2. The English language should be improved to ensure that your international audience can clearly understand your text. The text is greatly improved from the first version although significant improvement is needed in the Result and Discussion. Some examples of where the language could be improved include lines 266-274, 301-305, and 325-334. Additionally, lines 202-203 are unclear. Is the correlation between MAP and genetic distance dependent on the correlation between geography and MAP? Or did you run separate Mantel tests for both MAP and geographic distance?

3. Table 4 is not referenced and should be move to the supplement. It is improperly referenced on line 243 when Table 5 should instead be referenced.
Experimental design: no comment
Validity of the findings: In their rebuttal, the author's clarified, "Composition of different ploidy levels within a population at different longitudes was almost similar in another unpublished paper. Longitude was not highly correlated with ploidy level". The paper would benefit from including this analysis as it's currently unclear how the ploidy levels are structured across the populations. This information clarifies that the increasing genetic diversity with ploidy is likely due to the polyploid event rather than the pentaploids and hexaploids originated from populations of higher diversity.
Additional comments: The first revision of this article is a significant improvement from the previous version, however portions of the Results and Discussion should be improved for clarity. I have noted these sections in my review. Additionally, the raw flow cytometry data and inferred ploidy levels are needed for the analysis of genetic diversity across ploidy levels to be replicable.


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: NON-LINEAR GENETIC DIVERSITY AND NOTABLE POPULATION DIFFERENTIATION CAUSED BY LOW GENE FLOW OF BERMUDAGRASS [CYNODON DACTYLON (L.) PERS.] ALONG LONGITUDE GRADIENTS
Review round: 3
Reviewer: 1

Output:
Basic reporting: This third version of the manuscript is a marked improvement, particularly with regards to the writing. Clearly, efforts were made to improve the clarity of the ideas. There is also a reduction in the number of sentences lifted with improper/minor/insufficient modification from other published sources, which also had the benefit of improving the narrative flow of the manuscript. Still, the paper abounds with grammatical, spelling, punctuation, and word choice errors, some of which are new to this third version of the manuscript.

Your inclusion of the raw data as requested by Reviewer 2 is a valuable addition to the manuscript, but its value is limited somewhat by the refusal to carry out certain analyses with it. I agree with Reviewer 2's assessment that this manuscript would be strengthened by an analysis showing whether ploidy level is correlated with longitude, but you have elected instead to analyze this data in a separate paper.  I am left to believe that you excluded this analysis to increase publication count.
Experimental design: The methods section is more complete and has greater detail. Recommended analyses by myself and Reviewer 2 were not carried out, in particular the ploidy level/longitude analysis. I also suggested the addition of a partial Mantel test (test the correlation between genetic distance and another distance matrix, while controlling for other distance matrices), but instead, you cut the sentence from the Results section that prompted this suggestion.

In my second review of your manuscript, I again attempted to explain my problem with the idea of longitude being a meaningful environmental gradient around which to serve as the basis for your manuscript. I would like to address your rebuttal to this note. Starting with the second paragraph of your rebuttal to this section, you clarified your methodology of using Mantel tests between genetic diversity and precipitation, temperature, and geographic distances. You noted that precipitation, temperature, and geographic distance all vary across longitude. This was my point as well, and it does not bolster the importance of longitude. Your testing of the effects of precipitation, temperature, and geographic distance is appropriate, and makes sense, yet throughout the manuscript, it is longitude that is discussed as a gradient of ecological importance. This paragraph does not make a case for longitude as a biologically-relevant variable.
Validity of the findings: I have no additional comments.
Additional comments: I have an additional note to make regarding your response to my question regarding the relevance of longitude as an environmental variable. In the first paragraph of your response, you stated:

"Understanding the population genetic pattern and process of gene flow requires a detailed knowledge of how landscape characteristics structure populations. Higher temporal resolution can be provided using population genetic sampling and measures for detecting genetic relationships within continuously distributed populations in a landscape gradient (Landguth et al., 2010; Blair et al., 2012)."

I had difficulty understanding these sentences. What is the population genetic pattern of gene flow? How does temporal resolution fit into this question? Why are Landguth 2010 and Blair 2012 cited here, but not in your manuscript? After looking around online, I came across Manel 2003, "Landscape genetics: combining landscape ecology and population genetics". This is the first sentence of the abstract of that paper:

"Understanding the processes and patterns of gene flow and local adaptation requires a detailed knowledge of how landscape characteristics structure populations."

The next two sentences are from Bolliger 2014, "Landscape genetics since 2003: status, challenges and future directions":

"These individual-based methods provide much higher temporal resolution for detecting landscape genetic relationships (Landguth et al. 2010; Blair et al. 2012). This makes individual-based approaches particularly valuable for analyses within continuously distributed populations, or in gradient landscapes."

It became clear that your rebuttal paragraph was pieced together from the sentences of other published literature. The effort to synthesize this content into your own words was insufficient, leading to a puzzling paragraph that failed to explain or support your case. The sentences were similar enough to their sources that they were able to be quickly tracked down to their sources, despite being uncredited. You cited neither Manel 2003 nor Bolliger 2014, the sources from which you drew these segments, yet cited Landguth 2010 and Blair 2012 because Bolliger 2014 did.

I observed this style of writing in the prior version of the manuscript, and commented on it in my second review. You replied in your rebuttal that the whole manuscript had been carefully checked and revised, but I have doubts that the manuscript is truly free of improper incorporation of the unacknowledged work of others. I leave it to the editors to determine if this is the case.


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: NON-LINEAR GENETIC DIVERSITY AND NOTABLE POPULATION DIFFERENTIATION CAUSED BY LOW GENE FLOW OF BERMUDAGRASS [CYNODON DACTYLON (L.) PERS.] ALONG LONGITUDE GRADIENTS
Review round: 3
Reviewer: 2

Output:
Basic reporting: 1. Although the language has been greatly improved, there are still many typos and grammatical errors that must be resolved to improve clarity. Lines that require improvement include:
52: What are you “describing the evolutionary” significance of?
58-65: These sentences are confusing. You begin by saying longitude is the driving factor of some species distributions and then explain this is only because specific environmental variables are correlated with longitude. These sentences can be improved by first emphasizing that longitude is correlated with environmental variables and then continuing with examples.
87 and 89: “is” should be “are”
248: Which population?
251: I believe the authors mean “positive” rather than “negative” according to Table 4.
258, 360 and 405: “exited” should be “exists”
259: “differences in” should be added after “significant”
298-299: This sentence is unclear.
310: Currently phrasing suggests higher FST is the cause of local genetic differentiation. This should be rephrased to state higher FST indicates differentiation.
379-382: This sentence is unclear.
387-388: “because longitude might be easily affected by ecological isolation” should be replaced with “because populations were ecologically isolated”.

2. 330-332: McMillian’s theories apply to North America. How does this apply to your region of study?
Experimental design: 1. 197-200: Why were the populations grouped in this manner? This STRUCTURE and UPGMA results suggest these are not genetic groups therefore it’s unclear what their comparison accomplishes.
If these groups have biological meaning, how were the genetic diversity parameters calculated for each group?

2. 255-261: The authors should include the p-values for comparisons made.

3. I agree with Reviewer 1’s previous review that a mantel test should be conducted between genetic distance and geographic controlling for precipitation distance in order to test the author’s hypothesis that geographic distance determines genetic differentiation.
Validity of the findings: 1. 284: The authors argue that higher genetic diversity of populations at mid-longitudes could result from higher “communication” between populations. This is contradictory to the low levels of gene flow reported at line 215.

2. 289-291: The authors argue that the PCoA and Mantel tests show genetic clustering occurs along the longitudinal gradient yet the PCoA shows populations from across the entire cline form clusters rather than with populations geographically nearby. The clustering in the PCoA is contradicted by the positive correlation between genetic distance and geographical distance. As reviewer 1 suggested, this analysis should be re-run controlling for precipitation distance to disentangle this relationship.

3. 391-394: The relationship between ploidy, genetic diversity, and longitude were not tested. The authors only tested the relationship between ploidy and genetic diversity. The phrasing of this sentence should be improved to clarify that diversity increases with ploidy, not ploidy across longitude.
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: A VARIABLE-RATE QUANTITATIVE TRAIT EVOLUTION MODEL USING PENALIZED-LIKELIHOOD
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is well-written and describes a new method using Penalized Likelihood to infer variation in rates of BM across the tree. The paper adequately describes the approach and provides some exploration of its behavior.
Experimental design: The paper is well-written and describes a new method using Penalized Likelihood to infer variation in rates of BM across the tree. The paper adequately describes the approach and provides some exploration of its behavior.
Validity of the findings: Results are interesting and will be helpful for the reader interested in applying the method.
Additional comments: Lines 141 to 143: I understand this example is here just to show the overall expectation under this model when rates get higher. Would be good to include a warning of the huge variation in rates here. From 0.186 to 368. A rate of 368 is so fast that the phenotype value becomes almost a random draw because the multivariate normal distribution is extremely wide. This figure might also give the false impression that this method will estimate unrealistic rates of trait evolution, which I think is not the intention of the author. So, it might be important to say that.

Figure 3: The same comment made above applies here. Is it possible to provide an example with a rate variation that is closer to what we observe in empirical studies? The figure shows that the method is capable of recovering the correct distribution of rates (with lambda = 1), but it would be better to have an example with rate variation inspired by empirical data. For example, having a range of BM rates equal to the range estimated under some data set.

Lines 156 to 162: Alternatively, the author could have shuffled the rates of the branches in Figure 2 to produce a case of uncorrelated rates with the exact same rate variation. The result should be very similar, however.

Figure 5: The results here are interesting. It is possible to see a different behavior of the model when the rates are uncorrelated. The penalty of lambda quickly result in practically a homogeneous trait evolution model (i.e., a single BM rate applied to the whole tree). This rate seems to be very close to the average rate of the (although to see the true mean rate we would need to weigh it by the length of the branches). Any idea of why this is happening?

Figure 7: Please include the explanation for the black and gray dots in the Figure caption.

Figure 8: Please include the explanation for the black and gray dots in the Figure caption.

Lines 262 to 269: Here the author reiterates the results shown in the previous section. However, there is no discussion about which properties of the model are likely the reason behind this pattern. It would be helpful if the author could extend this topic and discuss in more depth why the model behaves in this way and the possible reasons behind the difference in the results when rates evolve through BM and rates are uncorrelated.

Lines 270 to 275: How this result compares with other approaches that are able to estimate varying rates of BM across a tree without predictor regimes? For example, Eastman et al. (2011 Evolution 65:3578-3589) approach of RJMCMC to fit varying rates of a BM in a phylogeny, implemented in geiger::rjmcmc.bm is able to sample the posterior distribution of rate regimes across the tree. Other options would be BAMMtraits (by Dan Rabosky and colleagues) and bayOU (by Josef Uyeda – but with restrictions to model a BM process instead of an OU). It would be interesting to compare the output from a RJMCMC approach with the Penalized Likelihood method.
	Although the author makes it clear that this method is intended to explore the data, and RJMCMC is a very distinct approach, users will ask this question when choosing which approach to use and it would be very helpful to have the perspective from the author here. If the objective is an exploration of the rates of trait evolution across the tree, then a data-driven approach such as RJMCMC can provide an alternative result like the one described here. A contrast and comparison with other approaches already available is necessary here.

About the ‘multirateBM’ program. Currently, it seems to only be available through the github repository for “phytools” and not via the standard installation using “install.packages”. This needs to be noted in the paper. It would be also very helpful to improve the help page for the function. More specifically, more details about the use of lambda (in the “Details” section). The help function also does not have any “Examples”, which are very helpful for the users. It seems that the same empirical analysis performed here can be added as an example in this function (the data seems to be also available in the package).

Finally, scripts for the plots and simulation done here have not been made available (or their availability was not made clear enough in 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: A VARIABLE-RATE QUANTITATIVE TRAIT EVOLUTION MODEL USING PENALIZED-LIKELIHOOD
Review round: 1
Reviewer: 2

Output:
Basic reporting: Clear English, perhaps a little too conversational. Mostly sufficient references, but not in relation to some important concepts (such as cross-validation, previous studies of similar models in the financial literature.)
Experimental design: Definitely within the scope of the journal. The research question is theoretical: Can we build evolutionary models with varying rates of evolution over the tree? The paper certainly brings to light a knowledge gap, and is a step closer to filling that gap. Mostly rigorous and very technical. The functions are available in the author's R package, which is leading software for these kinds of analyses.
Validity of the findings: The findings are valid, as far as they go. These models are difficult to fit and suffer from "survivor bias:" Our conclusions are only based on extant taxa. The full evolutionary history of the study organisms might lead us to different conclusions. Unfortunately, a good fossil record is rarely available! This is a problem with the entire field and I do not expect this paper to correct that misconception.

Conclusions are justified, so far as theoretical studies can be. The statistical techniques are well-known and sound. The conclusions are well stated and link back to the original model.
Additional comments: Interesting paper! It could lead to even better work. Please see my attached document.


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: ESTIMATING THE IMPACT OF CLIMATE CHANGE ON THE POTENTIAL DISTRIBUTION OF INDO-PACIFIC HUMPBACK DOLPHINS WITH SPECIES DISTRIBUTION MODEL
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript has some issues in the clarity, it needs some references and I have some comments about the figures. Please, see "General comments for the author" section for all my comments.
Experimental design: I have some comments about the methods. Please, see "General comments for the author" for more information.
Validity of the findings: No comments.
Additional comments: The research has valuable importance for biodiversity. I am not able to review the language, but the text is, in general, well written, and understandable. I include some suggestion to contribute to the manuscript, please find below:

General suggestion: My suggestion is to change the IPHD for Sousa chinensis or S. chinensis throughout the text.

Abstract:
Clear and objective, it is given the important and relevant information of the manuscript.
Line 26, the information "As an IUCN critically endangered species", is not correct. At the IUCN (and accordingly with the introduction of the present manuscript) the category of Sousa chinensis is VULNERABLE. Please, correct.

Lines 28 and 29: What is the relevance of the term "to our knowledge"? I think that it is implicit, and you do not need to add this term in the abstract. If you remove it, your sentence will be clearer and objective.

Line 28: The threats of human disturbance and environmental pollution to this population have been documented extensively.
In the introduction section (see the lines below) you only give one reference for the extensive documentation, please provide more references or change this sentence.

Key words: The keywords must be more objective and need to reflect the manuscript content and help it be found online. Suggestion: the words "Species distribution models; Ensemble model and Potential distribution" are implicit and/or present in your title (e.g., title: Estimating the impact of climate change on the potential distribution..." and "[...] dolphins with species distribution model distribution model". My suggestion is that you can add some words about your manuscript (e.g., marine fauna, conservation, greenhouse gas emissions, human impact, etc.). Also, in your results the projections of the dolphin also reveal the gain of habitat, thus I think that the word "Habitat contraction" can be changed to "future projections".

Introduction:
Line 47: "Indo-Pacific humpback dolphins (IPHD), Sousa chinensis, belong to the porpoise family of cetaceans are also known as "mermaids'' and "water pandas".
 What are known as mermaids and water pandas? All the cetaceans or Sousa chinensis? Please, be clear.

Lines 50, 51, 52, and 53: These areas, which have intensive commercial fisheries, are usually rapidly developing and are easily polluted by industrial production and the lives of local residents; the corresponding consequences of habitat degradation may lead to population declines or even put this species at risk of extinction (Li, 2020).
I do not understand, what happens to the local residents? And the habitat degradation may lead to which population declines? Which species? Please be clear. Also, the reference is needed before the semicolon (i.e., [...] of local residents (REFERENCE?); [...].

Also, in the abstract, you say "The threats of human disturbance environmental pollution to this population have been documented extensively"
Please, provide more references or modify your abstract.

Line 54: "In recent years, the numbers of records on strandings or deaths of IPHD have increased in China" (REFERENCE).
Please give the reference

Line 55: The threats of human disturbance and environmental pollution to this population have been documented extensively ((IUCN, 2019).
Please, update the IUCN reference.
Also, include the correct citation for the inclusion of Sousa chinensis in the IUCN: Jefferson, T.A., Smith, B.D., Braulik, G.T. & Perrin, W. 2017. Sousa chinensis (errata version published in 2018). The IUCN Red List of Threatened Species 2017: e.T82031425A123794774. https://dx.doi.org/10.2305/IUCN.UK.2017-3.RLTS.T82031425A50372332.en. Downloaded on 26 May 2021.

Line 56 and 57: and understanding the species distribution is a prerequisite for plan formulation (REFERENCE).
What do you want to say to understand the distribution? Do you want to know the species distribution? To predict the species distribution for the future? Please, be clear.
Also, give the reference

LInes58 and 59: A species lives in a certain environmental niche space, so environmental changes greatly influence species distribution (REFERENCE).
Please, give the reference.
Also, why do environmental changes have a great influence? Please, be clear.

Lines 58 to 67: Please rewrite this paragraph. The phrases are lost (e.g., The distribution of top marine predators is related to a variety of environmental determinants, such as ocean depth, salinity, distance to the shore, and sea surface temperatures. Global climate change has caused significant changes in marine environmental conditions over the past decades)
Also, Please, give the references.

Lines 71 and 72: Currently, SDMs are applied broadly in the life and environmental science fields (References).
Please, give the references. In what kind of studies, the sdms are applied? Give some examples.

LIne 75 and 76: Accordingly, the use of SDMs in conservation biology and biodiversity assessments is ever increasing (Araújo et al., 2019).
Please, give more examples here.

Line 77:  In this study, we developed SDMs and built an ensemble model.
Ensemble for the algorithm or the AOCMs?
Please, specify.

Line 85 and 86: In addition, it provides an essential reference to solve marine conservation planning problems.
This manuscript has, indubitably, great importance, but I do not think that is an essential reference, because the conservation plans can be elaborated without ECMS studies. My suggestion is: "It provides an ADDITIONAL (or important) reference to solve marine conservation planning problems''.

Material and Methods:

Line 89: The figure does not have that information. Please see the lines below.

Line 123: e.g.
E.g., ('exempli gratia') means "for example". You just used three AOGCMs, the correct term is "i.e.," (id est) that means "namely".

Line 124: CSM4, HadGEM2-ES, MIROC5.
Please, provide the institutions where the AOGCMs were generated.

Line 148: To integrate the advantage of each model, we built an ensemble model that was based on the weighted average of the predictions from the selected models and used this ensemble model to predict IPHD distributions under present and future climate conditions.
The ensembles were also generated for the AOGCM, correct? Please, give this information in the methods.

Line 152: by using a threshold that maximized the TSS value
What threshold was used?

Line 158: variable(Zhang et al., 2019.
Please, add a space between "e" and "(" [i.e.,  variable (Zhang et al., 2019).].

Results:
Line 166: The figures 3 and 4 are supplementary data.

Line 166 and 167: The AUC and  TSS values of any individual model were lower than those of the ensemble model.
Do you have any figures to illustrate? That would be great in the supplementary data.

Line 175: The Figure 5 is also supplementary data.

Line 176 and 177: The Figure 6 is also supplementary data.

Discussion

Lines 195 and 96: Utilizing georeferenced presence/pseudoabsence data and the corresponding environmental data, we innovatively developed an ensemble model for IPHD to predict the present and future potential distributions.
Your study has great importance, but the methodology of ensemble models has been used for many years. Even though this study was the first to use that methodology for Sousa chinensis, I am not sure about that word. You can simply write: "we developed an ensemble model" and it's ok and still important.

Line 208, 209, and 210: we recommend using an ensemble model to predict potential species distributions and habitat suitabilities (Araújo and New, 2007; Thuiller et al., 2009; César and Pedro, 2011; Shabani et al., 2016).
You recommend something in that phrase, so why the references? Are those examples of studies that used ensemble models? Please, be clear.

Line 213: for example, the coast of Malaysia, which is also a suitable habitat for white dolphins
These sentences are not necessary. It does not contribute to the sequence of the text.

Line 226: i.e or e.g.?

Line 231: considerable biological and ecological responses
Please, can you give some examples? What is the difference between the East China Sea to other marine habitats?

Line 245 and 246: Because of the data availability, the realized niche of IPHD, such as human activities and dietary structure, were not considered in this study. Stomach content analyses in previous studies have found that humpback dolphins consume a wide variety of pelagic and demersal fishes (Ning et al., 2020).
The methodology used in this paper does not permit the analysis of biotic variables. My suggestion is to remove this phrase.

Line 257: disorders(Xu et al., 2020).
Please add a space between "s" and "(". i.e: disorders (Xu et al., 2020).

Line 264 and 265: Protected areas have been considered to be an effective in situ strategy for conserving biodiversity and ecosystem services (REFERENCE).
Please, give the reference.

Line 267: (2017-2026))
Please, correct. Remove one ")"

Line 268: The
268 adverse effects of climate change on the protected areas of other animals have been elucidated (D’Amen et al., 2011; Zhang et al., 2020b).
What animals?
Also, include an e.g. before the references or, please, provide more references.

Figures:

Figure 1: What would you like to illustrate with this map? If the distribution of Sousa chinensis, please, include the proper information in the caption of what species you are illustrating the distribution. Also, please, include the occurrence points of Sousa Chinensis.

Figures 2, 3, 4, 5, and 6: My suggestion is that figures become supplementary data.

Figure 7: Please correct: Binary outputs to Binary output.
Figure 7A: Please correct: Binary outputs to Binary output.
It is necessary to inform how you make the binarizations, was it based on which thresholds? 10%? Lower presence training?

End of revision


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

Input:
Title: ESTIMATING THE IMPACT OF CLIMATE CHANGE ON THE POTENTIAL DISTRIBUTION OF INDO-PACIFIC HUMPBACK DOLPHINS WITH SPECIES DISTRIBUTION MODEL
Review round: 1
Reviewer: 2

Output:
Basic reporting: “Estimating the impact of climate change on the potential distribution of Indo-Pacific humpback dolphins with species distribution models” is a good manuscript. The study brings up a worrying scenario for the future conservation of the species, the analyses are largely adequate, and the text is professionally written. However, some adjustments are necessary for different parts of the manuscript for its effective publication. My first comment is the conflict in the number of occurrence records in Line 31 on the Abstract (83 occurrence records) while in Line 96 on Material and Methods (82 of which were within our study area) that should be checked. The Abstract could inform more details about the timelapse to forecast under different future climate scenarios. The Introduction used adequate references. I suggest inserting some references to Line 46-47 and Line 58-59. I think that Objectives (Line 77-86) can be rewritten to make it clearer the real goals and expectations of the manuscript. We already have forecasting models for the target species in a smaller geographic area and with fewer algorithms. Citing them can help in developing hypotheses to answer with a weighted ensemble model, which does not always get the best results as suggested in Line 207 to Line 210. I suggest Vasconcelos & Doro 2016 (10.1007/s11284-016-1401-8) as an example to reformulate de the goals of the study.
Experimental design: The experimental design is very well described for the Study Area, IPHD Data Collection, Environmental Variables, Resolution, and Future Projections. But the description of the weight ensemble model could be improved. Only in the legend of Figures 3 and 4, the reader can find out the threshold for AUC and TSS were select to excluded models that have been utilized in the weight ensemble model, cited in Line 166 in the Results. It was not clear if the ensemble model was made in the biomod 2 package as well. I would like to point out the ODMAP protocol (https://odmap.wsl.ch/ ) that provides a checklist for authors detailing key steps for model building.
Validity of the findings: In Line 37 and in Table 2, the authors mention that over 80% of the suitable habitat in the present day will be lost in all RCP scenarios in the future. This is a worrisome scenario, but the results may be inflated by the high overprediction of the models due to the environmental variables used. Unfortunately, there are no biotic variables for the study area that could refine the model for the target species (see Hunt et al. 2020 cited in the references). Areas, where the species has never been observed in the current climate conditions and were lost in the future climate scenarios, may inflate these results. For conservationist proposals, stability areas are important to report. In Table 2, the authors could report the percentages of new areas and areas of stability to Sousa chinensis, if it is possible. A minor comment is about the known absence points. The authors do not point out whether the known absence points were correctly predicted by the models for the current climate conditions. This could strengthen the validity of the models.
Additional comments: Figure 1 could be more informative, or it could be deleted. The graphs in Figures 3 and 4 are usually displayed as box plots. The article should avoid indicating that ensemble models are the best as quoted in lines 207 and 210.  Hao et al. (2020) demonstrate a case where this type of model has not shown the best performance over individual models (https://onlinelibrary.wiley.com/doi/epdf/10.1111/ecog.04890). Ensemble models are important to reduce uncertainties, but it should be emphasized that evaluate the predictive ability of models is just as important.


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: COMMON MOTOR PATTERNS OF ASYMMETRICAL AND SYMMETRICAL BIPEDAL GAITS
Review round: 1
Reviewer: 1

Output:
Basic reporting: General Comments: This paper is well-written only at the former part of the whole manuscript, and it is interesting for us that whether the muscle control mechanisms are equivalent between the trailing and leading legs in different gaits. But some statements were not supported by your own data. There are many critical issues on this manuscript, in particular, statistics, results and the latter part of the discussion, and conclusion sections. The most significant issue is that this research completely lacks metabolic data, so I think that the structure of the 'story' should be re-constructed.

Specific comments;
1.	In the conclusion section of the abstract, the authors stated about metabolic cost of skipping, but they did not measure metabolic data. This statement should be deleted.
2.	Introduction is well-organized. Its research necessity and hypothesis are logically explained, but the discussion section does not specify what data is the most significant in your study.
3.	In the methodological section, the authors measured EMG from 7 muscles. In particular, GM has two heads, so the authors should specify which head they focused.
4.	Are these 7 muscles for EMG analysis are good enough compared to other previous studies?
5.	Gait speeds were expressed as km/h. It should be replaced as m·sec-1.
6.	There is a serious problem in statistics. You need to compare the data with two-way ANOVA. Why did the author use one-way ANOVA for comparing these data sets? I cannot agree with this statistics.
7.	In line 307, a term “module 2 is module 3 in Fig.4. Please check this.
8.	In this analysis, the authors used kinematic analysis. They quantified the external work (Wext), but internal work was not analyzed. Why not? I think that not only the inverted pendulum but also the recovery rate of the mechanical work may be able to support your idea why the energy cost of skipping is so expensive than other gait.
9.	In Fig. 1, are there any significant differences? If there is, please put * or #.
10.	F values are completely lacking from the result section.
11.	I do not understand the linkage of each figure, because only Figs. 2, 4, and 7 appeared in the discussion section. I assumed that several figures should be in the supporting information.
12.	Were your hypotheses established? In Line 370 and 443, you stated that 'According to…'. I assumed that both hypotheses were established. But what results (or Figure) support your statement?
13.	The third hypothesis appeared in the conclusion section. The structure is highly confused.
14.	I also feel strange at the conclusion section, because several articles are referenced. This section should be concluded based on your own data.
15.	The latter part of your conclusion section never proved high energy cost of skipping. These statements should be deleted.
16.	I could not find out any advanced interpretation based on your own data sets in the discussion section. The motor control study always requires neuromechanical evidence or physiological mechanisms to prove your hypothesis. Again, the research focus is good, but the data do not always support statements in the discussion and conclusion sections. For example, which synergies determine the metabolic cost of walking, running, and skipping? (although the metabolic data is lacking…) Are those equivalent among different gait even if the gait speed is the same at 6.5km/h? And why? Yes, synergies are necessary to simplify complicated muscle control systems during different gait patterns. So I think that the 'story' should be simplified whether the synergies happen at the same muscle regions during the same gait cycle among walking, running, and skipping.

Minor comments;
1.	In line 408, ')' was doubly used. Check the spelling. This kind of minor mistake can be seen in Line 429 (need a space between ';' and 'they').
2.	New lines are not necessary since Line 421 to Line 446. These are minor issues, but more elaborations should be conducted before submitting a manuscript.
Experimental design: Well structured, but the metabolic information is completely lacking.
As stated in the basic reporting, I highly concerned about statistics.
Validity of the findings: Viewpoint is interesting, but an advanced interpretation or newly-explained physiological mechanism is not found.
Additional comments: General Comments: This paper is well-written only at the former part of the whole manuscript, and it is interesting for us that whether the muscle control mechanisms are equivalent between the trailing and leading legs in different gaits. But some statements were not supported by your own data. There are many critical issues in this manuscript, in particular, statistics, results, and the latter part of the discussion, and conclusion sections. The most significant issue is that this research completely lacks metabolic data, so I think that the structure of the 'story' should be re-constructed.

Specific comments;
1.	In the conclusion section of the abstract, the authors stated about the metabolic cost of skipping, but they did not measure metabolic data. This statement should be deleted.
2.	Introduction is well-organized. Its research necessity and hypothesis are logically explained, but the discussion section does not specify what data is the most significant in your study.
3.	In the methodological section, the authors measured EMG from 7 muscles. In particular, GM has two heads, so the authors should specify which head they focused on.
4.	Are these 7 muscles for EMG analysis are good enough compared to other previous studies?
5.	Gait speeds were expressed as km/h. It should be replaced as m·sec-1.
6.	There is a serious problem in statistics. You need to compare the data with two-way ANOVA. Why did the author use one-way ANOVA for comparing these data sets? I cannot agree with the statistics used in this manuscript.
7.	In line 307, a phrase "module 2" may be "module 3" in Fig.4. Please check this again.
8.	In this analysis, the authors used kinematic analysis. They quantified the external work, but the internal work was not analyzed. Why not? I think that not only the inverted pendulum but also the recovery rate of the mechanical work may be able to support your idea why the energy cost of skipping is so expensive than other gaits.
9.	In Fig. 1, are there any significant differences? If there is, please put * or #.
10.	F values are completely lacking in the result section.
11.	I do not understand the linkage of each figure. For example, only Figs. 2, 4, and 7 appeared in the discussion section. I assumed that several figures should be in the supporting information.
12.	Were your hypotheses established? In Line 370 and 443, you stated that 'According to…'. I assumed that both hypotheses were established. But what results (or Figure) support your statement?
13.	The third hypothesis appeared in the conclusion section. The structure is highly confused for me. Note that PeerJ is a multidisciplinary journal across wider research areas.
14.	I also feel strange about the conclusion section, because several articles are referenced. This section should be concluded based on your own data.
15.	The latter part of your conclusion section never proved the higher energy cost of skipping than other gaits. These statements should be deleted.
16.	I could not find out any advanced interpretation based on your own data sets in the discussion section. The motor control study always requires neuromechanical evidence or physiological mechanisms to prove your hypothesis. Again, the research focus is good, but the data do not always support statements in the discussion and conclusion sections. For example, which synergies determine the metabolic cost of walking, running, and skipping? (although the metabolic data is lacking…). Also, are those equivalent among different gait even if the gait speed is the same at 6.5km/h? And why? Synergies are necessary to simplify complicated muscle control systems during any gait pattern. So I think that the 'story' should be simplified whether the synergies happen at the same muscle regions during the same gait cycle among walking, running, and skipping.

Minor comments;
1.	In line 408, ')' was doubly used. Check the spelling. This kind of minor mistake can be seen in Line 429 (need a space between ';' and 'they').
2.	New lines are not necessary from Line 421 to Line 446. These are minor issues, but more elaborations should be conducted before submitting a 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: COMMON MOTOR PATTERNS OF ASYMMETRICAL AND SYMMETRICAL BIPEDAL GAITS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Terminology should be improved throughout the manuscript. If raw data (enveloped EMG signals) is involved in the manuscript, it is suitable to help readers understand the methodological proceedings.
Experimental design: Data recording from bilateral legs is questionable. Statistical analysis should be improved. The current version uses parametric test for small sample size data.
Validity of the findings: Interpretation of findings should be more clearly written.
Additional comments: The manuscript examined the motor modules during skipping. I think that the purposes of the manuscript are significant in neurophysiological and motor control studies. However, I have some concerns regarding terminology and methodology. I suggest that the authors improve ambiguity and the manuscript should be more clearly written.

Major comments
1. Introduction is ambiguous and written redundantly. I suggest that the authors should make introduction section more briefly. For example, second paragraph in introduction, description regarding the metabolic cost of skipping is not very important for this study, because this study did not collect the data of energy expenditure during locomotion.

2. I could not understand how the authors collected EMG data during skipping. The authors should explain more clearly. EMG recordings were done from bilateral legs, but walking, running, and skipping are bilateral symmetric. So, the bilateral EMG recordings are not need to compare the motor modules between locomotor movements. It is enough to collect from one leg. Please justify your study design about EMG recording. In addition, I was confused “preferred leg”, “leading leg”, and “trailing leg” during skipping. In the case of stepping over an obstacle, analyzing differences in muscle activation between leading and trailing legs are significant. However, the authors compared the motor modules between walking, running, leading leg, and trailing leg. The authors need to explain the EMG processing in this study how the EMG data in leading and trailing legs during skipping was sampled showing a typical example.

3. Statistical analysis is questionable. The number of the extracted modules by NNMF in locomotion is different between speeds, locomotor movements, and types of modules. As shown in figure 2, sample size (the number of synergies for each type of module) is not fixed. Thus, I suggest that non-parametric test is appreciate in this study. Furthermore, I could not understand why the authors done one sample t-test to sort the type of modules. Similarity of the modules across gaits and speeds was evaluated by cosine similarity. Is the maximal value of cosine similarity not enough to sort the modules?

Minor comments
Abstract
L49, Is skipping asymmetry movements?
L50, This sentence is method.
L52, How did you identify motor modules from EMG data? The authors should write it in method section.

Introduction
L80, Movement of skip is bilateral asymmetry?
L106, Mistake citation, Yokoyama et al., 2019.
L117, Mistake citation, Saito et al., 2018b is running study.

Methods
L167, Foot note is expressed as number.
L215, Which is the preferred limb? Preferred limb means dominant limb? How did you identify the preferred limb during walking and running?
L216, The preferred limb was used as trailing leg. What meaning of this sentence?

Results
L275, The authors show difference in gait parameters among different types of locomotion. Why don’t you compare the parameters between bilateral legs during walking or running? Were gait parameters similar between leading and trailing limbs? In the manuscript, the authors demonstrate walking and running are symmetry.
L294, The authors used 4 types of modules for analysis. How many modules are involved in each averaged data of Figure 3? The authors should show the number of modules (sample size) which included in mean of activation timing and weighting.

Discussion
L338, I was confused that much terms exist in the manuscript such as trailing leg, leading leg, stance phase, forelimb, hindlimb. What is different between these terms. I suggest that the authors should define these terms in introduction or method sections.
L360, This sentence is not necessary.
L386, The extracted synergies between present and previous study were shared, but the number of EMG recordings between present and previous works were quite different. Capellini et al. recorded 32 muscles included lower-limb and trunk muscles and Yokoyama et al. recorded 16 muscles during locomotion. This is methodological issue in this study. The authors should discuss effect of number of EMGs on the motor module extraction by NNMF.


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: COMMON MOTOR PATTERNS OF ASYMMETRICAL AND SYMMETRICAL BIPEDAL GAITS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Many statements are still redundant. Also, if you want to refer to the mechanical efficiency, you needed to measure metabolic data from all 14 participants. As you may know, there is a big gap between muscular synergies and locomotion efficiency, even if you succeeded to take the metabolic data from all participants. You can and should re-construct the 'story' of the whole manuscript.
Experimental design: More ingenuity is necessary.
Validity of the findings: The story of this paper cluttered so much, so it is very difficult for me to find out where the most important part is. Please remind that you stated more than 6400 words in this paper. That is too many. At most, 4500-5000 words including references (e.g. Steele, Tresch, & Perreault, (2013) in the main text) are good enough to examine your study questions.
Additional comments: The story of this paper still cluttered so much, and it has not yet got together. Many statements are still redundant. My recommendations for your future submission are as follows.

1) Please focus only on the EMG data obtained from three different gaits. Mechanical and metabolic data are not necessary any more, because you could obtain only 4 metabolic data.
* Are mechanical and metabolic data truly necessary to examine your original research questions?

2) A simple comparison can be conducted only at 1.8 m/sec.
** Other gait speeds are not comparative among three different gaits, so that these data should be in the supplemental information. If so, anybody can understand 1-way ANOVA is an appropriate statistical method.

3) Many redundant statements should be deleted to complete within 4000-4500 words.
** For example, L121-L134 and L492-L503 are not related to your main focus.

4) Are all figures necessary in 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: COMMON MOTOR PATTERNS OF ASYMMETRICAL AND SYMMETRICAL BIPEDAL GAITS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Terminology should be improved in the manuscript. Raw EMG data is needed to understand the methodology.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Manuscript was improved more clearly. However, current version of the manuscript is difficult to understand yet. I have some concerns to improve the manuscript below.
Specific comments
1. I could understand what skipping mean in the manuscript. However, “Skipping” will confuse the readers yet. I suggest that the authors use “Galloping” or “Unilateral Skipping” instead of “skipping” throughout the manuscript.

2. The authors should explain how individual participants familiarized galloping before the experiment. I expect that some participants did galloping awkwardly. Or, all participants could galloping well without any trials?

3. The authors should show typical example of raw data (i.e., envelop EMG signals) as a function of the percentage of a step cycle. I suggest that the figure involving the illustration of gallop-like-skipping movement is suitable to help readers understand the methodologies in this study.


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

Input:
Title: COMMON MOTOR PATTERNS OF ASYMMETRICAL AND SYMMETRICAL BIPEDAL GAITS
Review round: 3
Reviewer: 1

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


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

Input:
Title: LIVING SHORELINES ACHIEVE FUNCTIONAL EQUIVALENCE TO NATURAL FRINGE MARSHES ACROSS MULTIPLE ECOLOGICAL METRICS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript was clear, interesting, and well referenced.
Experimental design: The experimental design was clear and the methods were described in sufficient detail (as long as the comments below are addressed).
Validity of the findings: The findings are valuable and conclusions are well stated.
Additional comments: Summary:
I enjoyed reading this manuscript and I think it will make a very valuable contribution to the field. I have mostly minor comments. My only major comment is that I think the paper would greatly benefit from a figure(s) showing the raw data. The authors only present the z-scores and occasionally the range in z-scores, but they don’t provide any indication of the absolute values of fish biomass, for instance, or the variation across sites. This paper will be more broadly applicable and useful for other researchers if the authors can also present the average biomass, nutrients, abundance, etc. across all of the sites.

Minor comments:
Introduction:
•	Lines 34-35: Change to: “Losses are likely to be exacerbated where these conditions overlap with extensive watershed development”
•	Line 39: Change “Whereas” to “While”
•	Lines 55-58: I don’t agree with the use of the term nature-based features. Hardened shorelines can contain nature-based features (i.e. flower pots on seawalls for added habitat value), but the authors present these as distinct shoreline alternatives. I think the term nature-based infrastructure is more commonly and generally used and would be more appropriate here. But, I acknowledge that there is a diversity of terminology used in the field and not always consistently, so perhaps this is personal preference. The authors don’t have to respond to this, just something to consider.
•	Line 60: Change to “2017) and areas with greater wave energy are likely to need more highly engineered structures.”
•	Line 65: Change to “Nevertheless, the absence of an assessment..”
Methods:
•	Line 80-85: More detail is needed here on the individual sites. I would like to see a table that details the age of the living shorelines, structural materials used, width of marsh, average tidal amplitude, etc. This should be easily compiled from the supplementary data.
•	Line 86-87: A recent citation that might be helpful here showing that the vast majority of living shoreline studies have investigated fewer than 5 living shoreline sites: Smith, C., Rudd, M., Gittman, R.K., Melvin, E., Patterson, V., Renzi, J., Wellman, E. and Silliman, B., 2020. Coming to terms with living shorelines: A scoping review of novel restoration strategies for shoreline protection. Frontiers in Marine Science, 7, p.434.
•	Lines 95-96: How many cores were taken per transect? I think its only 1 but I would be explicit here. This is also a little confusing- saying that you collected cores along transects would lead me to believe that you collected multiple cores per transect. Were the cores a consistent distance from the marsh edge?
•	Lines 118-119: If the traps were set at high tide and puled at low tide wouldn’t they have a longer average soak time (i.e. ~6hrs)?
•	Lines 122-123: Again, this seems like a short soak time, though twice as long as the minnow traps despite being deployed for the same tidal range
•	Lines 127-129: What about fish? Did you only use the fyke nets to look at crabs?
•	Lines 129-131: I don’t really understand this methodology, so this needs to be clearer. Were you estimating the area of the entire marsh or just what was being sampled by the nets?
•	Line 137: Change to “Blue crabs”
•	Line 139: What does counted and weighed in composite by sampling effort mean? Why aren’t all of the nekton measures standardized to effort?
•	Lines 168-170: How long were the cameras deployed for during each survey event at each site?
•	Lines 174-176: 3 to 5 cameras where- at each site? Across all sites? During each sampling event?
•	Lines 168-181: It would be useful to give an overall range of the total number of days that were sampled at each site
•	Line 212: Can you add a sentence here describing why you chose the z-score approach. I’m guessing its because there was really high variability among the difference pairs of sites?
Results:
•	Line 241: Change to: “Among the four metrics (percent organic matter, C, N, and P), all paired…”
•	Line 252: I think it should be |z| in parentheses
•	Lines 283-285: Can you/did you look at the individual functional equivalence scores over time. It is very possible that some metrics (i.e. soil composition) will change significantly over time, whereas others that develop more quickly may not, which could confound the overall trend. I think investigating this for all of the metrics could be a useful addition.
•	Lines 283-285: It may not be significant, but looking at Figure 2 suggests to me that there is a trend of z-score increase with increasing age.
Discussion:
•	Lines 287-288: I’m not sure that you can draw this conclusion based on your data. You only have 2(?) sites that are two years or younger at the time of sampling and the majority of your sites are significantly older than that. Since you are calculating metrics across all of your sites, your z-score estimates are influenced by the majority of older sites that might have higher z-scores. Figure 2 suggests that one of your young sites reached functional equivalence and the other had not.
•	Lines 309-328: Interesting!
•	Lines 365-368: nice!
•	Lines 370: Change to: “lost from the degradation of natural fringing marshes”
Figures and Tables:
•	Supplementary dataset: Meta-data doesn’t include the units for many of the measurements and I think the table is missing data for the mussels in only the marsh for living shorelines.


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: LIVING SHORELINES ACHIEVE FUNCTIONAL EQUIVALENCE TO NATURAL FRINGE MARSHES ACROSS MULTIPLE ECOLOGICAL METRICS
Review round: 1
Reviewer: 2

Output:
Basic reporting: please see below
Experimental design: please see below
Validity of the findings: please see below
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: LIVING SHORELINES ACHIEVE FUNCTIONAL EQUIVALENCE TO NATURAL FRINGE MARSHES ACROSS MULTIPLE ECOLOGICAL METRICS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Clear, short, to the point, well-referenced
Experimental design: well designed
Validity of the findings: conclusions well stated and follows the results
Additional comments: No additional comments


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

Input:
Title: SCREENING AND IDENTIFICATION OF NOTCH1, CDKN2A, AND NOS3 AS DIFFERENTIALLY EXPRESSED AUTOPHAGY-RELATED GENES IN ERECTILE DYSFUNCTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article must be written in English and must use clear, unambiguous, technically correct text.
Experimental design: no proper Experimental design
Validity of the findings: no clear conclusion is given
Additional comments: Author performed reanalyzed work
 GEO accession no GSE10804 was previously analysed, work done and published.
1.Screening and identification of critical biomarkers in erectile dysfunction: evidence from bioinformatic analysis (PMID: 32161689 PMCID: PMC7050549 DOI: 10.7717/peerj.8653)
2. Transcriptional profiling of human cavernosal endothelial cells reveals distinctive cell adhesion phenotype and role for claudin 11 in vascular barrier function (PMID: 19622796 PMCID: PMC2765067 DOI: 10.1152/physiolgenomics.90354.2008)

Re analysed work is not acceptable Meanwhile, Author  not provided  Differential gene expression (DEGs) table with probe id, logFC, pValue, adj.P.Val, t value and Gene Name, which are more fundamental and basic in this work. No evedance in this work without this DEGstable.
Author not performed construction and analysis of target genes - TF regulatory network and  target genes - miRNA regulatory network


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: SCREENING AND IDENTIFICATION OF NOTCH1, CDKN2A, AND NOS3 AS DIFFERENTIALLY EXPRESSED AUTOPHAGY-RELATED GENES IN ERECTILE DYSFUNCTION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors have written the manuscript with a good flow to address the hypothesis at hand
Experimental design: The experiment design is validated with enough number of biological replicates and statistical analysis
Validity of the findings: The results have been obtained from previously published data and have enough replicates to address statistically relevant information. The findings are then validated in animal model of the disease. They have been validated using qPCR and western blot approaches. However, there is still some information that needs to be added to strengthen the manuscript.
Additional comments: The authors have done a good job at putting the data together as well as at extracting the relevant data from the previous datasets. However, there are some key points that need to be addressed and have been added as comments in the reviewed version.
Please make sure to add better representative images for the IF staining.


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: SCREENING AND IDENTIFICATION OF NOTCH1, CDKN2A, AND NOS3 AS DIFFERENTIALLY EXPRESSED AUTOPHAGY-RELATED GENES IN ERECTILE DYSFUNCTION
Review round: 1
Reviewer: 3

Output:
Basic reporting: Overall the manuscript needs more work to improve the readability, e.g. more professional English descriptions and clearer expression:

Line 41-42: Analyzing GEO seems a bit vague, at least list the type and number of samples used.

Line 49: 20 ARGs identified ultimately is a bit unclear - this seems not a proper summary of the whole Results section.

Line 54-56; Line 85-87 : Grammer and sentence structure issues.

Line 105: Here it says 3 samples for the ED group, but later in Line 204 it says 4 samples.
Experimental design: 1. I have some concerns on the GSE10804 dataset used in this project, which only contains 4 ED vs. 8 non-ED samples. Usually the DEGs identified from such a small sample size are prone to false positives.
2. Line 215m, after 20 ARG DEGs were identified, only 11 DEGs were used for enrichment analysis, is there a reason for only using a subset?
Validity of the findings: The autophagy related genes (ARGs) used in this manuscript lacks a clear definition. According to line 114, 381 ARGs were pulled from GeneCard by searching with the keyword "autophagy". However, the keyword "autophagy" gives us 6,346 results from GeneCard when I tried to replicate the procedure.
Additional comments: The therapeutic biomarkers has great values, and I believe this study will be of interest to scientists and clinicians involved in ED research in general. There are some areas the authors could modify to improve readability and clarity, as outlined above.


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

Input:
Title: SCREENING AND IDENTIFICATION OF NOTCH1, CDKN2A, AND NOS3 AS DIFFERENTIALLY EXPRESSED AUTOPHAGY-RELATED GENES IN ERECTILE DYSFUNCTION
Review round: 2
Reviewer: 1

Output:
Basic reporting: The reporting for the manuscript has improved through revisions
Experimental design: The experimental design has been updated and clarified by the authors to support their hypothesis
Validity of the findings: They have updated the manuscript based on the reviewers' suggestions
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: IN VITRO EFFECT OF RESIN INFILTRANT ON RESISTANCE OF SOUND ENAMEL SURFACES IN PERMANENT TEETH TO DEMINERALIZATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is clear ad straightforward. English needs some minor corrections

The literature review is adequate and appropriate for the paper.

The structure and figures are well presented and relevant to the hypothesis.
Experimental design: The experimental design is stand for this type of studies.

The research question is clearly stated although the originality of the study is not too unique.

The research was developed following the methodology commonly used for these studies. The methods are adequately described.
Validity of the findings: The results are clinically relevant confirming the value of the infiltration technique

The conclusions are based on the obtained results/
Additional comments: No additional comments