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: INTEGRATIVE ANALYSIS OF MIRNA–MRNA NETWORK IN IDIOPATHIC MEMBRANOUS NEPHROPATHY BY BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The author's goal is to integrate publicly-available mRNA and miRNA datasets to identify potential biomarkers or therapeutic targets for idiopathic membranous nephropathy. Once they have identified and analyzed 2 datasets, they seek to confirm their findings in validation datasets. The basic flow of the manuscript is to identify differentially expressed (DE) mRNAs and miRNAs, find the DE mRNAs that are negatively correlated with the DE miRNAs, conduct biological annotation and pathway analysis and then validate their findings.

The authors should be applauded for their ability to take published data, re-analyze it and make novel observations. This approach should be more frequently used by other investigators as the amount of data available currently greatly exceeds the amount of in-depth analysis available. In addition, integrating 'omic data is currently a hot research area. However, just because an analysis can be done doesn't mean it should be done or that it contributes to the goals of the manuscript. These are my major areas of concern with this manuscript, namely, that it is short on biological or clinical context and it isn't always clear why (and sometimes how) an analysis was performed. More details in the comments to the authors.

In general, the manuscript is well-written, but there are areas that are not idiomatic. For example, the authors say that genes are 'remarkably' expressed when the general term used is 'significantly'.
Experimental design: As stated, I like the approach of re-analyzing public data and integrating miRNA and mRNA data to discover novel biological insights. However, there are a number of areas where greater detail and/or concern exist:
Validity of the findings: Please see below.
Additional comments: Figure 1- The labels for volcano plots and heatmaps are incorrect.
     Why does 1D use a different color scheme?
     For figure 1 the authors state that 3415 miRNAs were differentially expressed, while 43 were 'remarkably' up-regulated and 15 were down-regulated. I don't know where the 3415 number comes from or what it means, but I think that mammals are only believed to have ~2000 miRNAs.

Figure 2- The role of the 'immune-associated genes' is one of the areas where the authors need to provide more detail and context.
     One presumes that the genes in the red circle of 2A come from the analysis performed using Funrich, miRDB and miRwalk. Did the authors add the results from these three tools together? If so, why? Much, much more detail is needed here. Why did they need to use 3 tools for this analysis?
    In the text, the 139 'key genes' are described as those that overlap between the predicted targets and the DE mRNAs, but also as those that are inversely correlated with the miRNAs. Both can't be true. Again, more details and context are needed here to fully understand the author's thought process.
   It also seems the authors just picked DE mRNAs that were expressed in the opposite direction as the miRNAs. This is the best they can do because the datasets were not generated at the same time, but it should be described as a significant limitation.
     The text says 58 genes came out of this analysis, but the figure says 59.

Figure 3- The authors describe the red and green colors, but what does yellow mean? There is no description of the colors used in 3C and a more thorough discussion of the meaning of the results is needed.
     Figure 3 is a figure that I also question how it contributes to the manuscript. It is clear these networks can be generated, but it isn't clear how they are supporting the results of the study.

Figure 4- Again, colors are used with no explanation. In the text, the authors recite the results they get, but what does it mean that these pathways were found? Anythings?
     Basically no context is given for the bottom part of figure 4. The one line title really lacks the information necessary to fully understand this figure.

Figure 5- much like figure 4 it needs much more explanation for the reader to understand why it is included.

Figure 6B- Why is the interaction of hub genes important?

Figure 7- In the .pdf version, figure 7 is basically unreadable while figure 8 looks really nice. The authors should remake figure 7 as they did in figure 8.

Figure 8- the y-axis needs to be labeled. The authors should double-check their statistics as well. miR-155-5p and 146a-5p are exactly the same, as are miR-204-3p and miR-23b-5p. It seems unlikely.

Figure 9- I really am not sure what this figure is trying to tell me. There needs to be a lot more detail.


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: INTEGRATIVE ANALYSIS OF MIRNA–MRNA NETWORK IN IDIOPATHIC MEMBRANOUS NEPHROPATHY BY BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors have conducted a study with paired miRNA and mRNA analyses. The language is clear and they also report having used a professional editing service. The overall design and reporting is appropriate.

Minor point: The introduction is too thin and it is not true that there is no knowledge about the pathophysiological mechanisms: Line 22-24 in abstract and line 51-52 in introduction. Please also mention and refer to the autoantigens PLA2R and THSD7.

The article has more figures than needed to tell the story. Figure 2, 4 and 5 could be shown as supplemental figures instead as they doesn't add that much anyways.
Experimental design: The experimental design seems appropriate with integration of different miRNA and mRNA datasets and appropriate analyses and figures.

Minor point: The normal control biopsies should be explained in more detail. Are these per indication biopsies that turned out to be "normal" after pathological evaluation or are they true normal biopsies of healthy volunteers?
Minor point: Some of the figures have low resolution and if possbile should be uploaded as a scalable digital format rather than picture format - otherwise the networks interpretation for the readers will be poor.
Validity of the findings: The findings are not validated with qPCR or IHC/protein level, but MiR-155-5p has been described in other renal diseases, in inflammation and in kidney cancer. Thus the findings in this study is probably correct. The authors also point to this in their conclusion. How the overexpression of MiR-155-5p is believed to implement the diagnosis of IMN is more unclear (line 240).
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: INTEGRATIVE ANALYSIS OF MIRNA–MRNA NETWORK IN IDIOPATHIC MEMBRANOUS NEPHROPATHY BY BIOINFORMATICS ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have significantly improved the manuscript and largely addressed the reviewer's concerns. They do note that they used an English editing service, but it doesn't appear that this was applied to the new sections of the manuscript as they contain many errors. Overall, I have minor concerns as outlined below:

1) The supplemental figures do not have legends.

2) Figure 2A- every miRNA/mRNA pair is in opposition. This is the predicted mechanism of action, but one wouldn't expect perfectly clean data. That is, there are likely some mRNA that are down-regulated when the miRNA is down-regulated, etc. Did the authors only show the interactions that were in opposition? If so, this should be noted.

3) Figure 2B- the 'Score' is not defined. In Figure 3B the 'highest degree of interaction' is mentioned, but this should still be better defined for the reader.

4) Figure 3 doesn't mention that these are immune-related genes anywhere in the legend.

5) Related to the above concern, in the text the authors describe the 'degree' and the table talks about the 'score' of the interaction. The text also mentions that 9 hub genes had scores >5, but then a 10th gene with a score of 4 is shown. This should be removed or the text changed.

6) GSE33288 is listed and it should be GSE133288.

7) Figure 4- in the text the authors state that FOS, JUN, BTG2 and NR4A1 were significant, but IL1A and MAFB were shown to be significant in the figure as well.

8) Figure 4 and 5- the y-axis is 'relative expression'. Relative to what? I don't believe they are actually showing relative expression, but probably normalized microarray values.

9) As miRNAs are thought to regulated mRNAs, I think it makes more sense to flip figures 4 and 5 in the order.
Experimental design: See comments above
Validity of the findings: See comments above
Additional comments: See comments 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: INTEGRATIVE ANALYSIS OF MIRNA–MRNA NETWORK IN IDIOPATHIC MEMBRANOUS NEPHROPATHY BY BIOINFORMATICS ANALYSIS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The reporting is adequate and the authors have corrected the introduction part regarding the background. Although, there are a few typographical errors that have been included in the new version that need to be sorted out during the proofs.
Experimental design: My concerns for the paper regarding figures have been corrected.
Validity of the findings: No 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: PHYLOGENETIC RELATIONSHIPS OF THE GENUS MISCHONYX BERTKAU, 1880, WITH TAXONOMIC CHANGES AND THREE NEW SPECIES DESCRIPTION (OPILIONES: GONYLEPTIDAE)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The English needs revision. I have made a few edits/suggestions in the pdf, but it needs to be read more carefully.

Also, there is room for improvement for the figures. The trees are not very readable, colors are difficult to see and aligning the names on the right doesn’t seem to work. Fonts need editing. Why not using the same font and size for all the trees? Also, there is no need to show every tree, many of which are very similar. It would be better to select some of the relevant tree, edit them properly for readability, and mention the others in the discussion (or add them as supplementary information).

The three maps should be combined into a single figure. I didn’t get the idea of why should they be separate, with huge overlap between them.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This is a thorough taxonomic revision of a genus of Gonyleptidae, Mischonyx, using a combination of multiple Sanger-based molecular markers and a new morphological data matrix. The data are analyzed using standard phylogenetic methods and the taxonomic results are translated into a classification, new generic assignments, and resulting in new species descriptions. The taxonomic part is well developed. There is also a dating analysis used to discuss some biogeographical hypotheses. Unfortunately, the fossil record for this part of the Laniatores tree is nonexistent, so the authors opt to us a mutation rate for their dating analyses. To me this is the weakest part of the study.

This will make another nice contribution to Laniatores systematics and biogeography after some edits and minor corrections (see below and in attached pdf):

I have made some grammar suggestions (in the pdf) but the paper needs to be thoroughly reviewed for language.

Gene names should be spelled out, and only abbreviated after they have been properly named (see my suggested corrections in the methods 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: PHYLOGENETIC RELATIONSHIPS OF THE GENUS MISCHONYX BERTKAU, 1880, WITH TAXONOMIC CHANGES AND THREE NEW SPECIES DESCRIPTION (OPILIONES: GONYLEPTIDAE)
Review round: 1
Reviewer: 2

Output:
Basic reporting: Afterwards an extensive revision of the ms #52148 submitted to PeerJ: “Phylogenetic relationships of the genus Mischonyx Bertkau, 1880, with taxonomic changes and three new species description (Opiliones: Gonyleptidae)”, I have some recommendations for the authors.

The ms is clear and concise on its objectives, Introduction and Myschonyx background sections offer to the reader all basis to understand the main issue. Literature revised is appropriate and well referenced along the text.
Personally, I am pleased with the idea of the approach of morphological, molecular and total evidence analyzed separately by MP, ML and Bayes, currently there are few phylogenetics works on Opiliones including those kind of evidence data.
Experimental design: But, my major criticisms for the work, is about on methods as follows:

First. The authors on the Phylogenetic inferences on methods section emphasized the use of two optimal criteria, Maximum Parsimony (MP) and Maximum Likelihhod (ML), analyzing Morphology (Morpho), Molecular (Mol) and Total Evidence (TE). For Morpho, they analyzed through ML, the authors only mentioned: “…using the best model found by the program, which uses BIC …”, later for Mol and TE, they stated: “The program selected the best substitution model for each gene partition under the BIC … using the program ModelFinder …” Here I considered is relevant to know which are these selected models and why they were selected, in nowhere else is anything mentioned again about the models used. To analyze morphology separately or in a concatenated matrix concatenated through ML is recommended to select Mk model accounting for ascertainment bias allowing gamma-distribution rate variation across characters (Klopfstein & Spasojevic, 2019). But this information is not specified in the text, and should be clarify.

Second. Is not clear for me, why the authors only emphasize the use of MP and ML for the phylogenetic reconstruction, wherein these two methods have some similarities in the way how they estimate the phylogeny. In this regard, I recommend the inclusion of Bayesian Inference through Mr. Bayes to analyze the same three data sets. In this way, the third topology obtained surely would be different to those under MP and ML, and the authors would have more results for discussion and not only focusing on taxonomic decision.

Third. In the section Phylogenetic inferences, the authors say: “We used a parsimony method to analyze character change because, as pointed by Chen & Kuntner (2014), the aim is to understand the evolutionary changes of characters rather than the probability of particular ancestral states on the phylogeny”. Later they say: “To analyze character change throughout the phylogeny, we used Winclada 1.6.1.”, and almost the end of this section, they say: …we analyze the character changes through the phylogeny using parsimony on Winclada 1.6.1”.
In the first place, there is no specified method to estimate character change, which mapping criteria was chosen in this study? ACCTRAN, DELTRAN?
Also, there are many evidences that parsimony methods for inferred character-state transformation find the obvious intuitively answer, ignoring two important sources of error: mapping uncertainty and phylogenetic uncertainty (Felsenstein, 1988; Frumhoff & Reeve, 1994; Ronquist, 2004).
With this last I do not mean that the parsimony methods for reconstruction are not adequate, however, I do not consider necessary use the same criterion for mapping on both MP and ML topologies, because there are not significant differences between these topologies. Instead, I recommended compare character change using different approaches (e.g. Parsimony vs. Likelihood or Bayesian) mapping on either MP, ML or Bayes tree.

Fourth. On the figures. Currently, there are many software to do more visually attractive and understandable trees. In the present work, I have the impression that the trees obtained were edited as little as possible, the names of species are hard to see, and in the mapped trees, the number of character/state is not possible to see in detail. On the Figures 4, 7 and 12 the labels say: “The values near the nodes are the Bootstrap values of each node”, but, near the nodes are two values: E.g. 97.4/100, 86.1/50, 99.9/69 … ¿Which is the correct Bootstrap value? What does it mean this strange notation? On Figure 5, Most parsimonious trees, How many trees? It looks like as the strict consensus. On Figure 8, the node values are not the 95% HDP, these values are the node ages.

REFERENCES
Felsenstein J. 1988. Phylogenies and quantitative characters. Annual Revision of Ecology and Systematics. 19: 445-471.
Frumhoff PC, Reeve HK. 1994. Using phylogenies to test hypotheses of adaptation: A critique of some current proposals. Evolution. 48: 172-180.
Klopfstein S., Spasojevic T. 2019. Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological matrix. PLoS ONE: 425090.
Validity of the findings: No comment
Additional comments: Dear Editor,

Afterwards an extensive revision of the ms #52148 submitted to PeerJ: “Phylogenetic relationships of the genus Mischonyx Bertkau, 1880, with taxonomic changes and three new species description (Opiliones: Gonyleptidae)”, I have some recommendations for the authors.

The ms is clear and concise on its objectives, Introduction and Myschonyx background sections offer to the reader all basis to understand the main issue. Literature revised is appropriate and well referenced along the text.
Personally, I am pleased with the idea of the approach of morphological, molecular and total evidence analyzed separately by MP, ML and Bayes, currently there are few phylogenetics works on Opiliones including those kind of evidence data.

But, my major criticisms for the work, is about on methods as follows:

First. The authors on the Phylogenetic inferences on methods section emphasized the use of two optimal criteria, Maximum Parsimony (MP) and Maximum Likelihhod (ML), analyzing Morphology (Morpho), Molecular (Mol) and Total Evidence (TE). For Morpho, they analyzed through ML, the authors only mentioned: “…using the best model found by the program, which uses BIC …”, later for Mol and TE, they stated: “The program selected the best substitution model for each gene partition under the BIC … using the program ModelFinder …” Here I considered is relevant to know which are these selected models and why they were selected, in nowhere else is anything mentioned again about the models used. To analyze morphology separately or in a concatenated matrix concatenated through ML is recommended to select Mk model accounting for ascertainment bias allowing gamma-distribution rate variation across characters (Klopfstein & Spasojevic, 2019). But this information is not specified in the text, and should be clarify.

Second. Is not clear for me, why the authors only emphasize the use of MP and ML for the phylogenetic reconstruction, wherein these two methods have some similarities in the way how they estimate the phylogeny. In this regard, I recommend the inclusion of Bayesian Inference through Mr. Bayes to analyze the same three data sets. In this way, the third topology obtained surely would be different to those under MP and ML, and the authors would have more results for discussion and not only focusing on taxonomic decision.

Third. In the section Phylogenetic inferences, the authors say: “We used a parsimony method to analyze character change because, as pointed by Chen & Kuntner (2014), the aim is to understand the evolutionary changes of characters rather than the probability of particular ancestral states on the phylogeny”. Later they say: “To analyze character change throughout the phylogeny, we used Winclada 1.6.1.”, and almost the end of this section, they say: …we analyze the character changes through the phylogeny using parsimony on Winclada 1.6.1”.
In the first place, there is no specified method to estimate character change, which mapping criteria was chosen in this study? ACCTRAN, DELTRAN?
Also, there are many evidences that parsimony methods for inferred character-state transformation find the obvious intuitively answer, ignoring two important sources of error: mapping uncertainty and phylogenetic uncertainty (Felsenstein, 1988; Frumhoff & Reeve, 1994; Ronquist, 2004).
With this last I do not mean that the parsimony methods for reconstruction are not adequate, however, I do not consider necessary use the same criterion for mapping on both MP and ML topologies, because there are not significant differences between these topologies. Instead, I recommended compare character change using different approaches (e.g. Parsimony vs. Likelihood or Bayesian) mapping on either MP, ML or Bayes tree.

Fourth. On the figures. Currently, there are many software to do more visually attractive and understandable trees. In the present work, I have the impression that the trees obtained were edited as little as possible, the names of species are hard to see, and in the mapped trees, the number of character/state is not possible to see in detail. On the Figures 4, 7 and 12 the labels say: “The values near the nodes are the Bootstrap values of each node”, but, near the nodes are two values: E.g. 97.4/100, 86.1/50, 99.9/69 … ¿Which is the correct Bootstrap value? What does it mean this strange notation? On Figure 5, Most parsimonious trees, How many trees? It looks like as the strict consensus. On Figure 8, the node values are not the 95% HDP, these values are the node ages.

REFERENCES
Felsenstein J. 1988. Phylogenies and quantitative characters. Annual Revision of Ecology and Systematics. 19: 445-471.
Frumhoff PC, Reeve HK. 1994. Using phylogenies to test hypotheses of adaptation: A critique of some current proposals. Evolution. 48: 172-180.
Klopfstein S., Spasojevic T. 2019. Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological matrix. PLoS ONE: 425090.


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

Input:
Title: PHYLOGENETIC RELATIONSHIPS OF THE GENUS MISCHONYX BERTKAU, 1880, WITH TAXONOMIC CHANGES AND THREE NEW SPECIES DESCRIPTION (OPILIONES: GONYLEPTIDAE)
Review round: 2
Reviewer: 1

Output:
Basic reporting: To Editor and authors,

After a second revision of the manuscript entitled: “Phylogenetic relationships of the genus Mischonyx Bertkau, 1880, with taxonomic changes and three new species description (Opiliones: Gonyleptidae)”, I have the following comments.

The manuscript has improved too much, with the language revision, all the paragraphs in the document are clearer. However, reviewing the document with tracked changes, there are still small errors in the writing, e.g. two continuous end points, errors in some italics, etc.
On the phylogenetics methods, with the new additions, it is now understandable how the authors obtained the different topologies.
On discussion section, changes on the divergence time and optimality criteria analysis choosing only a tree ML3 tree, have made this part of the manuscript comprehensible to the reader.

However, despite the best of the manuscript, there are still small details to be considered accepted, which are:
1.- On abstract and conclusions, the authors do not mention almost anything about divergence and biogeographic inferences, placing greater emphasis on the phylogenetic and taxonomic part only. I recommend a larger paragraph mentioning more about time divergence, which is a very important part of the manuscript.
2.- Trees visualization. On the previous version of the manuscript, I made the suggestion to change the current trees for others with a better visual quality, this in order to better convey the idea that each tree represents. In this sense, the overall design of the trees did not change at all, or fuse all of them in only one or two trees. There are many packages in R to make very illustrative and nice trees, for example, the dated tree could be accompanied with an ancient distribution map, some picture of one species, etc. Trees with character changes have the number of character and character state very small on the branch, and also the design is “wide”, spanning a lot of white space unnecessarily. Figure 23 Total Evidence Parsimony hypothesis, values near the nodes are the bootstrap values, but, on each node there are two values, the bootstrap one and another after the slash, please clarify what values are those.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: To Editor and authors,

After a second revision of the manuscript entitled: “Phylogenetic relationships of the genus Mischonyx Bertkau, 1880, with taxonomic changes and three new species description (Opiliones: Gonyleptidae)”, I have the following comments.

The manuscript has improved too much, with the language revision, all the paragraphs in the document are clearer. However, reviewing the document with tracked changes, there are still small errors in the writing, e.g. two continuous end points, errors in some italics, etc.
On the phylogenetics methods, with the new additions, it is now understandable how the authors obtained the different topologies.
On discussion section, changes on the divergence time and optimality criteria analysis choosing only a tree ML3 tree, have made this part of the manuscript comprehensible to the reader.

However, despite the best of the manuscript, there are still small details to be considered accepted, which are:
1.- On abstract and conclusions, the authors do not mention almost anything about divergence and biogeographic inferences, placing greater emphasis on the phylogenetic and taxonomic part only. I recommend a larger paragraph mentioning more about time divergence, which is a very important part of the manuscript.
2.- Trees visualization. On the previous version of the manuscript, I made the suggestion to change the current trees for others with a better visual quality, this in order to better convey the idea that each tree represents. In this sense, the overall design of the trees did not change at all, or fuse all of them in only one or two trees. There are many packages in R to make very illustrative and nice trees, for example, the dated tree could be accompanied with an ancient distribution map, some picture of one species, etc. Trees with character changes have the number of character and character state very small on the branch, and also the design is “wide”, spanning a lot of white space unnecessarily. Figure 23 Total Evidence Parsimony hypothesis, values near the nodes are the bootstrap values, but, on each node there are two values, the bootstrap one and another after the slash, please clarify what values are those.


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 LIGHT’S IN MY EYES: OPTICAL MODELING DEMONSTRATES WIND IS MORE IMPORTANT THAN SEA SURFACE-REFLECTED SUNLIGHT FOR FORAGING HERONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript was a joy to read. Very clear and unambiguous language throughout.

The first paragraph of the introduction is a bit thin on references while describing some things that I am sure there is established literature on? Perhaps some references to the properties of glint would be useful here. At least for the uninitiated, especially as we’re told that it’s wrong to call it glare. What’s the difference, and what do you base that claim on?

Otherwise, the introduction provides very clear and useful background for this work, though perhaps “James A. Rogers (1983) Foraging Behaviour of Seven Species of Herons in Tampa Bay, Florida, Colonial Waterbirds, 6, pp11-23)” ought to be included in the introduction?

The article structure is well presented and clear. Raw data are easily accessible and the code provided is clear. The manuscript is also self contained and presents clearly and unambiguously what the hypothesis, methods, results, and conclusions are.

I would suggest a different title. While the use of "quantitative optical models/radiative transfer modeling" looks to be novel and was really useful in showing what level of glint the birds were likely to experience, the story that I find most exciting is that they seem to not be bothered by glint. I think a title focusing on that would bring this work to the attention of an audience interested in bird vision.
Experimental design: This work is original as far as I can tell, which is odd as it seems such an obvious thing to investigate. Definitely relevant and meaningful. I am impressed with the clear hypothesis and focused investigation put into testing the hypothesis.

This study is based on a lot of field work collected over a long period of time. The data are purely observational, so there are little to no ethical concerns. Efforts were made to account for observer error, which is quite important in this kind of work and modern technology was used to obtain very detailed information on things that are not easily discerned in the field (e.g. elevation of the sun). A tool to measure actual strength of light on site and perhaps images of water surface for later analysis of wind disturbance might have been useful, but considering the results, it’s unlikely that these things would have changed the outcome much.

The methods are clearly described and could be replicated.
Validity of the findings: While not an expert on the statistics used, the data are robust and the statistical analyses reflect what is fairly clear from the very first plot of the data. I wonder if it is possible to use ordinal analyses on the wind/orientation data as there seems to be a trend towards stronger wind having stronger effect as it increases in strength? When the model is not informed of a trend in the wind classifications, it simply finds that the strongest wind is different from the others. Am I interpreting that correctly?

A fairly large section of the discussion focuses on polarised light as a method of seeing through the glint. This was also my first thought (and google search) and as such it points out a rather glaring (pardon the pun) hole in the literature with regards to exactly how birds see through the surface of the water, when it seems glint does not bother all of them. The authors suggest that herons be used as model animals to investigate this and that makes sense to me.
Additional comments: I was delighted to review this manuscript. It presents such a clear hypothesis and tests it so thoroughly. I'm no expert on bird vision, so I can't really speculate on whether your findings were to be expected or not. They certainly surprised me, especially considering the scarcity of data suggesting birds are better able to see through glint than e.g. humans.


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 LIGHT’S IN MY EYES: OPTICAL MODELING DEMONSTRATES WIND IS MORE IMPORTANT THAN SEA SURFACE-REFLECTED SUNLIGHT FOR FORAGING HERONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript asks and answers an interesting question: do herons orient their body relative to the sun to optimize viewing conditions while hunting?

General Comments:
Strike angle: In the introduction, the authors mention a viewing angle looking 40 degrees downward. Is there any information on the strike angle taken by herons? For example, do they strike at 40 degrees (which is more out than down), or do they strike more perpendicular to the water’s surface (70-90 degrees)? And what effect would that have on glint? From personal experience, it is easier to see into water from directly above than to see into water out in front of me. Perhaps herons don’t orient away from glint because they are looking down, not down and away.

Minor Comments:
Line 20 – I would not go so far as to say ‘ubiquitous’.
Line 21 – Change ‘signals’ to ‘cues’. A signal means that both parties receive a benefit or that information is intentionally being displayed by the sender.
Line 20-22 – This sentence is generally difficult to read with so many commas.
Line 26 and 32 – the ‘spp.’ should not be italicized since it is not Latin.
Line 28-29 – Earlier, the authors implied that this strategy would not work well. I suggest they remove the earlier sentence and turn this sentence into a proper hypothesis and prediction.
Line 44 – The ‘hereafter’ is unnecessary since the authors already called it ‘glint’ and define it.
Line 48 – Have the authors consider what is already known about how archer fish do the same thing but in the opposite direction? Temple et al. 2010 in PRSLB, Ben-Simon et al. 2012 in J of Vision and in J of Exp Bio, among others
Line 66 – additional and opposing to what other challenge?
Line 67 – the order in which information is revealed makes this section difficult to read… maybe just get rid of lines 65-66 since you talk about the trade-off later anyway.
Experimental design: The methods are carefully chosen and well executed.

General Comments:
Statistics: I have not used GEE statistics before, but I understand that it is good for avoiding pseudoreplication in longitudinal studies (repeated measures of an individual over time), which is exactly what the authors have here. So the statistics used are appropriate. My question though is regarding the data in Figure 5. The authors compare the wind speed categories two at a time. But wind speed is ordinal, and therefore, it would be valuable to have a test that determines significance (or not) of all four categories together. There appears to be an overall trend, but is that trend significant, as a whole? Wind speed, in truth, is continuous not categorical. I would like to see a comparison made where the step-wise relationship between wind speed categories is recognized.

Line 245 – How are there three estimates of alpha error, but only one estimate of beta error? Also power (1-beta error) is irrelevant if the result is significant because the null hypothesis has been rejected, so there is no chance of committing Type II error (incorrectly accepting the null).
Validity of the findings: The conclusions are interesting and useful.

Comments:

Line 269-275 – The logic here needs some work. Being able to detect polarization is not the same as filtering polarized light. Quite the opposite in fact. If herons were able to see and detect polarized light, they would be guaranteed to fall victim to glint. If herons were not able to detect polarized light, it wouldn’t mean anything one way or the other.
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: CRYPTOCENTRUS STEINHARDTI (ACTINOPTERYGII; GOBIIDAE): A NEW SPECIES OF SHRIMP-GOBY, AND A NEW INVASIVE TO THE MEDITERRANEAN SEA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper has several grammar and spelling errors, particularly some in the scientific names. There is not enough background or context given to support the conclusions, and not enough literature surveyed. The figures are good, and the data has been shared, but the hypothesis that the described individuals represent a new species of Cryptocentrus is not sufficiently supported.
Experimental design: The research is within the aims and scope of the journal, and the question is well defined, but the investigation is not rigorous enough and the methods need more detail.
Validity of the findings: The data are clearly given but they are not robust and the conclusions are not well-supported.
Additional comments: This contribution describes morphological and genetic characteristics of three fish individuals trawled from the eastern Mediterranean and assigned to the shrimp goby genus Cryptocentrus. The authors describe the species as new and postulate that it arrived in the Mediterranean from the Red Sea via the Suez Canal. This dispersal pattern is not unknown, there are several examples of such Lessepsian migrants including two other shrimp gobies (Vanderhorstia mertensi and Cryptocentrus caeruleopunctatus), but it is unusual to have a new species that presumably arrived from the Red Sea described first from the Mediterranean. Unfortunately, the authors do not make sound arguments for any of their claims, and a more comprehensive and careful consideration of the characters and diversity of shrimp gobies would be needed to definitively describe these individuals as a new species. The three individuals from the trawl are all damaged, and so the authors use DNA sequences to assist with identification. However, their methods are incompletely described and the resultant phylogeny has many very poorly supported nodes, making their phylogenetic conclusions unreliable.

   The morphological argument that the specimens represent a new Cryptocentrus species rests on first establishing that it is a Cryptocentrus, and then on determining that it is new. As the authors discuss, the generic diagnoses for shrimp goby genera are not always reliable, and in this case they use molecular data to place the new individuals among other goby species. They sequence the mitochondrial COI and cytb genes, although only the COI is used for phylogenetic reconstruction. The description of the molecular methods is very brief and inconsistent: is the tree an ML tree or Bayesian? The figure caption says ML but the description of replications given in the methods is more consistent with a Bayesian analysis.  There are almost no details given about how the sequences were alighned, concatenated, how models were identified, and how the trees were run. Why wasn't cytb included in the phylogeny? Other cytb data for Cryptocentrus are available. Much more detail is needed here, but unfortunately, it may not result in a better phylogeny. The phylogeny given is very poorly supported and it's really not possible to say much more than the new individuals are probably part of the Cryptocentrus lineage.

   The authors also need to provide much more, and more accurate, morphological comparisons between the new individuals and known species. For instance, they discuss the character of transverse (rather than longitudinal) papillae rows on the head, and state that the Asterropteryx lineage (including shrimp goby genera such as Amblyeleotris, Ctenogobiops and Vanderhorstia) is characterized by longitudinal papillae rows, while the Cryptocentrus lineage has transverse papillae rows, and they cite Thacker et al. 2011. That paper says the exact opposite of what the authors describe: transverse papillae rows are shared by Amblyeleotris, Cryptocentrus, Myersina and Stonogobiops, they are not clade-specific and cannot be used to assign species to shrimp goby lineages. This is a pretty large mistake and makes me question the accuracy of the rest of the morphological comparisons. The authors go on to argue that the new individuals are distinguished from species of Cryptocentroides in having a wide gill opening, extending to below the preopercular margin, as opposed to a restricted gill opening, extending to below the pectoral fin base. Those don't sound very different, an illustration would be very helpful. Is that the only character that diagnoses Cryptocentroides? The new individuals are separated from Myersina by the degree of nape scalation. How variable is that, and are there other characters typical of Myersina? What distinguishes Cryptocentrus from Vanderhorstia or Tomiyamichthys, and which of those characters are present in the new individuals? This is covered briefly but needs expansion. The authors provide little detail and no  citations; this section needs to be greatly expanded so that the generic assignment is solidly supported.

   Finally, the authors compare the new individuals to Cryptocentrus species possessing fewer than 70 lateral scales (most Cryptocentrus have more), but none of those species are present in the Red Sea. The comparisons and differential diagnoses need to be expanded and Red Sea species must be considered; many species have wide ranges of lateral scales, the new individuals might be within the range of intraspecific variation for some Red Sea Cryptocentrus. I'd recommend looking carefully at Cryptocentroides arabicus and Cryptocentrus fasciatus. It is also possible that the new individuals are from previously known Lessepian migrant species Cryptocentrus caeruleopunctatus, there is so little detail given, and no discussion of variation, that it is impossible to know how the new individuals compare.


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: CRYPTOCENTRUS STEINHARDTI (ACTINOPTERYGII; GOBIIDAE): A NEW SPECIES OF SHRIMP-GOBY, AND A NEW INVASIVE TO THE MEDITERRANEAN SEA
Review round: 1
Reviewer: 2

Output:
Basic reporting: All comments are on the attached pdf.
The manuscript needs work as it relies almost entirely on genetic samples of 3 specimens (COI) and almost no morphological comparison. It may indeed be a new species but authors need to convince the reader properly. They have not demonstrated that their "comprehensive morphological and anatomical examinations" show this.
Experimental design: Plenty of genetic info but considerably lacking in the "comprehensive morphological and anatomical" information it is supposed to contain. See comments in pdf.
Validity of the findings: See comments in pdf.
Additional comments: Please convince the reader that this really is a good species with good morphological comparison with its congeners in the western Indian Ocean, especially the Red Sea.


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

Input:
Title: CRYPTOCENTRUS STEINHARDTI (ACTINOPTERYGII; GOBIIDAE): A NEW SPECIES OF SHRIMP-GOBY, AND A NEW INVASIVE TO THE MEDITERRANEAN SEA
Review round: 1
Reviewer: 3

Output:
Basic reporting: No addition comments.
Experimental design: In general good article with another new species described from non-native area.
All corrections and suggestions are visible through tracking changes in 3 files.
Some corrections are needed.
Validity of the findings: Authors found a new species for science without doubt.
But its and Lotilia relationships to other Cryptocentrus species were not resolved by present analysis and an additional study is needed, making question of generic name of part of Cryptocentrus species opened.
Additional comments: The description of new species is provided in shortened style but enough to see details of morphological characters. But some mistakes are present, for example authors wrongly assigned shrimp-gobies genera to Asterropteryx "lineage", i.e. the genus is not associated with shrimps. Authors need to be more careful with such conclusions.
All corrections within Word files.


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: CRYPTOCENTRUS STEINHARDTI (ACTINOPTERYGII; GOBIIDAE): A NEW SPECIES OF SHRIMP-GOBY, AND A NEW INVASIVE TO THE MEDITERRANEAN SEA
Review round: 2
Reviewer: 1

Output:
Basic reporting: In this revision, the authors have made many improvements over the previous version, including expanded morphological comparisons and improvements to the text. The molecular analysis is unchanged, but is better explained and the shortcomings are better acknowledged (the name Myersina is still misspelled in Figure 3, and Ctenogobiops is misspelled on line 180). Overall, the writing is clearer and it reads well.
Experimental design: The research is within the aims and scope of the journal, and the question is well defined. The MS has been updated in response to reviews with additional data and comparisons to other Cryptocentrus species, both the congeners in the Red Sea and all of the species in the Cryptocentrus "low scale count" group. The Discussion has also been expanded with more comparisons to other shrimp goby genera and some discussion of their diagnostic characters (or lack thereof). These are excellent additions and greatly strengthen the argument that the species is new.
Validity of the findings: The arguments for the novelty of C. steinhardti are good, much stronger now with the added comparative material. The molecular results are unchanged and are still basically inconclusive, but the supporting text makes it clear that Cryptocentrus is in need of revision and that the phylogeny is not particularly robust.
Additional comments: The authors have added significant material that greatly strengthens the paper, well done.


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: CRYPTOCENTRUS STEINHARDTI (ACTINOPTERYGII; GOBIIDAE): A NEW SPECIES OF SHRIMP-GOBY, AND A NEW INVASIVE TO THE MEDITERRANEAN SEA
Review round: 2
Reviewer: 2

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: Please see the attached PDF.


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

Input:
Title: CRYPTOCENTRUS STEINHARDTI (ACTINOPTERYGII; GOBIIDAE): A NEW SPECIES OF SHRIMP-GOBY, AND A NEW INVASIVE TO THE MEDITERRANEAN SEA
Review round: 2
Reviewer: 3

Output:
Basic reporting: no additional comments.
Experimental design: no additional comments.
Validity of the findings: no additional comments.
Additional comments: The article after first review was improved but there are some places where additional corrections are needed. All my corrections, comments and suggestions are visible in attached Word file.


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

Input:
Title: CRYPTOCENTRUS STEINHARDTI (ACTINOPTERYGII; GOBIIDAE): A NEW SPECIES OF SHRIMP-GOBY, AND A NEW INVASIVE TO THE MEDITERRANEAN SEA
Review round: 3
Reviewer: 1

Output:
Basic reporting: See below
Experimental design: See below
Validity of the findings: See below
Additional comments: I have read the revision materials and am happy to Accept 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: CRYPTOCENTRUS STEINHARDTI (ACTINOPTERYGII; GOBIIDAE): A NEW SPECIES OF SHRIMP-GOBY, AND A NEW INVASIVE TO THE MEDITERRANEAN SEA
Review round: 3
Reviewer: 2

Output:
Basic reporting: In general no additional comments except for formatting.
Experimental design: no comments
Validity of the findings: no comments
Additional comments: Few corrections (mostly commas) were made through MS and visible in Corrections.
I was sure authors can check Instructions of preparation of References according journal format, but authors omitted it.
Therefore I made formatting of references following journal rules.
All corrections are visible in MS.


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

Input:
Title: THE CLINICAL DIAGNOSIS OF ACHILLES TENDINOPATHY: A SCOPING REVIEW
Review round: 1
Reviewer: 1

Output:
Basic reporting: Dear editor,
dear authors,
thank you for the invitation to review your paper, which I enjoyed a lot. The article structure, the literature reference and the study design had a high quality and your article will give good recommendations for researches for study designs and outcome parameters for future clinical studies in the field of Achilles tendinopathy
Experimental design: You have chosen a scoping review design which is totally appropriate.
Validity of the findings: Your conclusion are well stated and linked to the original research questions.
Additional comments: Here are some specific comments:

l.91. Full stop after „April 2021“.
l.119. „asymptomatic Achilles tendinopathy“ might be a misleading terminology. since „tendinopathy“ includes a dysfunctional or symptomatic state (see your definition ll. 55-58). Perhaps, „ asymptomatic Achilles tendon states“ might be more suitable.
l.164. „will“ instead of „with“

table1: As far as I understand you are referring to the study of Vicenzino et al. (8) so you would need to cite this at this point. However, since your study is about Achilles tendinopathy I would rather recommend to adapt this table and exclude unrelevant scores such as the DASH score.
Moreover, I would recommend to give researches at this point direct examples of scores or questionaires for every core health domain  e.g. participation (Tegener activity scale) as you also named some in the discussion. Thus researaches will directly know what to do to improve their study design, when they have a look at table 1.

table 6: Why you did not include VISA-A here as you did e.g. in table 7( e.g. the study of Gatz et al. used VISA-A)?


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 CLINICAL DIAGNOSIS OF ACHILLES TENDINOPATHY: A SCOPING REVIEW
Review round: 1
Reviewer: 2

Output:
Basic reporting: The present manuscript was well structured with clearly results and conclusions of this current topic.

Just a few suggestions for the autors to improve tje quality of the manuscritp:

Please, add some studies about tendinopathy and ultrasound imaging (for example Romero-Morales et al. “Comparison of the sonographic features of the Achilles Tendon complex in patients with and without achilles tendinopathy: A case-control study”. Physical Therapy in Sport.) and more studies related with ultrasound imaging findings and tendinopathy.

Please, authors should write the conclusion section more “conclusive”, just with the main findings.

At last, congratulations for this excellent work.
Experimental design: Well designed.
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: INFLUENCE OF PLEISTOCENE CLIMATIC OSCILLATIONS ON THE PHYLOGEOGRAPHY AND DEMOGRAPHIC HISTORY OF ENDEMIC VULNERABLE TREES (SECTION MAGNOLIA) OF THE TROPICAL MONTANE CLOUD FOREST IN MEXICO
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall, the manuscript is clear but some section appear to be vague.
The methods section needs more clarity in reporting: bioclimatic variables, skyline plots.
The literature references are a bit insufficient and some references are missing to support the results.
The results are relevant to the hypothesis being tested, but the discussion shifts too much in the direction of species delimitation in the study system.
Experimental design: The research question is well defined.
Methods need more clarity and some choices need to be properly justified.
Validity of the findings: The sequence data have been deposited in GeneBank, but still not available. It is not clear if it would be possible to reconstruct the haplotypes with the sequences in GenBank.
Additional comments: I have now read the article "Phylogeography, lineage divergence, and paleodistributions support glacial refugia for an endemic vulnerable tree (Magnolia schiedeana) of the tropical montane cloud forest" twice, and I found it interesting and relevant in the context of cloud forest phylogeography in Mexico. Overall, the background is adequate and the methods are robust, but there are some issues here. However, I found myself reading the discussion and struggling between two main arguments: the phylogeographic history on the one hand, and the taxonomy of Magnolia schiedeana on the other. To me, too much focus is given to the latter and, according to the references cited, the present data are not the most adequate to test hypothesis around this issue. Regarding this point, authors appear to be going back and forth between accepting and not accepting the species separation. Finally, I found some flaws in the interpretation and discussion of the results, which might come down to a lack of clarity, but these weakens the relevance of the present work.

Below are more detailed concerns:
Lines 79-83: This is correct to a certain point. Yes, this is a (simplistic) expectation, but it has to be accompanied by a congruent time frame (see Ornelas et al. 2016). The dry refugia debate is  centered around the last glacial period, and thus a demographic expansion pre-dating this period cannot be taken as evidence for this particular model (see the demographic expansion in Ramírez-Barahona & Eguiarte 2014). Also, Rogers & Harpeding (1996) should not be cited here.

Lines 94-96: The paper cited here for the age of the family (Azuma et al. 2011) –there is a typo in the year– does not have a divergence time analysis. Besides being unsupported, the 100 My age provided here seems a bit too old. The Angiosperm Phylogeny Website has crown Magnoliaceae to be younger than 100 Mya (this age is more in line with te stem age of the family); for instance, see the ages in Magallón et al. (2015) and Ramírez-Barahona et al. (2020), which appear also to be much younger. Please substantiate the North American origin.

Lines 165-168: the sequence data are not yet available, but if I'm understanding correctly only unique sequences were deposited, correct? My question is how would one reconstruct the haplotypes for individuals here? I'm not sure this would be possible with the information provided.

Lines 267: typo – substation rates

Lines 283-285. I'm having trouble with the testing data for the distribution models. Given the taxonomic uncertainty in the complex, these testing data are surely taxonomically messy as well. I find it inconsistent that authors only used 'occurrences from specimens collected in this study' for training 'due to taxonomic uncertainty' (typo in line 277 – uncertainly), but then choose to disregard this for the testing data. Please justify. Why not go with another strategy, 26 records are few, but still can be used to produce robust models; or why not extract data from other specimens vetted by the authors (or other experts).

Overall in the results and discussion, it is hard to follow all the acronyms for the states, I would suggest to spell them out in full. But, it is also hard to follow the discussion if not familiar with the geopolitical limits of Mexico. I would rather keep the discussion more broad in term of geography.

Lines 306-312. It is not clear which variables were downloaded. I'm assuming that for the LGM, the CHELSA variables were downloaded (based on the reported resolution). If so, I believe it is not ideal to use these in combination with the PMIP, because CHELSA and PMIP are based on different principles and algorithms. It can be done, but it is not ideal, so authors should be explicit about this choice. Also, I assume authors are using a single GCM on which the Paleoclim variables were constructed (if I recall correctly, this a version of CCSM). This has important consequences for downstream interpretations of the demographic history, so the choice should be properly justified.

Lines 369-375. These results should be backed up by a proper statistical test (e.g., discriminant analysis).

Lines 395-396. How was the timing of this sudden increase determined? This is a crucial point, because all the discussion hinges precisely on this timing. Going to figure 3, this definition of the ages for the sudden expansion is not clear.

Lines 444-446. It is clear that there is genetic structure, but this is far from being concordant with species delimitation.

Lines 461-465. Continued from the above comment. Here authors point the other way, that population genetic data does not support species delimitation. Also, this goes to my overall concern about the focus on the taxonomy of the species. I do not see how the present data is better to tackle this problem that the one used by Rico & Gutierrez-Becerril (2019) – this reference is missing from the reference list.

Lines 465-472. What is the relevance of all this? There are hints at some comparison being made, but the argument for doing so is not clear.

Lines 482-484. This is interesting. Does this mean, that the present data does not favor the segregation of M pedrazae?

Lines 487-493. This passage exemplifies the lack of clarity in the discussion. This section is vague and really speculative and without key information to back up the arguments. The TMVB might have restricted gene flow, but the time frame is critical here.

Lines 494-497. Authors are going back and forth between supporting the segregation of the two species and not supporting it.

Lines 517-525. Again the age cited appear to be too old (see Nie et al. 2008, Ramírez-Barahona et al. 2020), which would impact the proposed scenario. By the way, all this appear to be too vague and unsubstantiated. But the point here, is why is this history relevant? There is no connection between this passage and what comes next about population expansion during the last 300,000 years.

Lines 530-534. Which inter-glacial are you referring to here? Again, this concerns me because it is unclear how the estimated ages were determined. This is not clear from the skyline plots. Also, the statement on lines 533-534 does not hold with the evidence provided.

Lines 543-546. Ok, but see Ramírez-Barahona & Eguiarte (2014) to see that using different circulation models impacts the patterns seen in the species distribution models. So, the ensuing discussion is biased.

Lines 558-562. Sorry to be blunt, but this argument is plain wrong. As far as I'm concerned, the various species designations are not based on any population genetics. The only way that expansion-contraction dynamics can be linked to species designations would be to test that these species are in fact distinct genetic clusters.

Lines 566-587. These are a bit vague and authors should maker concrete proposals.

Figure 2. How was the ancestral haplotype defined (H23)? The colors here confused me because they do not correspond to the ones in figure 1. Are the colors related to inferred membership? The PCA plots need the % variance stated somewhere.

Figure 3. How where the location of the vertical lines defined in the skyline plots? These lines appear to mark the sudden expansion of the lineages, but this is not clear. Also the skylines show that after that period of time, demographic expansion continued, although authors state in the discussion that things were stable. Does M pedrazea merit analyses by its own?

Figure 4. The results presented here, to me, are not fully exploited in the discussion. Something else more complex appears to be happening here, which is not apparent in the skylines.


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

Input:
Title: INFLUENCE OF PLEISTOCENE CLIMATIC OSCILLATIONS ON THE PHYLOGEOGRAPHY AND DEMOGRAPHIC HISTORY OF ENDEMIC VULNERABLE TREES (SECTION MAGNOLIA) OF THE TROPICAL MONTANE CLOUD FOREST IN MEXICO
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors study the Tropical Cloud Forest ecosystem and the implications of the climate oscillations of the Quaternary in the phylogeography and the historical demography of a vulnerable endemic tree, Magnolia schiedeana in Mexico. The authors apply genetic analysis in four regions of the chloroplast DNA and reconstruct the past distribution of the species with niche modelling. They aim to test the hypotheses of glacial refugia versus dry refugia. All in all, this work has good potential to be published with some further refinements in the analyses and the writing. In particular, the writing requires improvement for clarity as the text becomes ambiguous in parts and includes grammar or syntax errors. It would thus profit from the edits of a native speaker.
The background presented in the introduction requires improvement in logical flow and better link between the general research context and the specifics of the study area and species. Sometimes the text is hard for the reader to follow, e.g. the part referring to the dry refugia and the moist forests as theories explaining the dynamics of populations in response to climate oscillations.  The latter is a key point that should be carefully addressed and in a more eloquent manner as it is tightly related to the hypotheses of the research presented so that the reader can better follow the research.
In the last paragraph of the introduction, the authors mostly present their technical aims rather than more general scientific questions. As such, they have not sufficiently linked the research objectives to a more general context in the sense of what new does this research bring beyond the knowledge regarding the study species - why is it interesting in a more general way.
Experimental design: Most of the methods used are in general sufficiently described but there is room for improvement particularly in improving the link between the genetic data and the ecological analysis. It would also be interesting if the authors could show the niche overlap of the projections in % over time in the last paragraph of the results (e.g. with ecospat package) and test with statistical tests whether the number of pixels has significantly changed. Please see the uploaded word file for some more specific comments.
Validity of the findings: Please see the uploaded word file for some more specific comments.
Additional comments: No additional comments


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

Input:
Title: INFLUENCE OF PLEISTOCENE CLIMATIC OSCILLATIONS ON THE PHYLOGEOGRAPHY AND DEMOGRAPHIC HISTORY OF ENDEMIC VULNERABLE TREES (SECTION MAGNOLIA) OF THE TROPICAL MONTANE CLOUD FOREST IN MEXICO
Review round: 1
Reviewer: 3

Output:
Basic reporting: In this paper the authors assessed the phylogeography, historical demography and Quaternary distributions for an endemic and endangered species of the Tropical Montane Cloud Forest (TMCF), Magnolia schiediana. The study is based in four chloroplast DNA regions and past species distribution models. They found phylogeographic structure corresponding to three lineages: west, central-east and south TMCF of Mexico. Genetic data and past SDMs suggest a demographic expansion from Veracruz that occurred in the Pleistocene (~200,000 – 300,000 years ago). According to the authors, their results support the Pleistocene refugia hypothesis for species from the Tropical Forest in Mexico.

The manuscript is written in clear unambiguous, professional English, with a few details that can be easily addressed (see general comments). For readers that might not be as familiar with the geography of Mexico, I suggest using the complete name of the Mexican states throughout the text instead of abbreviations.
Literature and references are sufficient and according to the field background, and enough context is provided.

The manuscript is well structured. The figures and tables are clear, but I suggest eliminating Table 1 from the main manuscript, because small sample size may represent a caveat for population comparisons and conclusions at the population level. Also, I recommend adding a figure of the Bayesian phylogeny in the main text, but if authors consider that this figure won't add to the study, at least include it as supplementary material (see general comments).

The aims of the study are stated in the introduction. The analyses are adequate and results are very interesting as presented by the authors. Analyses are in accordance to the objectives, but I have some concerns regarding the conclusions provided by the authors and suggest performing a formal hypothesis test by means of an ABC framework (see validity of the findings section). In addition, given the small sample size for some localities the scale of the analyses should be reconsidered (see comments below).

Sequences have been deposited to GeneBank and accession numbers are provided in the manuscript. Moreover, sequence alignment is included as supplementary material.
Experimental design: This research is within the scope of the journal, the research question is well-defined. The authors clearly state the knowledge gap filled by this study. Also, the authors provide a clear statement of the objective of the study. Nevertheless, re-phrasing the aims in terms of the hypotheses tested by their analysis may provide a wider public; i.e. “In this study we (i) tested the phylogenetic relationship between M. pedrazae, M. schiediana and M. schiediana var. Oaxaca; and (ii) we used a phylogeographic approach and past species distribution models to characterize the historical demography and changes in distribution ranges of these taxa". I would add (iii) using an ABC framework to test the dry-refuge vs. moist-forest hypothesis (see section 3).

Finally, one of the objectives was to identified populations that should be priorities for conservation based on their levels of genetic diversity. Nevertheless, a small sample size for some localities may bias these conclusions; thus, providing conservation guidelines at the population level should be avoided, conservation guidelines could and should be provided but at a wider regional level.

Methods are mostly well explained and conform to technical standard, but a few details should be added. In particular I’m concerned about the small sample size for some populations (i.e. one locality in Veracruz and one in Puebla has n=1, M. pedrazae var Oaxaca has n=5). This has important implications when estimating levels of genetic diversity and genetic structure at population levels and, therefore, all analyses and result should be conducted only at the lineage level. This should also be considered for implications for conservation.
Validity of the findings: The benefit to literature is clearly stated, all underlying data have been provided and the analyses are robust.

Nevertheless, some conclusions should be revised, and alternative interpretation of the results should be considered. In this sense, the data presented by the authors may be providing better support to the moist-forest hypothesis:

Past species distribution models shown in figure 4 suggest that range was smaller during the LIG (not the LGM), because this is the time when we can see the smaller suitable area for the presence of the species. Then the models suggest that for the LGM the species expanded towards the south reaching Oaxaca (possible secondary contact with the lineage found in Oaxaca?), and remained there through the Early Holocene (EH); then from the EH to the Mid-Holocene (MH) a displacement of the species distribution into the north reaching SLP (possible secondary contact with M. pedraza?). These models support downslope migration and expansion promoting population connectivity through the LGM according to the moist-forest hypothesis as stated in Ramirez-Barahona and Eguiarte (2013). According to Fig. 4 we can see a slight range contraction from the MH into the present species range, which could relate to upslope migration and range fragmentation in accordance to the moist-forest hypothesis (Ramírez-Barahona and Eguiarte, 2013). These results taken together with genetic data suggest that lineages pre-dating the LGM would be present (reported divergence time for M. schiediana is 11 mya) and show marked differentiation, but these lineages would have an overall wide distribution (no IBD when Oaxaca is removed from the analyses further supporting a moist-forest hypothesis) (Ramírez-Barahona and Eguiarte, 2013). Genetic diversity would be favored (high overall genetic diversity, with at least four haplotypes with high frequency [H03, H02, H36 and H12]) and lack of genetic structure (one genetic cluster with wide distribution for M. schiedeana according to BAPS, with an area of higher genetic diversity in TLA and MI, and may be even GO, which agrees with areas of environmental stability in the distribution models), and signals of demographic expansion before the LGM (> 200,000 ya), followed by range expansion after the LIG, from the LGM to the Holocene (high number of low frequency haplotypes connected by few mutational steps in the haplotype network).

Of course, not all signals completely agree with the moist-forest hypothesis, because under this hypothesis we wouldn’t expect signals of demographic expansion (Ramírez-Barahona and Eguiarte, 2013), and neutrality tests, mismatch distribution and skyline plots all suggest demographic expansion for M. schiediana.

Therefore, and considering that the authors have very good data, I strongly suggest conducting a formal hypothesis testing based on an ABC framework (Cornuet et al., 2008, 2010, 2014; Knowles 2009; Bertorelle et al., 2010) that would assign a probability to each scenario and make an explicit test for the dry-refuge vs. moist-forest hypotheses and facilitate scenario choice. This will also allow testing if current levels of genetic variation and genetic structure in M. schiediana could be explained by other geographic or geologic events that do not relate to Pleistocene climate change.
Additional comments: Line 9-10. Please mention in the abstract the number of populations and individuals included in the analysis.

Line 50. Please consider changing phrasing to: “; which implies that it is highly vulnerable to climate change”

Line 58. Please consider changing this phrase to “These processes led to complex…” instead of “These processes had led…”.

Line 63-66. Please review the text “The dry refugia states that cooler conditions during the Last Glacial Maximum (LGM ~23-14 ka) shifted species migrations to the lowlands but the prevalence of arid conditions led to species displacements and contractions into glacial refugia; subsequently population expansions and long-distance recolonizations took place with the increase in temperature and humid conditions in the Holocene…)”. Please make the dry refugia hypothesis more explicit, because I got a little confused when reading the text.

Lines 120- 122. Please mention the total number of populations or localities included in the analysis.

Lines 136-143. Is there any information regarding mechanisms for seed and pollen dispersal? Are there any reports about the dispersal distance?

Line 145. In the Sampling and DNA sequencing section, please provide the total number of samples per taxon used in the analyses. How many M. pedrazae, M. schiedeana and M. schiedeana var Oaxaca individuals were analyzed?

Lines 152-153. Did the authors consider a distance between sampled individuals to avoid or minimize chances of sampling only closely related individuals?

Line 203. Some of the localities listed in Table 1 show a very low number of samples (n=1), therefore, genetic diversity is not well sampled for these locations and comparisons and conclusions at the population level should be avoided. I suggest moving this table to supplementary materials and focusing the paper and its conservation implications only at the lineage level.

Line 225-227. Please include original references to the methods employed by BEPC: Manolopoulou et al. 2011 and Manolopoulou and Emerson 2012. Also, please provide the underlying assumptions for this test. This is particularly important because the test assumes that there is phylogeographic structure and that current population structure is explained by founder events followed by migration (isolation by distance model) (see Manolopolou et al. 2020). The latter implies that the data supports the Pleistocene refuge hypothesis; therefore, there is a bias regarding the dry-refuge vs. moist-forest models. Perhaps, the authors should test first which of the two models or hypotheses has the best support given their data and depending on that implement this test.

Line 235. Please make it explicit that the program BEPC estimates the best number of migration events.

Lines 240-241. I recommend performing Mantel tests before BEPC, to support that data is consistent with an isolation by distance model and justify the use of BEPC analysis.

Lines 277-291. Please make the final number of occurrence points for each taxon used for the analysis explicit and clarify whether data for the three taxa or only for M. schiediana was used to build the models.

Lines 306-313. Please explain how the AOGCM to be used in the analyses was defined or provide an argument to justify the use of a particular AOGCM.

Line 320. Please explain where the 106 individuals came from; is it because of the outgroup? In methods section, the authors mention a data matrix of 96 individuals including some sequences downloaded from the GeneBank.

Lines 323-324. Please provide the results from MrBayes analysis (phylogenetic tree) as a figure in the main manuscript.

Lines 345-348. As previously mentioned (Line 203), some of the localities listed in Table 1 have only one sample. Genetic diversity at the population level should be taken with caution since these measures are particularly sensitive to sample size, and comparisons and conclusions at the population level should be avoided. I suggest moving table 1 to supplementary materials (or totally removing it from the manuscript) and focusing the paper only at comparing and assessing genetic diversity at the lineage level.

Lines 358-363. Instead of explaining the genetic clustering obtained with BAPS from a population perspective, the authors should emphasize that the three genetic clusters correspond to regions of the TMCF, which can be classified into south, central and north, and also is consistent with the classification of three taxa: M. pedrazae, M. schiediana and M. schiediana var Oaxaca.

Lines 363-369. As I mentioned above, I have some concerns regarding the BPEC analysis because of the assumptions underlying the analysis. In this case in particular, data suggest the presence of three lineages, which could have diverged in a different site each; therefore, we cannot rule out the possibility of more than one ancestral location. I recommend avoiding making inferences regarding ancestral haplotypes or ancestral locations, at least at this point.

Line 370-375. I recommend conducting a statistical analysis, such as MANOVA, to test for statistical differences in the environmental envelope occupied by each lineage (Nakazato et al., 2010 AJB 97(4):680-693; Di Febbraro et al. 2017 J Biogeog 44:2828-2838).

Lines 376-377. As mentioned above, sample size for some populations is very low and I recommend taking analyses at the population level with extreme caution and, if possible, avoiding making conclusions and inferences at this level. Please keep only pairwise FST between lineages or taxa.

Lines 378-383. It is very interesting that M. schiediana var Oaxaca show the highest level of genetic differentiation and that IBD analysis losses power when removing this data. Nevertheless, according to table 1 only 5 individuals from one locality from Oaxaca were included in the analysis and the geographic distance of this locality to the other taxa seems considerable (Fig 1). Does this provide enough evidence in itself to infer that this group or lineage is well-supported or might this be an effect of having samples from only one site in Oaxaca?

Line 396. Please add ya after ~250,000.

Lines 392-396. For the Bayesian Skyline Plots, each lineage may show a distinct independent historical demography, as seems to be the case for the data shown by the authors. I recommend keeping M. schiediana and M. pedraza separate for the historical demography analyses, because joining the data may produce a bias if the signal of demographic expansion for one of the lineages is very strong. It is interesting that signal of population expansion occurred about the same period (but temporality should be interpreted with caution; see comment on Lines 530-534) for both taxa, further suggesting they have constituted a different lineage for a long time perhaps even before the Pleistocene (moreoever since authors mentioned that divergence for M. schiedeana was estimated 11 Mya).

Lines 415-420. It is not clear if the model and past projections show distribution changes for the three taxa or only for M. schiediana. Please, clarify this in the methods section and in the legend for figure 4. Also in figure 4 legend define the meaning of MH, EH, LGM and LIG.

Lines 481-485. Data suggests that M. schiediana var. Oaxaca could have been isolated for a longer time. We should take these results with caution because we cannot rule out that sampling could be causing some bias since only one locality (N=5) from Oaxaca (and with a long distance from the other sampling sites; fig 1A.) was included in the analysis. I see that authors mention the need to gather additional data in lines 511-512, but suggest this caveat of the data should be considered since the beginning of the discussion.

Line 517. Please clarify “high mid-latitudes”. The term is ambiguous, so I recommend providing a latitude interval or threshold.

Line 521. Does “icehouse conditions” refer to glacial conditions?

Line 525-527. I recommend providing the date of divergence of M schiedeana in the introduction or in the study species sections. This will provide context to the results of the past species distribution models and historical demography data.

Lines 530-534. Results from Bayesian Skyline plots should be taken with caution, because (1) small sample size at least for M. pedrazae and M. schiediana var Oaxaca, which reduces the power of the analysis; and (2) transforming x-axis to time based on a standard substitution rate estimated for angiosperm chloroplast. Rates of molecular evolution vary considerably (see Smith and Donoghue, 2008 Science 322(5898):86-89; Gaut et al. 2011 Annu Rev Ecol Evol Syst 42:245-266; Lanfear et al., 2013 Nature Communications 4:1879), and this has an effect on the estimated dates. Therefore, the discussion should focus on consistent signals of demographic response across lineages instead of focusing on the date per se.

Line 533-542. Please, for a better context, provide dates of divergence for the three lineages included in the study (if available from the literature), because if the divergence pre-date the climate changes of the Pleistocene this would have implications for the interpretation of the results. The results from past species distribution show interesting shifts in species distribution during the distinct periods and may even support hypotheses of secondary contact between lineages during these times or the possibility of incomplete lineage sorting or divergence associate to Pleistocene climate change. Nevertheless, if M. schiedeana diverged 11mya, it is possible that M. pedraza and M. schiedeana var Oaxaca diverged before the Pleistocene. Estimates of the dates of divergence between lineages are needed for the reader to better-understand the processes that have affected these taxa.

Line 543. Please, change to “According to the glacial refugia hypothesis, …”.

Lines 543-562. Is it possible to have multiple refugia instead of just one? Please, perform a sum of the models to have a better visual representation of the areas of environmental stability that might have been refugia.

Lines 570-577. Given the small sample size for some localities, the genetic diversity of some sites might be underrepresented. Therefore, providing conservation guidelines at the local level may not be adequate, and conservation implications should be mention only on a broader regional level.


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

Input:
Title: INFLUENCE OF PLEISTOCENE CLIMATIC OSCILLATIONS ON THE PHYLOGEOGRAPHY AND DEMOGRAPHIC HISTORY OF ENDEMIC VULNERABLE TREES (SECTION MAGNOLIA) OF THE TROPICAL MONTANE CLOUD FOREST IN MEXICO
Review round: 2
Reviewer: 1

Output:
Basic reporting: no further comments
Experimental design: no further comments
Validity of the findings: The interpretation of the  results and conclusions are more cautious and some limitations of the data are identified.
Still, I have an issue with the circulation model used for the SDMs.
Additional comments: This is the second time reviewing this paper, and I congratulate the authors for being positive to my previous comments. The authors have done a great job revising their paper, which in my opinion is now a stronger paper with relevant results. These data would be a great addition to the growing evidence on cloud forest phylogeography in the region.
Some comments:
1) Lines 360-362. This is a erroneous interpretation of the results presented in Guevara (2020), who shows that different circulation models give contrasting results. I'm would recommend authors add a sentence or two in the discussion stating that the results and interpretation of SDMs are based on a single GCM, and thus caution is warranted. Or something like along these lines.
2) Lines 599. change 'do' for 'does'.
3) Figure 2. Authors should consider changing the colors in the figure, to make these less primary, and to keep in mind that it might be difficult to discern between colors if color-blind.
4) Figure 4. Same as above for the colors. Also, it would be nice to highlight the scenario with the greatest support (perhaps a square around the scenario).


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

Input:
Title: INFLUENCE OF PLEISTOCENE CLIMATIC OSCILLATIONS ON THE PHYLOGEOGRAPHY AND DEMOGRAPHIC HISTORY OF ENDEMIC VULNERABLE TREES (SECTION MAGNOLIA) OF THE TROPICAL MONTANE CLOUD FOREST IN MEXICO
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have overall improved their manuscript. Yet, some of the comments from the previous round of review have been partly addressed and particularly some of the methodological issues. Nevertheless, the concept and topic addressed are relevant, contribute to the field, and merit publication.
Experimental design: The methods used to address the questions are relevant. However, the niche analysis has room for improvements as already suggested in the previous round of review.
Validity of the findings: The findings are highly recommended to be refined in the light of improvements in the analysis of the projected distributions.
Additional comments: Please find below specific comments that could improve this work.

L. 325: How did you define this radius? Is it e.g. the average density of occurrences?
L. 330: All occurrences or only the ones from GBIF?
L. 340: Based on the paper you cited in your response:

"collinearity shift and environmental novelty can negatively affect Maxent model transferability. We therefore recommend to quantify and report collinearity shift and environmental novelty to better infer model accuracy when models are spatially and/or temporally transferred."

This is one more reason to keep a lower threshold for collinearity in variables.

L. 341: A threshold of 0.85 is still too high. You could at least lower it at 0.75 e.g. see Elith et al., 2012. This will also help you reduce the number of variables which is way too high for so few occurrences. Therefore, there is high risk of model overfit and low transferability in time and space.

L. 358-368: Comparisons of niche and space overlap under different resolutions over space and time cannot be objective as the resolution can drammatically alter predictions of SDM. Please see Randin CF, Engler R, Normand S et al. (2009) Climate change and plant distribution: local models predict high-elevation persistence. Global Change Biology, 15,1557–1569.

For Mid Holocene there is a dataset from worldclim paleodata at 30s resolution you could use. See here http://www.worldclim.com/paleo-climate1. For other climate layers you could downscale the data.

L.369-371: For what % of the study area the variable values are beyond the calibration range (novel climate)? You could test this before projecting and select for the variables with the best transferability for more objective projections of the models.

L477: The ratio of occurrences should have been something around 70% training and 30% testing. Not the other way round...For such a small number of occurrences, this number of variables is excessive.  A rule of thumb is one variable per 20 occurrences... See Guisan et al 2017, Habitat suitability models in R (book)

L. 479: Did you let the algorithm decide the type of features? It would be easier for a model to extrapolate the simpler it is e.g. you could exclude hinge features at least (if not threshold too) and leave Q, L, P, T.

L.653: The last paragraph is very interesting as it gives a clear hands-on recommendation.

Minor comments:
L.126: Please correct to "considerable"
L. 247: Please correct to "Manolopoulou" in the second citation


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

Input:
Title: INFLUENCE OF PLEISTOCENE CLIMATIC OSCILLATIONS ON THE PHYLOGEOGRAPHY AND DEMOGRAPHIC HISTORY OF ENDEMIC VULNERABLE TREES (SECTION MAGNOLIA) OF THE TROPICAL MONTANE CLOUD FOREST IN MEXICO
Review round: 2
Reviewer: 3

Output:
Basic reporting: Authors made a good job addressing my previous comments. There are still a few issues and typos, see General comments for the author.
Experimental design: Overall genetic and spatial analyses are adequate, and previous comments have been addressed.

Authors followed my suggestion of running an ABC framework to explicitly test the dry-refugia and moist-forest hypotheses. Nevertheless, more detail is needed in the method section so analyses can be replicated. Moreover, the authors mention that the five tested scenarios were “considered as the most plausible given the observed relationships of divergence and admixture among the three lineages”. Regarding the original question of testing two biogeographic hypotheses, I suggest considering at least two divergence scenarios (or group of scenarios), one that considers divergence associated with Pleistocene climate changes (t2 and t1), as already done; and another that considers divergence associated to vulcanism in the Transmexican Volcanic Belt (t4 and t3) (see for example, Pérez-Crespo et al. 2017 J Biogeog 44:2501-2514; Ramírez-Barahona and Eguiarte 2014 J Biogeog 41:2396-2407).

In addition, in the results section authors mentioned that two scenarios (2 and 5) obtained equal probabilities, and type 1 and type 2 error rates were high. To select between these scenarios, authors performed two additional runs in DIYABC where each scenario was alternatively removed from the analysis. This is not an adequate method to select between these competing scenarios and a different approach should be used (see Beaumont et al. 2002 Genetics 162:2025-2035; Beaumont 2010 Annu Rev Ecol Evol Syst 41:397-406; Bertorelle et al. 2010 Mol Ecol 19(13):2609-2625; Robert et al. 2011 PNAS 108:15112-15117). In this sense, from the methods section it is not clear if previous runs were conducted to test different combinations of summary statistics and parameter values to adjust scenarios. The selection of summary statistics is important, because it will add or subtract power to the analysis. In addition, by conducting previous runs we can identify if tested scenarios are sufficiently different so the analysis will be able to distinguish between them or identify if some of the parameters should have wider or narrower distributions. Conducting previous runs to adjust summary statistics and parameter distribution and adding scenarios with deeper dates of divergence will probably solve this issue.
Validity of the findings: Previous comments have been addressed but see comments on experimental design regarding the ABC analyses.
Additional comments: Line 25. Correct italics in the s of populations.

Line 117. Please change “at the north of Oaxaca” to “in northern Oaxaca”.

Line 260-263. Please add a references that support the use of MANOVA and Tukey tests to assess environmental differentiation.

Lines 291-303. It is important to provide detailed information on the summary statistics, paramater values and parameter distribution used when conducting coalescent simulation such as DIYABC, because the quality of the results will depend on the quality of initial data (see Bertorelle et al. 2010. Molecular Ecology 19(13):2609-2625 https://doi.org/10.1111/j.1365-294X.2010.04690.x). Moreover, authors should provide all information so the analysis can be replicated. Therefore, methods used to run DIYABC need a more detailed explanation. Please, define the distribution model used for each parameter (uniform, logistic, etc.) in addition to the median, maximum and minimum values for each parameter (N1, N2, N3, NA, t1, t2, ra) defined initially to run DIYABC. Particularly as time is an important parameter being tested, please define the mean values and confidence intervals defined for t1 and t2 in both generetion time and its equivalent in geological time.

Line 323. Please change “spatial accuracy sufficient to produce” to “spatial accuracy to produce” or to “they have sufficient quality and accuracy to produce”

Lines 322-330. Please explain why using a thinning of 3 km for one dataset and 5 km for the other.

Line 333. Please provide a justification for using CHELSEA.

Line 342. Please review this sentence “and the Pearson’s correlation threshold of 0.85 using NTBOX v0.1.4.5 R package (Osorio-Olvera et al., 2020) was performed…” It is a little bit odd.

Lines 348-351. Also review sentence “Some levels of…, resulted in 100 candidate niche models” Perhaps change to “Some levels of…, which resulted in 100 candidate niche models”.

Line 362-368. Selection of climate input data for species distribution modelling could influence the results (Bobrowski and Schickhoff, 2017). Therefore, please provide a justification for using data from WorldClim in some cases and data from CHELSA in other cases to obtain the species distribution models and to perform past projections.

Line 417. Regarding results from AMOVA, where you say that “… a slightly lower proportion of the genetic variance and genetic differentiation were observed relative to the other two groupings” Do you mean relative to the two lineage grouping? because I see in table 2 and in the results that FCT value for the three lineage grouping is higher than FST for no grouping but lower than FCT for three lineages grouping.

Lines 432-434. That haplotypes H10, H17 H22, H23, H36 and H40 were assigned to M. schiedeana pop. Oaxaca is not clear from Fig. 2. Only one haplotype from population Mi is colored yellow in panel 2D. In the haplotype network (panel 2B) haplotypes H43,H44 and H45 are assigned to the M. schiedeana pop. Oaxaca cluster.

Lines 435. Supplemental S2 shows pairwise FST values. I’m not sure why it is cited here.

Lines 453-456. Bayesian skyline plot show a steeper expansion for M. schiedeana than for M. pedrazae. Is the result for M. pedrazae signficant?

Lines 463-467. For DIYABC results, the logistic regression shown in supplementary materials, shows equal probabilities for scenario 2 and scenario 5, as well as high type 1 and type 2 error rates. Therefore, the correct implementation should be treating both scenarios as equally possible, and results should highlight both of them. Of course, running DIYABC while eliminating scenario 5 will result in scenario 2 having the best probability, and the opposite if scenario 2 is excluded, because this type of analysis will only contrast and assign a probability to the scenarios that are fed to the program. We should remember that we are only selecting the best scenario among those that are being tested and, we should not treat these scenarios as the absolute truth because we cannot rule out that there are other untested scenarios that might be equally plausible or even have a better fit to the observed data. Therefore, the proposed method to discrimate between scenarios 2 and 5 do not seems adequate. Previous runs should be conducted to adjust parameter values and to assess if selected summary statistics have enough power to differentiate between competing scenarios, this will result in higher reliability for scenario choice; and if even then the analysis is unable to discrimate between scenarios 2 and 5, then both shall be presented as equally plausible (please read Beaumont et al. 2002 Genetics 162:2025-2035; Beaumont 2010 Annu Rev Ecol Evol Syst 41:397-406; Bertorelle et al. 2010 Mol Ecol 19(13):2609-2625; Robert et al. 2011 PNAS 108:15112-15117).

Line 524. Change “due to is slow-evolving” to “due to its slow-evolving”.

Lines 571-574. It is difficult to assess if estimated dates of divergence are reliable, because of lack of detail regarding the description of methods and some methodological issues regarding scenario choice. Moreover, apparently the main differences between the tested scenarios related to identifying the ancestral lineage but not to differences in times of divergence. In this sense, since Magnolia section diversified ~10 Mya and signals of population expansion in M. schiedeana were dated ~250,000 ya, it would be interesting if competing scenarios also included differences in times of divergence, and test for divergence driven by Pleistocene climate changes (dates in accordance to t2 = LIG and t1 = LGM) vs. divergence driven by vulcanism pulses of the TMVB (t4 and t3).
Lines 581-583. Please make it explicit in the methods section that tested scenarios also considered changes in effective population sizes (varNe).

Line 588. Please change prolong to extend

Line 598. According to line 303, the five tested scenarios were considered as the most plausible given the observed relationships of divergence and admixture among the three lineages. Nevertheless, as I understand it, the ABC approach was implemented to explicitly test the dry-refugia and moist-forest hypotheses; thus, scenarios should include differences in times of divergence and changes in effective population sizes (for example, Pérez-Crespo et al. 2017 J Biogeog 44:2501-2514; Ramírez-Barahona and Eguiarte 2014 J Biogeog 41:2396-2407). If these changes are already considered in the five analysed scenarios, this should be explained in the methods section.