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: FUNCTIONAL ANALYSIS OF LNCRNAS BASED ON COMPETITIVE ENDOGENOUS RNA IN TONGUE SQUAMOUS CELL CARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Some sections of the manuscript, especially the methods section lacks clarity. Figure 1, 2, and 3 can be combined into a single figure with multiple panels. The volcano plots can be moved to supplementary figures. Figure 4 is redundant and can be moved into supplementary. Also, Figure 7, 8 and 9 can be combined into a single figure with multiple panels.
Experimental design: The study aims to find out the roles of lncRNAs as part of putative competing endogenous RNA network in tongue squamous cell carcinoma. While the overall design of the study is well defined and the results support the conclusions, I would like to point out some aspects where the manuscript can be more clear.
1. In the Methods section, proper description of the TCGA dataset should be given. Instead of "RNA sequences", the authors should mention whether they used RNA-Seq v2 and/or miRNA-seq dataset from TCGA, and in which format the RNA-seq data was downloaded; was it raw count or RSEM or FPKM? Also, the authors mentioned "Before conducting differential expression analysis, we processed the data and deleted the RNA and miRNA data that were not expressed"; was there a cut-off for expression or number of samples (e.g. remove genes with < 1 FPKM in 90% of samples)?
2. They mentioned about multi-variate analysis with mRNAs in the ceRNA network. But no figures or tables are included that shows the result of the multi-variate analysis. How was the risk scores and what was the significance of individual factors in the multi-variate analysis?

Minor comments:
1. Instead of "three types of lncRNAs", the authors could write "three lncRNAs".
2. In the abstract: "Three kinds of lncRNAs are involved in the regulation of disease by affecting cytokines and the immune system." : this should not be definitive as further validations are needed to support this statement. Rather the authors can write "The enrichment study indicates that these three lncRNAs are involved in the regulation of disease by affecting cytokines and the immune system".
Validity of the findings: The study supports the conclusion. But some clarifications are still needed (as stated above) before the manuscript can be accepted for publication.
Additional comments: The study aims to find out the roles of lncRNAs as part of putative competing endogenous RNA network in tongue squamous cell carcinoma. While the overall design of the study is well defined and the results support the conclusions, I would like to point out some aspects where the manuscript can be more clear.
1. In the Methods section, proper description of the TCGA dataset should be given. Instead of "RNA sequences", the authors should mention whether they used RNA-Seq v2 and/or miRNA-seq dataset from TCGA, and in which format the RNA-seq data was downloaded; was it raw count or RSEM or FPKM? Also, the authors mentioned "Before conducting differential expression analysis, we processed the data and deleted the RNA and miRNA data that were not expressed"; was there a cut-off for expression or number of samples (e.g. remove genes with < 1 FPKM in 90% of samples)?
2. They mentioned about multi-variate analysis with mRNAs in the ceRNA network. But no figures or tables are included that shows the result of the multi-variate analysis. How was the risk scores and what was the significance of individual factors in the multi-variate analysis?

Minor comments:
1. Instead of "three types of lncRNAs", the authors could write "three lncRNAs".
2. In the abstract: "Three kinds of lncRNAs are involved in the regulation of disease by affecting cytokines and the immune system." : this should not be definitive as further validations are needed to support this statement. Rather the authors can write "The enrichment study indicates that these three lncRNAs are involved in the regulation of disease by affecting cytokines and the immune system".
3. Figure 1, 2, and 3 can be combined into a single figure with multiple panels. The volcano plots can be moved to supplementary figures. Figure 4 is redundant and can be moved into supplementary. Also, Figure 7, 8 and 9 can be combined into a single figure with multiple panels.


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: FUNCTIONAL ANALYSIS OF LNCRNAS BASED ON COMPETITIVE ENDOGENOUS RNA IN TONGUE SQUAMOUS CELL CARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Major reviews:
The authors could update the reference literature. For example, in line 57 when they mention oral carcinomas the latest reference was published in 2012. This recomendation is for the lncRNAs too. During the introduction they spent a lot of time describing the mechanism of ceRNA, which is very important. However I would suggest to reduce without losing contend about the mechanism and highlight more the studies that link lncRNAs and tumorigenesis. I would recommend to rearrange the introduction to stay straight to hypothesis. Otherwise it remains fuzzy and the propose is not clear in the end.
Minor reviews:
Regarding the figures 1,2, and 3, please clarify what rows and columns represent. And it would be benefic if the authors put color bars according to the diagnosis of the sample, it would become clearer if these differentially expressed transcripts are able to group samples according to their diagnosis.
Improve the resolution of figures with GSEA analysis, it is really hard to see something.
Tables would be great if each gene are repsented in a line with the name description together.
Experimental design: Major review:
It would be great if the authors describe better how they proceed in the analysis. For example, they used TCGA samples, what kind of files raw sequencing data, processed samples.
1-) The authors performed some clustering analysis or used MDS (multidimensinal scale) to check outliers samples? If they don't I strongly recommend perform that.
2-) Why do the authors used the ENsembl annotation and not the GENCODE annotation once they are working with noncoding RNA.
3-) They check for technical bias in the expression data? If they don't I strongly recommend perform that. And if there is some of these they would have to correct it.
4-) When performing the model of differentially expressed genes, the interest variable was the diganosis, and what about the ajusted variables like sex, age and other? This would make a huge difference in this model .
5-) Perform cut offs using Fold change is not a good strategy, unless the authors show the expression value. For example, a Fold change of 2 in genes that have average expression of 5, would require that control and case have 5 and 10 respectively, however for a gene with average expression of 1000, it would requiere that expression should be 1000 and 2000. In this last case a Fold Change of 1.5 would requiere an average expression of 1500 and 1000, which is very meaningful.
6-) It would be great have a table with clinical variables, just to be aware if the dataset has some biological bias before starting the differentially expression analysis.
7-) In the netwrok analysis, what are the parameters used to measure the binding between miRNA and lncRNAs, what are free energy of binding, or there multiple bindings? If they only used what was described in the literature, it would should be clearer, and would be great knowning how large is this database to make a comparison if what they found is a good result or not.
8-) To perform the network the authors used a correlation measure? Because it is not enough to have the binding, but you have to know the dynamic as well. So I strongly suggest to perform a correlation analysis using expression data and then build the network.
9-) In figure 6, what are the criteria to define high and low expression?
It would be great to know the criteria of these, and show what is the rank of expression value of these RNAs according to each class others transcripts.
Validity of the findings: The results are meaningful, once this study reveals new potential targets and describe mechanisms that could lead to the tongue squamous cell carcinoma. The discussion is well structure and it easy to follow. The findings are useful in tha lncRNA area, as well as in cancer area. The conclusions are sticked to the point.
Additional comments: The main findings of these paper are of interest of scientific community and should be considered for publication. My main concern is about the technical questions, which could change the final results, however the main core of this study, probably, would not change. The disussion and conclusion are easy to follow and if the introduction and results were ajusted in that way would be great. Recommendations about figure and tables were already describe before.


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: FUNCTIONAL ANALYSIS OF LNCRNAS BASED ON COMPETITIVE ENDOGENOUS RNA IN TONGUE SQUAMOUS CELL CARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed all my concerns. But in many places the English should be checked carefully and corrected.
Experimental design: No further comments
Validity of the findings: No further 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: FISHER LINEAR DISCRIMINANT ANALYSIS FOR CLASSIFICATION AND PREDICTION OF GENOMIC SUSCEPTIBILITY TO STOMACH AND COLORECTAL CANCERS BASED ON SIX STR LOCI IN A NORTHERN CHINESE HAN POPULATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: Clear professional English language is used throughout the manuscript. Both Introduction and Discussion provide the appropriate context for the study. References are relevant and up to date.  Tables and Figures contain pertinent data, are well written and formatted. The authors are advised to detail what guided the choice of immunohistochemical markers tested in this study. Considering the large plethora of immunohistochemical markers, why were the ones included here prioritized versus others available?
Experimental design: The study is well designed and asks an original and meaningful question. The molecular methods are described in sufficient detail to be replicated. The investigation appears to abide to high technical standards.
The authors are requested to explain the assigned cut-offs for ki-67 and p53 immunostains. In clinical practice ki-67 is scored as an approximate percentage of tumor cell nuclei positive and p53 is interpreted as representing wild-type or aberrant expression. The cut-offs of >50% or <50% assigned by the authors may not be relevant.
It would be highly valuable to do MSI analysis of the tumor tissue in patients in the study group and the authors are advised to do so if possible.
No ethical standards for the study have been included. The authors are asked to specify if the subjects have consented to participate in the study and if institutional approval has been obtained.
Validity of the findings: The validity of the findings is limited by the small number of subjects. In addition, the study appears to include only the Chinese ethnic group and may not be representative of other populations. As only gastrointestinal cancer and controls were studied, it is not possible to ascertain if the STR loci implicated are specific for gastrointestinal cancer or might be associated with other cancer types.
Additional comments: Well-written and technically sound study with interesting findings.  The molecular data is the most relevant. The immunohistochemical and serum marker data have not been well developed in this work and does not appear to add much to the value of the publication.


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

Input:
Title: FISHER LINEAR DISCRIMINANT ANALYSIS FOR CLASSIFICATION AND PREDICTION OF GENOMIC SUSCEPTIBILITY TO STOMACH AND COLORECTAL CANCERS BASED ON SIX STR LOCI IN A NORTHERN CHINESE HAN POPULATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is an overall relatively well written, structured and cited manuscript. However, there are a few areas that could use improvement.

1) I feel that the introduction does not adequately explain why the six STR loci were chosen. Luckily the authors included this information in their discussion (lines 258-287) and I believe that this would be much more appropriate in the introduction.

2) The opening lines of the introduction (lines 63-72) are a little confusing as gastrointestinal (GI) carcinoma as a group is not defined. Additionally, the reference supplied says that GI carcinoma is A leading cause of cancer related deaths not THE leading cause and I think that is an important distinction to make in line 63. Some reference to the geographic and ethnic discrepancies in incidence would also be appropriate.

3) Line 84 should reference that the subsequent studies all tested for somatic alterations in STR loci.

4) The data presented in the "Establishment of discriminant function" section (lines 206-222) is quite difficult to read in its current form. Construction of one or more tables would help immensely.

5) Table 1 column two header currently has "Gastrointestinal cancer (n=30), n (%)" should be "... (n=19) ..."

6) Figure 4 is rather cluttered in my opinion and would better off split into two figures (one with the cfunc in the main paper, and the other with the loci in a supplemental table)
Experimental design: The question asked by this manuscript is quite interesting and worth exploring. However, I believe that the current structure of analysis is not fully able to answer it.

The authors combine 19 colon, rectal and gastric carcinomas and compare this against normal controls. While colon and rectal carcinomas are generally considered relatively comparable, gastric carcinomas are different enough (both clinically and genomically) that it is inappropriate in my opinion to group them together. Additionally, GI carcinomas also include pancreatobilliary, esophageal, small intestinal and hepatic carcinomas, none of which are represented in this manuscript. I believe that this article would be significantly stronger if the authors analyzed additional cases and separated out gastric from colorectal into separate analyses. If this was done a revision to "select gastrointestinal carcinomas" throughout the article would also be appropriate.
Validity of the findings: In the "Correspondence between STR typing and IHC markers" and "... and tumor markers" sections (lines 238-249) no statistical analysis is provided to support the claims of relation between the STR typing and either IHC or serum tumor markers. This should be performed and reported as such.
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: FISHER LINEAR DISCRIMINANT ANALYSIS FOR CLASSIFICATION AND PREDICTION OF GENOMIC SUSCEPTIBILITY TO STOMACH AND COLORECTAL CANCERS BASED ON SIX STR LOCI IN A NORTHERN CHINESE HAN POPULATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: Explaining the choice of IHC markers is a relevant addition to the manuscript (lines 332-346)
Experimental design: The authors choose to keep the 50% cut-off for Ki-67 and p53. This is acceptable albeit far from ideal for Ki-67.
It does not reflect tumor biology for p53. Advise the authors to either remove p53 from the paper or to score it was wild-type or mutant expression pattern.
Ethical parameters were appropriately included.
Validity of the findings: Authors have clarified the limitation of sample size and restricted ethnic subgroup included in the study.
Authors are advised to include in the Discussion the data provided to the reviewers: 'In addition to gastrointestinal cancer, we have conducted similar studies in other cancers, such as lung cancer and breast cancer. Some results are similar to the current findings, but not exactly the same. Potentially valuable STR loci found in other cancers are not exactly matched by these six loci.'
Additional comments: In my view, the serum and immunohistochemical markers are of little if any relevance for this study. I would be in favor of removing this data from this manuscript. Authors may consider further studies and submission of a separate manuscript correlating to serum and IHC makers  to this or some other journal with more solid data.


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

Input:
Title: FISHER LINEAR DISCRIMINANT ANALYSIS FOR CLASSIFICATION AND PREDICTION OF GENOMIC SUSCEPTIBILITY TO STOMACH AND COLORECTAL CANCERS BASED ON SIX STR LOCI IN A NORTHERN CHINESE HAN POPULATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: The reporting is much clearer with this revision. Great work!
Experimental design: I still believe that this will be a stronger study with more samples, but I accept the limitations that your institution has. The disclaimers at the end of the paper i think adequately inform readers that this is still a pilot study. I look forward to any follow up studies!
Validity of the findings: Edits addressed this section.
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: HIERARCHICAL GENERALIZED ADDITIVE MODELS IN ECOLOGY: AN INTRODUCTION WITH MGCV
Review round: 1
Reviewer: 1

Output:
Basic reporting: see below
Experimental design: see below
Validity of the findings: see below
Additional comments: This is a strong paper and I only have a few minor comments.

1.	Line 34: HGLMs may not only handle linear but also quadratic etc. relationships.
2.	Line 37: Did you mean something like “may vary across groups”?
3.	Line 182: typo in “average average”
4.	In some Figures (e.g. Figure 7), points are hidden by the prediction line. Can this be changed?
5.	Line 408: It should be made clear that the listed smoothers are the remaining ones not those being removed.
6.	A lot of Tables have broken links as indicated by “Table ??”.
7.	Line 438: It seems as if model 4 is slightly better than model 2 contrary to what the text says.
8.	Line 489: typo in “could could”
9.	Line 501: What’s a “model-to-model comparison” as compared to a “model comparison”?
10.	Line 509: Why are fitted vs. response plots less useful for non-gaussian families?
11.	Line 520 ff.: Could this be made a proper table with some notes? Also, there seem to be spaces in the category names in the table. I think it would be better to remove these spaces.
12.	Figure 14: It should be made explicit to which data this plot belongs. Also, it seems to be left and right not “Top” and “bottom” row.
13.	Figure 15: Maybe the y-axis should include explicitly that predictions are on the log-scale (not just in the note).
14.	Table 3: I think it’s a little bit concerning that the intercept only has not much worse (or even better) predictions despite a clear non-linear trend. Perhaps it’s worth discussing that a little bit more thoroughly.
15.	Line 619 (and all lines where you compare models based on AIC): On which basis do you decide when to models differ “substantially” in their AIC values?
16.	Line 657: Ist n_g and g ment to be the same? At least g is not introduced before it is used.
17.	Line 787: You say that gam() uses the Bayesian posterior covariance matrix. As gam() is frequentist I would naively expect this covariance matrix to be an *approximation* of the Bayesian posterior covariance matrix, or is it really an exact one? In any case, it can only be the mode of this covariance matrix unless we obtained the full posterior distribution somehow.
18.	Line 804: With the latest CRAN releases of mgcv and brms, factor-smooth interactions are now possible.
19.	Line 810: It may be helpful to describe in a little bit more detail how GAMs fit into the functional regression framework. For instance, in the term “function-on-scalar” it may be unclear for readers if x or y is the function / the scalar.

Comments regarding the R code:

1.	I think more spaces within lines of code as well more new-lines would help with the readability. I would recommend single lines not exceeding 80 characters.
2.	Longer comments are perhaps better put into their own lines
3.	It is saver not to abbreviate TRUE and FALSE by T and F respectively.
4.	Personally, I like the style
object <- fun(
   <arguments>
)
in order to prevent arguments from starting at the 40+ character in the line, but it’s just a matter of style that I don’t want to impose on anyone.
5.	Perhaps it would be beneficial to the readability if you used an Rmarkdown document instead of an R script to have comments outside of code chunks. As a bonus you could compile the document to html so that people can directly look at the results next to the code without having to run the code themselves.


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: HIERARCHICAL GENERALIZED ADDITIVE MODELS IN ECOLOGY: AN INTRODUCTION WITH MGCV
Review round: 1
Reviewer: 2

Output:
Basic reporting: No major comments, this is mostly very well written and structured.
Experimental design: The simulation study re. over/undersmoothing in Section V needs more work, in my opinion, or at least a much more circumspect interpretation of the result(s).
Validity of the findings: See above re. Section V, see attached for specific small points on model checking and representation of results.
Additional comments: See attached. Some typos, some snetences could be more clear, some minor aspects of results I could not reproduce or interpretations I did not share.


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: HIERARCHICAL GENERALIZED ADDITIVE MODELS IN ECOLOGY: AN INTRODUCTION WITH MGCV
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article provides an introduction to Hierarchical GAMs in mgcv, which will be useful to scientists interested in analysing data sets with a hierarchical structure. The article is generally clear, and it provides the right level of detail for the intended audience. I have only major comment about the presentation:

- In the paper you frequently refer to models 1 to 5, so that a forgetful reader is forced to frequently go back to their definition in Figure 4. I think that it would be better to use more meaningful labels for the models, such as:
1) G (*G*lobal only)
2) GIC (*G*lobal + *I*ndividual effects with *C*ommon penalty)
3) GIM (*G*lobal + *I*ndividual effects with *M*ultiple penalties)
4) IC (only *I*ndividual effects with *C*ommon penalty)
5) IM (only *I*ndividual effects with *M*ultiple penalty)
Obviously the labels above are just a suggestion, but the current 1 to 5 labels are making the discussion in the paper quite hard to follow.
Experimental design: No comment.
Validity of the findings: The examples used in the paper are clear and should be useful to any applied scientist wanting to start using HGAM in mgcv. I have two main comments.

1) When analysing the D. mendota data set, the author assess the four model considered using the RMSE on the test set. Table 3 shows that the GAM models do slightly better than the intercept-only model on the first 3 data sets and slightly worse on the Waubesa data. However, the Waubesa data contains a very large outlier, which has a strong influence on the RMSEs. Using the Mean Absolute Error leads to different results:

# A tibble: 4 x 5
  Lake    `Intercept only` `Model 1` `Model 2` `Model 3`
  <fct>   <chr>            <chr>     <chr>     <chr>
1 Kegonsa 1.7              1.5       1.5       1.4
2 Mendota 2                1.6       1.6       1.6
3 Menona  1.9              1.6       1.6       1.6
4 Waubesa 2.6              2.5       2.7       2.6

My point is that the reader might look at table 3, and conclude that it is not worth spending much time learning about HGAMs, given that their performance is very close to that of an intercept-only model on real data. To avoid this, it would be important to point out that table 3 (and probably table 2) are based on relatively small data sets with occasional very large (and unpredictable) responses. Hence it is difficult to see how (in the absence of additional information) any statistical model could lead to a much lower RMSE on the test set, relative to the intercept-only model.

2) Looking at Figure 18, one might get the impression that the bam() function is pretty useless, given that it is beaten by gamm and gamm4 for any group size. However, it would be important to point out that bam scales well (possibly better than any other fitting methods in mgcv) with the number of observations per group, especially if the discrete = TRUE option is used. It might also be useful to include the results of a comparison where the number of groups is held constant, and the number of observations within each group is increased.
Additional comments: I have some relatively minor comments and suggestions:

- Given that the paper is aimed specifically at ecologists, maybe the word "ecology" should appear already in the title.

L 105: "A penalty term is then added to the model likelihood", this is the log-likelihood, right?

L 109: "In the left plot λ was estimated" probably I am being pedantic but I would say that lambda is
            being "selected" not "estimated".

L 150: Here you are talking about the penalty used in TPRS. Maybe it would be useful to add a
           pointer to the relevant section in Wood's book or to add a formula for the penalty, which
           is described a bit vaguely at the moment.

Caption to figure 3: "This means these functions are in the null space of this basis" the intercept and
                                 linear term are in the null space of the penalty matrix, not of the basis. Of course
                                 the smooth could then be re-parametrized to separate null space and span,
                                 but I don't think you are mentioning the re-parametrization here.

L 364 "This increases the computational cost of the model (as there are more smoothing parameters to
           estimate), and means that the only information shared between groups is through the global
           smoother." Notice that information is shared also for estimating the variance of the
           observations, and for estimating the variance of the random effects (if these are included as in
           the formula following line 369).

L 369 I am a bit confused about what is happening here:
           y ~ s(x, bs="tp") + s(x, by=fac, m=1, bs="ts") + s(fac, bs="re")`
          In particular, the by-factor effects have a first order penalty hence their null space should be
          empty if these smooths have been centred (that is, if the constant function has been removed
          from their span). If this is correct, then what is gained by using "ts" rather than "tp"?
          Please clarify (I have a similar doubts about the plants and birds models).

L 379 "Using ts helps reduce this issue, as the only unpenalized null space terms will occur in
           the global smoother." maybe it would be clearer to say "Using ts helps reduce this issue,
            as the unpenalized null space terms will occur only in the global smoother."
            (I moved the "only" around).

L 417 "count ~ t2(week, latitude, species, bs=c("cc", "tp", "re"), k=c(10, 10, 6), m=c(2, 2, 2))"
            What is the meaning of using a 2nd order penalty for the random effect here? I guess that
            you had to set m to c(2, 2, 2) rather than c(2, 2)  because you need m to have the same
            length as the number of marginals, but the last 2 will not be used.
            Please clarify this in the text as a non-expert reader might get confused.

L 420 For bird_mod5 you are still using bs = "ts", but there is no identifiability issue here right?
          Please clarify or change to "tp".

L 516 "The k.check test shows that the default maximum degrees of freedom for the smoothers used in model 5 are sufficient for all species, as the p-value for the observed k-index" personally I prefer looking at whether EDF is close to k', rather than looking at the p-values. The reason is that the p-values can be highly variable under the null hypothesis (no residual autocorrelation), and can change from (say) 0.4 to 0.02 from one call to gam.check to the next. Further if one of the p-values is, say, 0.01 while edf=2 and k'=10 I don't see why one should consider increasing k further for this effect (while if edf=9.8, k'=10 I would consider increasing k even if the corresponding p-value was not significant).

L 537 "Note that there is no p-value for the random effects smoothers s(taxon) and s(taxon,year_f) as the k value  for this term is already set at its maximum." It would be worth pointing out that the p-values come from simulation-based tests for autocorrelation of the residuals. So this test cannot be performed for factors such as taxon (there is no natural way of ordering the residuals along taxon).

Table 3: "Table 3: Out-of-sample predictive ability for model 1-3 applied to the D. mendotae dataset. RMSE values represent the average squared difference between model predictions and observations for held-out data (zero predictive ability would correspond to a RMSE of one)" Are you sure that the RMSE should be 1 for a very bad model?

L 583 "This estimate would have no variance (as it is always the same regardless of what the data look like) but  would have high bias unless the true population mean happened to equal zero." should be "... unless the true population mean happened to equal to the predetermined fixed value for the mean." (I think you are mixing what you write in footnote 6 with the main text here)

L 650 "(i) the number of basis functions to be estimated" strictly speaking the basis function are fixed, their regression coefficients have to be estimated

L 849 "All code used to generate this paper, as well as prior versions of this manuscript, are available
       at: github.com/noamross/mixed-effect-gams." I would include this sentence also at the end of the abstract,  so that the reader will know immediately where the code is.

A list of typos:

L 144 " can be use for problems"

L 174 "one wanted estimate the interacting"

L 227 " but very different shapes. wiggliness measures"

In footnote 1 on page 9:  "it will will raise" and also "error message if passed data coded as character"

L 433 "Table ??. " Notice that the references to all tables are broken.

L 508 "The code for model 4 and 5 for the community zooplankton model is shown here:" but the formulas actually are at top of the page.

L 670 "need to be estimate"

L 686 "the funcion bam()"

Figure 18: Notice that the legend does not allow to distinguish between bam(discete = TRUE) and bam(discrete = FALSE)

L 846 "the intial idea"


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: HIERARCHICAL GENERALIZED ADDITIVE MODELS IN ECOLOGY: AN INTRODUCTION WITH MGCV
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have addressed all of my previous comments and I have no further suggestions.


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: HIERARCHICAL GENERALIZED ADDITIVE MODELS IN ECOLOGY: AN INTRODUCTION WITH MGCV
Review round: 2
Reviewer: 2

Output:
Basic reporting: All issues previously reported have been answered.

(Very) minor points (NB: page and line numbers refer to pdf with diffs):

p. 27, l. 578:
"The code for model 4 and 5 checking model S and I for the community zooplankton model is:"
<Code not actually shown>

p. 43 bottom/44 top:
- please refer to function "refund::pffr" not "fosr" - "fosr" is fairly limited and does not use mgcv::gam.
- please cite "Scheipl, Fabian; Gertheiss, Jan; Greven, Sonja. Generalized functional additive mixed models. lectron. J. Statist. 10 (2016), no. 1, 1455--1492. doi:10.1214/16-EJS1145. https://projecteuclid.org/euclid.ejs/1464710238" here, which is the more relevant reference for this instead of Scheipl/Staicu/Greven 2014.

p. 44, l. 985f.:
Maybe worth mentioning here that, starting from the current version, mgcv now does approximate fully Bayesian inference via a clever version of INLA as well  (mgcv::ginla).
None of us could ever hope to keep up with Simon Wood...
Experimental design: All issues previously reported have been answered thoroughly.
Validity of the findings: All issues previously reported have been answered thoroughly.
Additional comments: It was a pleasure to read the author's well-written and thoughtful rebuttal and the revised and much improved manuscript.
Congratulations on a very interesting and insightful paper.


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

Input:
Title: HIERARCHICAL GENERALIZED ADDITIVE MODELS IN ECOLOGY: AN INTRODUCTION WITH MGCV
Review round: 2
Reviewer: 3

Output:
Basic reporting: NA
Experimental design: NA
Validity of the findings: NA
Additional comments: I am happy with the revised version of the manuscript, and with the authors' reply to my comments. I have no further suggestions.


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: ON THE PRESENCE OF DIPTURUS NIDAROSIENSIS (STORM, 1881) IN THE CENTRAL MEDITERRANEAN AREA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Introduction
I feel that the introduction of the paper is poor and needs to be reorganized. I recommend the following points to develop:

a). DNA barcoding and its use for problematic species (See Hebert et al., 2003a,b).

b). Rajidae (skates) as a taxonomic problematic group due to their conservative morphological features (see Coulson et al., 2011). For this family, DNA barcoding has been used to the description of new species (e.g. Last & Séret, 2016), extirpation (e.g. Ball et al., 2016), as well as, expansion a species range (e.g. Ordines et al., 2017). Note that some of these examples are from lines 216-223.

c). Dipturus case. Add some examples about misidentification of this genus such as Dipturus batis (see Griffiths et al., 2010; Iglésias et al., 2010).

d). D. nidarosiensis misidentification. Development the study cases of this species in the Mediterranean (Cannas et al., 2010; Cariani et al., 2017; Ramírez-Amaro et al., 2017). Along these lines, the current distribution is the North East Atlantic Ocean (from Iceland, Faroe and northern Norway to Madeira and Mauritania) and the western Mediterranean Sea (from Alboran to southern Adriatic and Ionian seas). From lines 37-44.

e). Biology and red list of study species (enter information from lines 44-52).

f).The biology and ecology of D. nidarosiensis are poorly known in the Mediterranean, hence the importance of this paper.

Discussion
I feel that the discussion is poorly developed.
The main result of the present study is the expansion of geographic distribution of this species.
Remove lines 154-155.
Transfer lines 155-158 to the introduction
Lines 160-161: whose suggest that this species acceded through Gibraltar strait from the Atlantic Ocean?
Lines 161-164: according to the fishermen, the occurrence of this species in none usual, so it is likely this species has been confused with other Dipturus species. Develop this point.

In my view, the few and recent records of this species in the Mediterranean is due to the displacement of the trawling fleet toward deeper areas during the last years (see Marongiu et al., 2017). Develop this point.

Lines 176-177: add some examples from other species about the hypothesis that juveniles live in shallower water than adults.
Lines 188: add could be associated…
Lines 183-185: given the low number of samples analyzed, this paragraph is speculative.
Lines 201-202: long tail longer in juveniles than the adults apparently is common in skates, please add an example.
Lines 213-214: this hypothesis is speculative. Please provide some example of marine species where this connectivity pattern has been observed. These examples may reinforce their hypothesis.
Transfer lines 215-223 to the introduction.
Transfer lines 224-226-223 to the beginning of the discussion.

Proposed references:
•	Hebert et al. (2003a) Proceedings of the Royal Society Series B Biological Sciences, 270, 313–321.
•	Hebert et al. (2003b) Philosophical Transactions of the Royal Society of London Series B –Biological Sciences, 270, S96–S99.
•	Coulson et al. (2011) Molecular Ecology Resources, 11, 968–978.
•	Last and Séret (2016) Zootaxa, 4147, 477–489.
•	Griffiths et al. (2010) Proceeding of the Royal Society Biological Science, 277, 1497–1503.
•	Iglésias et al. (2010) Aquatic Conservation: Marine and Freshwater Ecosystems, 20, 319–333.
Experimental design: This manuscript proposes to use COI mitochondrial fragments to report D. nidarosiensis of Central Mediterranean. I am confused by the number of specimens analyzed. While in M&M are 8 specimens, then in results, the authors indicate that four of these samples were analyzed in a previous study (Cariani et al., 2017). It is necessary to clarify this point in M&M.
Lines 72: are the specimens deposited in a museum collection?
Lines 75-80: remove all these morphometric measurements and meristic counts from the text and only reference the table. Per example: All measurements are indicated in Table 1.
Lines 82-84: please describe, briefly, each maturity phase.
Lines 96: please add the software where the sequences were edited.
Lines 104-109: the authors used an adequate number of sequences to compare.
Validity of the findings: The authors argue that the results corroborate the hypothesis of the existence of the Norwegian in the Mediterranean, but this hypothesis has already been confirmed in previous studies (Cannas et al., 2010; Cariani et al., 2017; Ramírez-Amaro et al., 2017). So, this study implicates that this species extended its distribution to the Central Mediterranean.

The study fully provides the taxonomic and genetic identification of D. nidarosiensis in the area. All tables and figures are necessary and useful for readers. However, in the case of maturity phases, the authors could add pictures of internal reproductive traits and describe these in results. Genetic analyses (network and phylogenetic approaches) are well developed. Genetic identity percentage, according to the number of bases differences, could be added.
Additional comments: This article used morphological and genetic analyses to recorded, for the first time, Norwegian skate (Dipturus nidarosiensis) in the Southern Adriatic and Western Northern Ionian seas (Central Mediterranean basin). The authors argue that the results corroborate the hypothesis of the existence of the Norwegian in the Mediterranean, but this hypothesis has already been confirmed in previous studies (Cannas et al., 2010; Cariani et al., 2017; Ramírez-Amaro et al., 2017). So, this study implicates that this species extended its distribution to the Central Mediterranean.

Further, the authors claim that provide knowledge on its life history traits. I disagree with this objective. In my view, providing information on life history traits (e.g. fecundity, gestation period, age at maturity) implies a complex study, with more samples and applying statistical methods. In overall, I feel that the introduction and discussion of the paper are poor and needs to be reorganized. I hope they are of use to improve the clarity of the paper and the quality of the results and their interpretation.


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: ON THE PRESENCE OF DIPTURUS NIDAROSIENSIS (STORM, 1881) IN THE CENTRAL MEDITERRANEAN AREA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript explores the presence of Dipturus nidarosiensis in the Central Mediterranean, reporting the first occurrences of the species in the Southern Adriatic Sea. A full morphometric description of the eight reported specimens and their genetic characterization and species identification are provided, making the manuscript self-contained.
The English language should be improved because phrase construction is sometimes very confusing (e.g., lines 53-57, 104-107, 158-163, 211-212), hence a full-text revision by a native-English speaker is strongly recommended.
Experimental design: The structure of the manuscript conforms to PeerJ standards.
The Introduction is appropriate, and literature is well referenced and relevant. The research objectives are clearly stated and were met.
Methods are well supported by figures, but the terminology used for the morphometric measurements is not accurate – please use Ebert and Stehmann (2013) for reference. Suggestion: Total length; Disk length; Pre-first dorsal-fin length; Pre-second dorsal-fin length; Preorbital or snout length; Preoral length; Interorbital length; Internostril length; Disk width; Tail length; (…).
Conclusions are well stated but could be summarised to avoid repeating the Discussion (e.g. Line 239, “Moreover, morphological differences between adults and juveniles were highlighted.”, deleting the rest of the sentence.)
Figures are relevant and have high quality, but their legends could be improved: include species and location so that the legends support the figures/table entirely without the need to consult the text – suggestion: “Figure 1. Schematic representation of the morphometric measurements recorded for Dipturus nidarosiensis specimens caught in the Central Mediterranean Sea.”
The following change in Table 1 editing is suggested: give Percentage of total length in brackets so that the values are not mistaken for a range.
Validity of the findings: This work is an original research and is within the scope of PeerJ.
The results bring important new insights on the distribution and biology of a poorly-recorded skate species in the Mediterranean Sea and the species identification is confirmed through genetic analyses.
Additional comments: I suggest the manuscript is accepted for publication but only after a careful English language revision. I opted not to make corrections in the sentence construction because I am not a native-English speaker either.

Please also take into consideration the following remarks:
1.	Lines 18-19 and 39: The southern limit of distribution of the species is different between the Introduction (northern Mauritania) and the Abstract (northern Morocco) – please correct and include reference(s) in the Introduction.
2.	Line 30: The correspondence between these life stages (which should further be ordered chronologically) and the maturity stages defined in lines 83-84 and in Table 1 is not clear.
3.	Line 39: Correct “endemic to”.
4.	Line 48: Correct “length at first maturity”.
5.	Line 49: Complete the sentence: “(…) vulnerable to environmental and anthropogenic pressure” (for example).
6.	Line 68: “landings and onboard sampling of commercial vessels (…) operating in the fishing ports (…)”
7.	Lines 71-73: Re-order Figures 1 and 2.
8.	Line 86: Clarify which tissues were used for DNA extraction.
9.	Line 93: Correct “cycling” to “cyclic”.
10.	Lines 103 and 112 and Figure 6: Write “Median-Joining” and “Neighbour-Joining” (hyphened).
11.	Line 134 and Figure 4: Ebert and Stehmann (2013) describe teeth as follows: “Teeth in upper jaw in 41 to 44 rows, set in pavement in young and females, but in parallel rows in mature males.”
12.	Lines 142-147: The haplotypes codes used in the text do not correspond to the codes used in Figure 6.
13.	Lines 192-203: Mention that the values being analysed are in percentage of total length because it is erroneous to state that “Ltail is longer in juveniles than in adults” if absolute values are being considered.
14.	Lines 192 and 237: Avoid using “comparable” because it might make the reader question why statistical analyses were not made. “Similar” is a suitable alternative.
15.	Lines 204, 240 and Table 1: Correct “thorns”.
16.	References: Invert order of references Marano et al. 2002 and Marongiu et al. 2017.
17.	Figures 4 and 5: Correct “Particular” to “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: ON THE PRESENCE OF DIPTURUS NIDAROSIENSIS (STORM, 1881) IN THE CENTRAL MEDITERRANEAN AREA
Review round: 1
Reviewer: 3

Output:
Basic reporting: Please see general comments for the author.
Experimental design: Please see general comments for the author.
Validity of the findings: Please see general comments for the author.
Additional comments: Overall this manuscript is a worthwhile scientific contribution, however is not ready for publishing in its current form. It would need further work and suggest another round of reviewing.
It is strongly recommended that the authors undertake a major revision of the use of (Scientific) English throughout the whole manuscript and, having text reviewed prior to re-submission by a native English speaker would be beneficial.
The following examples are mere illustrations as the whole manuscript would need to be worked on and therefore, recommended a second review where more details can then be provided.
A more clear introduction would be preferable, with global species knowledge, problem specific to region, why this study would be beneficial including more knowledge about biology and the implications of reoccurrence in the Mediterranean have to any future management measures.

For example:
Line 26-29 for example something on the lines of “Juvenile and adult specimens were caught between 320 to 720 m depth, with total length ranging from 268 to 1422 mm and, total weight from 44.5 to 12540 g.”
Missing a stop at the end of sentence line 29.
Line 30 –“ the occurrence of individuals of both sexes and, at different life stages suggest ….”
Maybe avoid acronyms on the abstract, you could say from onshore and offshore programmes (I would imagine you mean market sampling data and observer programmes looking into discards data) and fisheries-independent scientific surveys.
Restructure sentence 27-29, suggest something like “Fish were caught around the pit of Bari in the Southern Adriatic Sea and, in the North West of the Ionian Sea.
First sentence of abstract similar to beginning of the Introduction, but in Introduction comes northern Mauritania and in the abstract Morocco. I would not necessarily start abstract with that sentence.
Throughout the entire manuscript et al is not in italics, it should be et al. ,
Line 39 – suggest something on the lines
Line 41 – references at the end of the sentence since some are repeated as they refer have data from different areas. Bit of consistency in naming convention e.g. “This species is considered endemic in the North East Atlantic and the Bay of Biscay” instead of North East Atlantic Ocean and Gulf of Biscay.
For example in line 46-47 “ Certaintly, in both the Atlantic and the Mediterranean” seems less formal than would be expected.
No consistency in the use of Atlantic (includes North West Atlantic, whole Atlantic), try to keep it to either Northeast Atlantic, in terms of Atlantic Coast all belong to NEA.
Methods section would need a more clear structure with English improved. “landings and embark on commercial vessels” could be something on the lines of “Samples of Dipturus nidarosiensis  were collected through onshore (e.g. market sampling) and offshore observer programmes and, from fisheries-independent surveys.
Use colour instead of color.
Line 80 – not down jaw – “lower” jaw – not consistent with legend of photos
It would be beneficial to have maturity stages description, is this maturity widely used, how would you distinguish from stage 4a and stage 4b… not sure how it would be able to see regenerating on this species? Or even the resting… The stage seems more of a teleost species than off an elasmobranch. If we have the description we could also see what would be the difference between stage 3a and stage 3b. Recommendation to look into ICES Workshop 2012 were 4 stages were agreed for this type of species: A– Immature, B Maturing (though biologically still immature), C Mature, D Active.
The agreement within the ICES WGEF would be that these are still valid and should be the ones used.

Another example of the English would be in the Ethical compliance, would recommend to confirm if the journal guidelines for formatting laws would be acceptable. Also “in any case to minimize pains on animals, that arrived on the vessel” You could look into something as “However, specimens brought onboard alive during the scientific survey were subject of anaesthetic as to comply with fish welfare guidelines under the Decree Law etc….
Line 127 Ministry of Healt should be “Ministry of Health2

Results
Similar to other sections would benefit of restructure.
What would you classify in your study as juveniles, sub-adults and adults? Maybe a total length associated with it between females and males would be useful.

Discussion
Needs further work.
Line 157 – et al should not be used on a pers, comm. As we cannot associate to an author if no surnames.
Line 158-161 having a bit of difficulty in following what you mean to say. “This sequence scenario, also a lot of hypothesis in the text and sometimes too many assumptions made when in reality sample size is rather low. Strong comment “corroborate the hypothesis?”. Would recommend the usage of the word suggest e.g. the results may suggest the existence of an ancient occurrence… though this would not be suitable at the start, this would be like a main point of discussion.
Start from the discussion of the results of the study itself and compare with others, then generalise what this could mean.
Line 169 “where the  D. nidarosiensis was found, the bottow shows….” Again should be more formal first “where D. nidarosiensis were found, the seabed present similar characteristics, e.g. canyonys and slopes with high depths, suggesting such features would be favourable to this species”.
Line 181 – may be useful have the common name before as to familiarise those with less benthic knowledge.
Line 186-205 mixed results with discussion
Line 216-223 – Would this be suitable to the discussion?
Conclusion
Again stronger conclusion needed, a lot of hypothesis put on discussion. A bit confused with the discussion and conclusion as they seem rather mixed like sentence in line 239-241 that would be a discussion not a conclusion.
Last paragraph repetition of the end of the discussion.
Suggest revision of the titles for each figure, not summarised and Copyright should be put on the photo itself with the year.
Figure 1 – meaning of all the parameters should be added to the legend DL, L1P, etc
Figure 2 – for example “Spatial distribution of Norwegian skate Dipturus nidarosiensis caught during 2010-2016”. Number corresponds to specimens code reported in Table 1.
Figure 4 “Detail of the mouth of (A) female with molar-like teeth and, (B) male with pointed teeth,
Figure 5 “Detail of the snout (A) dorsal and (B) ventral side.
Figure 6 change color for colour, North-Eastern Atlantic Ocean for North-East Atlantic. Add verb “is shown in Table S1”
Table 1 maybe something on the lines of “Summary of data collection: biological parameters (sex, maturity, morphometric parameters, weight and meristic parameters) and source information (commercial or survey, date, depth)”
Commercial should be used instead of landing
Suggest maybe add sex and maturity at a higher level, too far down the line if above then easier to compare females and males and different stage at maturity.
Suggest reducing the number of references. Suggest reading Griffits et al 2011 “levels of connectivity between longnose skate in the Mediterranean sea and the North-Eastern Atlantic Ocean” Conservation Genetics. May be of use considering that these two species may have been confounded in terms of identification.
It should be noted that these above are mere examples as major work is required.


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: ON THE PRESENCE OF DIPTURUS NIDAROSIENSIS (STORM, 1881) IN THE CENTRAL MEDITERRANEAN AREA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The MS was successfully improved, especially the Introduction and discussion sections.

Some comments:

Lines 138-139: MEGA is not a sequence editing software. Please modify this.
Line 213: change “diffusion” by “dispersion”
Lines 214-215: add in final sentence: , but more samples and analyses are needed to confirm this
Line 273: R. radata must be R. radiata, but now this species is named as Amblyraja radiata

Table 1: change “Medits” by “MEDITS”
Experimental design: Experimental design is well supported, and the number of COI sequences here analyzed was clarified.
Validity of the findings: The results bring important new insights on the distribution of D. nidarosiensis in the Mediterranean.
Additional comments: I have now carefully read the revision of this manuscript. The authors took into account the reviewers comments and. I find the manuscript clearer.


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: ON THE PRESENCE OF DIPTURUS NIDAROSIENSIS (STORM, 1881) IN THE CENTRAL MEDITERRANEAN AREA
Review round: 2
Reviewer: 2

Output:
Basic reporting: Although the subject of this manuscript is interesting, the changes made are not yet enough to make this work published in its current form.
The autors took time to change and improve the manuscript but confusing at times. And although some comments are made, exhaustive details may not have been provided as fear that manuscript could use a reform.
The abstract itself is poorly written and does not capture the main facts needed in an abstract.
Throughout the manuscript terms are not consistently being used, for example landings, discard surveys. I am not sure authors should call offshore observer programmes of "discard surveys", and landings should be clear that we are talking about commercial landings. Also when it comes to research surveys, it should be clear they are scientific surveys, and at some point it is used fishery-independent surveys, need to use one term to define things not several for same things. And these inconsistencies start already in the abstract.
Line 24-25 - "during several biological samplings" not sure author should say several biological samplings, should be more formal, for example something on the lines of: "Biological sampling was conducted on specimens collected through commercial landings, offshore observer programme and scientific surveys." I would not add MEDITS trawl surveys on the abstract (no need for acronyms straight away). Also abstract misleading in terms of the samples, they were already studied in another manuscript so it should also be made clear there that this is the case.
The sentence about the lengths and weights and depths did not change from before even after being suggested by reviewer. And improvements should be made.
There is no need to say in the abstract were the fish were caught... this type of details can be found in the methods.
Strongly dislike the sentence "only partially explored or completely unexplored by fishery and/or researcher vessels" and this sentence occurs more than just in the abstract it should change and it is highly misleading. So is it partially explored by whom, is completely unexplored by whom? and also it should research vessels and not researcher vessels....
Line 37 "has been unnoticed" should be changed to "may have been"

Also inconsistency on the present and past tense use... sometimes verbs are put in the present and sometimes in the past. not very clear.

Introduction - Author should start with the main point of this manuscript... starting with species discrimination is just why? No need to start talking genetics as such.
Would suggest starting with species misidentification is a common issue among several different species, including the species we are interested in, then go to the possiblities of the genetics bring into helping uncovering these misidentifications.
Retract any personal comment on the introduction (here is time for facts not possibilities, these could be mentioned in a discussion section but never on an introduction), line 80-81.
line 86-87 - misleading, these issues are common to all elasmobranchs, so it does not make skates special in that way.
line 89-09 remove the on "the specimens".
line 96-97 elucidating / improving... stronger sentence needed elucidating is a bit over the top. removing also the collected data, I would say this study could futher inform on this species geographical distribution and life-history traits.
The examples here mentioned for the introduction are mere examples, as the introduction needs revamp.
Methods
Sampling starts again with the inconsistencies on what is an offshore programme, and there is no e.g. on here, we are talking about 8 specimens so either they were collected on a commercial vessel, or from the market, or from the survey.
And landings / sicentific surveys / market/ discards cannot all be called survey.
On the sampling it should be clear that some of these already have been studied before, is highly misleading on saying these are brand new methods when they are not.
Lines 112 to 115. are we using term of rays or skates, if needed then should be skates and rays, part of the introduction talks about skates no rays come here, misleading.
Gonadal maturity - it is used on the surveys but has been agreed by whom? for example is it an working group (e.g. under ICES, FAO, etc) protocol, or just related to this.. should be clear where it comes from.
Genetic analyses - line 123 - 124
should change to something on the lines of "Eight specimens were used for the genetic analysis, with four previoulsy analysed by xxx (code 1-4, table 1) and this study new material (code 5-8).
line 126-127 - Total genomic DNA was extracted from tissues samples using xxx, these samples (skin, white muscle) were collected from the ventral side of the pectoral fin (ca. 0.5 cm3 in size).
Results - poor section
statistics? which statistics, we are talking here about raw values, not treated numbers that suffered some statistical analysis so these should be rephrased...
Line 176-181 what do we mean with disc was wider than long? "typically for this species" this is already giving a "discussion" point, and it should not at all. We are merely describing facts in the results section.
"with a number of rows" how many misleading...
remove "included" before between 42-45
182-184 why again starting describing the adults, start from jhuveniles and go from there onwards...
187-188 - repetetion - this should come in the methods in terms of previously analysed not again on the results.
190 suggest "the combination of these data with those available .... Ocean, provided with a final alignment of ,,,,
Past and present mixed line 192 and 193 , was obtained, shows...
Sentence starting in line 192 should stop in South Africa. next sentence to start e.g. " It also showed six additional haplotypes, with four exclusive to xxx and two exclusive to xxx."
Discussion
Line 214 and 215 - how can we say "ancient" or "recent entry" not clear the distintion anywhere in the manuscript.
again 228 -229 needs to be changed, poorly constructed.
Sentences in the discussion starting with Indeed should be revisited, Please do not use "Indeed" that often and it the beggining of a sentence, it seems author is talking to reader instead of describing in written what they think it means.
line 241 - sub-adults should come before adults.
Sentence 243-246 - strong hypothesis .... too low number to suggest anything.... could still be mentioned but with a different approach like for example capture of juveniles only occured on the upper part of the slope, which may suggest juveniles may live in shallower water than sub-adutls and adults...
line 242 - how can you say is a stable local population?
Line 249-253 - these are results there is no evidence of any discussion point on these sentences... and to be honest what are the main difference? juveniles and adults are both in bathyal muds?? it may be that the area where you sampled the adults also a damaged area so you wouldn't have the sea pen in those areas... is highly misleading.
but again these are not discussion points they are results.
line 255 "appears to confirm" should be changed to something like "may support"
line 257-258 again repeat
I would suggest the author to start the discussion with points regarding the morphological parameters rather than genetics, as these are more simple and obvious to describe, with then genetics supporting the first impressions on the specimens.
line 268 - 269 - again a result not discussion point
line 275 - the thorns on the side of the tail in adults are commonly damaged (e.g. through age and damaged by other animals, but also on the capture event) so it is a bit unclear about the condition of the any of the specimens which means again unclear...
line 296-298 again repetition that we need more animals... 2 or 3 times on a discussion no need for this... you can circumnvent by using further data are needed.
line 311 - again start with juveniles
figure 1 - change positions to locations
figure 2 - rapresented change to represented
figure 3 - start with juvenile
figure 4 - remove "the" in "shown in the figure 4"
Table 1 - change title of the table to something like "summary of data collected from commercial landings and scientific surveys, NA: not available)
Table 1 "change survey" to "source", year on date to 2010 not '10, Landing and Medits, so which landings are from market sampling or from the observer programme (discards), if the distinction is given in the methods it should be clear from where these fish come from.
A footnote should be added to the fish which have previously been study in another manuscript.  or it should be added in the table caption/title.
Table 2
Gonads - rearrange table to female and male side by side as so you have one column from left to right: stage, maturation state, gonad, with female and male side by side. now in rows.
also inconsistentcy oocytes and eggs, formal term oocytes.
stage 2 how small is a nidamental gland supposed to be?  oviducts? uterus? plural and singular...
has this key been used by ICES, FAO or is just MEDITS surveys? has it been approved and scientific reviewed by experts
stage 2 male -"eventually????" not eventually,
yellow eggs? oocytes
any idea about size like < 5mm > 10 mm a bit more reference than just bit white, bit yellow...
sage 3b now we mention oocytes of different sizes???
stage 3 a male their internal structure are not is, we are talking about both claspers...
stage 4a reduced nidamental gland diameter
the whole key needs to be review in terms of english as it is poorly constructed with sentence instead of summary the facts. for example: stage 2 males - "clasper larger than stage 1 and skeleton flexible. Clasper extending past the posterior edge of the pelvic fins (i would imagine you are saying it is that, because if not they are still immature fish). Spermducts well developed, and starting to meander.

Think authors should see what is in terms of ICES WGEF matury key for skates and rays.
Matury keys have been agreed in 2012 workshop.
Experimental design: Ethical compliance - allows misinterpretation starting with all, misleads reader to all have been form fishery.
plus would say from "commercial fishing activity" so it needs rephrasing, like "All .... analysed in this study from commercial fishing activity (DCF xx), do not fit under....
However, specimens brough onboard alive during scientific survey (remove "the" were given an anaesthetic..... either say fishery-independent surveys or scientific surveys, choose one term.
On another note, there is no mention on the whole manuscript to which type of anaesthetic was given to the specimens and that this will not affect any of the results (and if there is, then it should be also mentioned), we should know which type of product was given to each specimen.
And what was the faith of the fish caught alive on the scientific surveys as with anaesthics we are talking about an decrease on their survivability... which I doubt it was as maturity was established which means fish were killed, therefore it was not an anaesthic but in reality killing the fish for the purpose of this study.
Validity of the findings: See above text.
Additional comments: See above 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: ONE-CLASS LAND-COVER CLASSIFICATION USING MAXENT: THE EFFECT OF MODELLING PARAMETERIZATION ON CLASSIFICATION ACCURACY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors present a systematic analysis about how modeling parameterization affect the classification accuracy of MaxEnt; if these parameter effects depend on the land-cover under analysis; and can we identify the best parameter setting for different land-cover classes and compare its performance with the default parameter setting. Overall, the study goals are well clear and logical. The article is well written, which is well structured and easy to follow. But the tables and figures still need to be improved.
Experimental design: The goal of this study is clear, and the experimental design is clear as well. But the results section need to be improved. Please see below for detailed comments.
Validity of the findings: Need to be improved. Detailed comments please see below.
Additional comments: General comments:
The authors present a systematic analysis about how modeling parameterization affect the classification accuracy of MaxEnt; if these parameter effects depend on the land-cover under analysis; and can we identify the best parameter setting for different land-cover classes and compare its performance with the default parameter setting. Overall, the study goals are well clear and logical, and the article is well written. However, the result and conclusion of the study are not very clear. Some major comments are showed as follows:
1.	As mentioned in Line 15-17, the classification accuracy is highly affected by the land-cover type being classified. However, the land-cover classes in this study seems to be too few. In addition, the class level of land-cover is too simple/coarse (e.g., the build-up includes many types of land-covers), which is not clear to thoroughly analysis the effects of modeling parameterization, especially in spatial heterogeneous areas. For example, the FC (feature classes) parameter is important on the final accuracy (Line214) and heavily dependent on the land-cover. Of which, L and Q features are both simple features, which are beneficial to spatially homogenous covers (e.g., built-up), but weaken for more heterogeneous covers (e.g., irrigated). However, for the weakness, we do not know the reason due to heterogeneous covers. To make the parameter effect on different land-cover classifications, it would be better to analysis the parameter effects with more land-cover types.
2.	Line 23, the SS (sampling size) has a positive effect on classification result. However, you did not give us the effect will exist to what extent. According to Fig.3, with the increase of SS, the K accuracy will increase. Therefore, we wondering whether you should to increase the sampling size from 100 to a larger value until the K value becomes stable. The comments are also suited for TP and RM parameters (Fig.2 and Fig.4).
3.	Except the setting of SS, TP, and RM parameters, it is not clear if there are some specific FC and BT parameters that can provide higher quality classifications based on the results (Line 301, Line 336-339). In other words, users will need to explore the optimal value of the most two important parameter by continuous trying. Therefore, how can results of this study give some guidance for setting the two parameters?
4.	Line 266-270, only around half comparisons (23/44) show that the best parameters outperformed the default parameters. It is really sounds illogical. The best parameter should possess best accuracy, at least equally well. Although you have given some discussions, which seems reasonable for the insignificant difference in the comparison result. However, for significant difference between the best parameter and default setting (e.g., MTP in fig.6a), it need more discussions.
Minor comments:
1.	Line 175, what is the class distribution of the randomly selected 1000 points?
2.	Line 50, “another issue” should be replaced by another word, such as however. Because from Line41 to Line 50, the content is about the strength of maximum likelihood algorithm.
3.	The Abstract did not show the clear result of the three goals of the study. Some specific parameter setting guidance should be given.
4.	Line 18, the sentence “but for heterogeneous land-cover …” is not result.
5.	Line 309, “heterogenous” should be “heterogeneous”, please check thoroughly.
6.	Please give full name of the abbreviations AUC, IF and NM (Line 365, Line 151, and Line185)
7.	Line 395-397. You suggest using manual parameterization could generate better land-classification accuracy outcomes. However, it is not consistent for irrigated grass (Line 275-277).
8.	Line 101, “depends” should be “depend”


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: ONE-CLASS LAND-COVER CLASSIFICATION USING MAXENT: THE EFFECT OF MODELLING PARAMETERIZATION ON CLASSIFICATION ACCURACY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is well written and well structured, but a few sentences should be revised language-wise. Most of the relevant literature is cited, and the context is provided for. The submission is ‘self-contained’.

It is not clear to me whether or not the raw data is being shared / already available somewhere.
Experimental design: The article is original primary research that falls within the aims and scope of the journal. It clearly fills a knowledge gap, which is well identified. The methods are sufficiently described to be replicable.
Validity of the findings: The findings are valid and meaningful, and the benefit to the literature is clear; data seems to be robust and the conclusions are well stated.
Additional comments: The article tests the effects of varying Maxent modelling parameters as well as parameters related to the modelling process. The large number of different models that were built do allow to draw conclusions on the effects of those parameters, specifically for the application of using Maxent for land cover classification.  As modelling algorithms are frequently applied without in-depth analysis of the effects of the modelling parameters used, the contribution is very valuable to anyone applying Maxent for land cover classification (or for species distribution modelling in general).

Here are some comments and suggestions for improvement:

Introduction
Line 70/71: “it has shown good performance” – Here it would be good to add some literature sources that have confirmed the good performance of Maxent, and maybe to add a sentence on why you chose to work with maxent because many other classifiers have also shown good performance and are widely used for land cover classification, e.g. SVM or regression trees.
Line 77/78: “the only published study on Maxent parametrization for land cover classification of which we are aware” – in a recent publication (Skowronek et al. 2018) we used Maxent to map an invasive species and tested the effect of varying feature class and regularization multiplier. The results were somewhat similar to your findings (see Skowronek S, Van De Kerchove R, Rombouts B et al (2018) Transferability of species distribution models for the detection of an invasive alien bryophyte using imaging spectroscopy data. Int J Appl Earth Obs Geoinf 68:61–72.  https://doi.org/10.1016/j.jag.2018.02.001).

Methods
Line 131: “as MaxEnd models can be sensitive to over-parametrization” – please provide a reference for this statement; a statement in Elith et al. 2011 suggests the opposite, mentioning that Maxent is rather robust and possibly able to deal with correlated input data. (“In particular, it is more stable in the face of correlated variables than stepwise regression, so there is less need to remove correlated variables” (see Elith, J., Phillips, S.J., Hastie, T., Dudík, M., Chee, Y.E., Yates, C.J., 2011. A statistical explanation of MaxEnt for ecologists. Divers. Distrib. 17, 43–57. http://dx.doi.org/ 10.1111/j.1472-4642.2010.00725.x.).
Line 158: You varied the sample size from 40 to 100 samples – I assume this is the number of presence points? What about the background points? How many background points did you use, how did you generate them, or did you use the respective presence points of the other classes as background? As the choice of the background plays an essential role this should definitely be explained.
Line 168: “All MaxEnt models were run using the random seed feature” – please provide a short explanation what the random seed feature is or a reference / where it is availabe.
Method section: Do you say somewhere what program/ software packages you used for the modelling? If not already included please add this information. Might also be helpful to include your full script as supplement.
Line 185: “IF and NM” – I assume those are the initials of the authors, maybe substitute the abbreviations by “the authors of this study” or the full names; the abbreviations are confusing.
Whole manuscript: You are using the abbreviations for fc, rm, ss, tp etc. throughout the text. However, these abbreviations are not really standard, or well known abbreviations, especially not to readers who have not used Maxent before. I suggest using the full expressions (feature class, regularization multiplier etc.) as much as possible, and only using abbreviations where really necessary, e.g. in graphics where you don’t have enough space, or in equations. Most people are not able to remember several previously unknown abbreviations along the whole article; it makes some parts of the text unnecessarily difficult to.

Results
Line 219/220: “was the largest differed” – please revise the sentence language wise
Line 223/224: “T, Q and TQ” – shouldn’t it be L, Q and LQ?
Line 261-266: sentence is difficult to read, please revise sentence structure.
Line 361-365: please revise language wise

Discussion:
Line 329-339: From your data, is there any conclusion you can draw on what type of threshold worked better for which land cover class? Or can you suggest what research would be necessary to approach this topic?
Also, there are a few more publications that have varied fc and rm in studies aimed at modelling species distribution, some of them could be included (see discussion in Skowronek et al. 2018).

Supplement
The supplements contain relevant tables showing an overview of the modelling results and parameters. However, the excel worksheet “Graphs” is only telling me that “this chart is not available in your version of excel”; I would suggest exporting the graphs as PDF instead of using Excel.


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: GENETIC DIVERSITY INCREASES WITH DEPTH IN RED GORGONIAN POPULATIONS OF THE MEDITERRANEAN SEA AND THE ATLANTIC OCEAN
Review round: 1
Reviewer: 1

Output:
Basic reporting: There is insufficient methodology in this submission to allow others to evaluate the study without consulting another study (Pilczynska et al. 2016) which is unacceptable. Include sufficient methods to be self-contained.
Experimental design: 1.	The hypotheses need to be better formulated (remove “might” at the very least). I would seriously think about the fact that the populations have maximum depth limits too so the populations at their deeper limit will suffer selective pressure too from some other factor –the Mediterranean populations were between 20-30m so I assume that collections were made near maximum depth limits for the species there. It is possible that maximum population stability is at some intermediate depth.
2.	I can’t assess the collection method used but I don’t think a linear regression is an appropriate test for the hypotheses (“We hypothesized that diversity was reduced in shallow populations due to higher environmental variability”).
3.	The authors state that depth ranges differed between Atlantic and Mediterranean populations but then lump them together for the analyses. They should have collected deep and shallow individuals at each site and compared them so as to avoid confounding space and depth.
Validity of the findings: 1. It is not clear to me what is the difference between the data in Figure 2 and Table 1 – aren’t they derived from the same dataset? Why are the scales different? What are the +/- in the Table? Are the data in Fig 2 means – if so why not include a measure of variation?

2. The ms focuses on temperature as the selective pressure as they can model it but other environmental factors may be selective and may also operate over a depth range too; pressure, density, salinity, other species, etc. So it is difficult to accept that temperature is THE factor in a correlation study in which temperature was not actually measured.

3. In order to be convincing that there is a clear pattern the reader would need to see more data, and from deeper and more points. At the moment the deepest sites (Lagos and Sacres 2, 60 m) actually have the lowest diversity and are amongst the least rich in alleles.
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: GENETIC DIVERSITY INCREASES WITH DEPTH IN RED GORGONIAN POPULATIONS OF THE MEDITERRANEAN SEA AND THE ATLANTIC OCEAN
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is clear and concise, novel for the species analysed and also for the findings. Literature lackes of several crucial references that would be essential to make a clearer interpretation of the data set. The comparison of the two areas is very interesting, but a more in-depth interpretation of the physical factors as drivers of the potential diferences in genetic diversity can be made. The future readers will find useful having a more accurate description of what may be the environmental constrains in the Atlantic and Mediterranean sea for the larval dispersion. Figures and tables are explicit and well done. See the pdf for further comments.
Experimental design: The experimental design is quite well conceived. However the real constraint is that both populations are a little bit difficult to compare, due to the fact that they are sampled at different depths in the twilight zone. This fact is not, however, a definitive problem for the manuscript. Genetic analysis are on line with previous works (and I congratulate the authors, Paramuricea clavata is difficult to analyse). See more comments on the pdf.
Validity of the findings: The original question has to be clarified. I find that the genetic diversity that the authors claim is increasing with depth in Paramuricea clavata has to be better explained. See more comments in the pdf.
Additional comments: I have one general comment for the authors that is really important: you do not take into account the reprodutive traits and the larval behaviour of the species. And this is, simply, essential. There are many works explaining reproductive cycle, effort, differences among populations, first larval stages, etc. It is supposed that your work is about connectivity, after all. And no relation between your findings and the potential larval dispersion (and the time of the year in which this happens) is written. I suggest to implement this information to enrico your conclusions (see 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: GENETIC DIVERSITY INCREASES WITH DEPTH IN RED GORGONIAN POPULATIONS OF THE MEDITERRANEAN SEA AND THE ATLANTIC OCEAN
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is written in a good english but present a lack in literature references and background about the previous works made on the same species and on the "refugia hypothesis".
The figures are not clear and need a revision.
Based on the hypothesis that Authors want to test, there is no a specific sampling design and based on their results, the discussion is to much speculative.
See my detailed comments on the general comments session.
Experimental design: see my comment on the general comments section.
Validity of the findings: see my comment on the general comments section.
Additional comments: Dear Editor,
The manuscript “Genetic diversity increases with depth in red gorgonian populations of the Mediterranean Sea and the Atlantic Ocean” by Pilczynska and colleagues investigate the change of genetic variability from shallow to deep populations of the red gorgonian Paramuricea clavata sampled both in the Mediterranean Sea and Atlantic Ocean. The main result of their study is that genetic variability varies with depth, but not that there is an increase in genetic variability with depth. One of the main concerns regarding this study is the choice of the sampled populations. Authors sampled populations at different depths in the Atlantic and at different depths in the Mediterranean Sea. If they want to test the effect of the depth on the genetic variability they should samples populations at the same depth in both basins or along a bathymetric gradient. Moreover, they should sample populations in the same area at two different depths to not be biased by a geographical sampling. They, in fact, use temperature time-series as a proxy for the depth effect but in my opinion, other parameters can play a role in the genetic variability pattern. Then, they cannot disentangle the effect of genetic connectivity in determining the patter of genetic variability because some populations could show less genetic variability because are more isolated than other. Finally, I think that some important references are missed in the manuscript because there are several studies that have studied the effect of the depth on Mediterranean gorgonian populations (e.g. Cánovas-Molina et al. (2018); Padron et al. 2018; Costantini et al. 2016; Arizmendi-Mejía et al. 2015; Costantini et al. 2011; Mokhtar‐Jamaï et al. 2011). All these information should be taken into account in the new version of the manuscript. Regarding the sampling design, I found it not really exhaustive. Based on the aim of the paper, in my opinion, Authors should have performed a sampling design specifically addressed to answer their question. Based on their sampling design other causes not related to the depth should explain the genetic variability pattern observed. Maybe a more exhaustive description of the sampled sites will implement the paper. Moreover, the Authors sampled a lot of colonies but at the end perform all results using only ten of them. Finally, they have to explain why they analyse only 5 of the 10 available species-specific microsatellite loci. Finally, Authors published in 2016 a similar work using some of the same populations analysed here and it is strange that they did not discuss ever the new results in function of the old ones. The discussion, in my opinion needs a complete revision. In fact, as said before, some important references are missed and a more detailed discussion of the high variability observed within basin and across depth should be taken into account. To me they cannot conclude that deep population of Paramuricea clavata represent refugia for shallow water populations (see for example the reduction of genetic variability at 60 m depth).

ABSTRACT:
Line 29: Delete “along the first tens of meters”. To me it is too precise, is not always like this. It depends on species and habitat and geographic zone.
Lines 32-34: is not completely clear. Rewrite this sentence.
Lines 39-40: “genetic diversity IN shallow and deep populations”

INTRODUCTION:
Line 63: add “of the population”
Line 66-68. Thermal stress is only one example of processes that can influence selection. Try to rephrase this sentence.
Line 68: “long time” instead than “long-term”
Line 80: It is not completely true that the deep refugia hypothesis is rarely tested. See for example (only to cite some of them):
Bongaerts, P., Riginos, C., Brunner, R., Englebert, N., Smith, S. R., & Hoegh-Guldberg, O. (2017). Deep reefs are not universal refuges: reseeding potential varies among coral species. Science Advances, 3(2), e1602373.
Bongaerts, P., Ridgway, T., Sampayo, E. M., & Hoegh-Guldberg, O. (2010). Assessing the ‘deep reef refugia’hypothesis: focus on Caribbean reefs. Coral reefs, 29(2), 309-327.
Van Oppen, M. J., Bongaerts, P. I. M., Underwood, J. N., Peplow, L. M., & Cooper, T. F. (2011). The role of deep reefs in shallow reef recovery: an assessment of vertical connectivity in a brooding coral from west and east Australia. Molecular ecology, 20(8), 1647-1660.
Moreover there are also studies made on Mediterranean and on gorgonians that evaluate the effect on the depth on genetic variability of the species that should be taken in account.
Line 94: Eliminate “and might…” It is too speculative without references.
Line 96: P. clavata populations
Line 97: I think that Authors have to explain why the compared Atlantic vs. Mediterranean populations. Do they expect different or similar results? Based on what assumptions? I think that they have to clarify better. Moreover, I think that we cannot disentangle genetic variability from genetic connectivity because maybe populations in the deep show high genetic variability because are more connected among them or vice versa.

METHODS:
Line 108: What Authors mean with “environmental gradient”? They mean “ temperature” or also other abiotic parameters? I think that they have to explicit better this part because is the more critical (see comment above). Moreover, is not completely true that in the Mediterranean the vertical distribution of Paramuricea clavata is within the first 30 meters. There are some populations below this depth (e.g. Spain, Gori et al. 2011; Ligurian coast, Padron et al. 2018; below 50 meters in the Calabria coasts (Bo et al. 2009)). In fact, the bathymetric distribution range of the species in the Mediterranean Sea goes from around 15 meters to more than 200 meters.
Line 109: How many colonies per site were sampled? Please specify.
Lines 112-113: what kind of “other sampling methods”? Please, explain. Based on the aim of the paper I think that more information regarding the sampling design should be given here.
Line 126-127: This analysis is not clear. What do Authors mean for “regional mean”?
Line 129: What kind of software the Authors have used to determine genetic variability parameters? And for the linear regression model?

RESULTS:
Line 150: Should be interesting to test the differences in terms of genetic variability between basins and between shallow and depth sites within basin. “Generally” does mean nothing from a scientific point of view; such as “nearly”.
Line 151: correct “max PA less than 4”. Max PA should be a specific value.
Line 151: Do Authors consider Espichel1 shallow o deep? Authors have to specify that here they talk about Espichel2 (based on what Author have written, 50-meter depth is considered “shallow water”). Moreover, also Espichel2 show a high value of genetic variability compared to the deeper populations (Sagre2 and Lagos). In the Material, Authors stated that deep populations are those found at 60-meter depth. I think that in the MM session Authors have to better explain what populations they consider shallow and depth and why.
Lines 152: What about the only other two deep populations (Sagres 2 and Lagos)? They do not show high values of genetic variability.
Lines 153-154: Yes, there is a significant correlation with depth in A and PA but still deeper populations showed low values compared to population found at 50-meter depth. Authors should describe better the correlation patterns.
Lines 157: 12°C
Lines 157: I think that this is the main result: “genetic diversity vary with depth”. Not that there is an increase of genetic variability with depth.

DISCUSSION

Lines 169: It is strange that Authors here did not use the existing references on gorgonians regarding the possible bottleneck. In fact, for example, a paper carried out by the same Authors (Pilczynska et al. 2016) does not show evidence of a recent bottleneck in the same shallow populations analysed here. Conversely, Padron et al. (2018) evidence bottleneck in some Ligurian populations at a deeper depth. I think that all this information should be discussed and taken into account in the discussion.
Line 171: Please, specify what is the “thermal threshold”.
Lines 174: Authors should explain that Boavida et al. is based on an ecological niche modelling. There are other references that should be taken in account here based on other papers carried out in particular on the northwestern Mediterranean Sea (e.g. Crisci et al. 2011).

Lines 178: The “refugia hypothesis” should be more detailed. More important references are missing here depending the contrasting results of this hypothesis and how it varies depending on the geographical areas and species.
Line 185: Why Authors did not test the presence of bottleneck? This is an analysis that should be added in the manuscript to confirm or not they results.
Lines 187-197: All this part should be rewritten. Authors should be discussing more in detail their results, explaining the differences that they observed among sites and among depth. They results do not allow to evidence a so clear common pattern of variability.
Line 203: It is the first time that the “connectivity” is taken in account in the manuscript. I think that this should be also introduced before.
Lines 216: Again, I don’t think that they can generalize here. They did not test other invertebrates. Maybe other species show a completely different pattern (see for example other gorgonians).
Lines 222: the paper is focus on temperature variability not “environmental” in general.
Lines 226: “higher and more variable”
Lines 227: as said before, the bottleneck hypothesis should be tested here.

Figure 3: This figure should be redesigned. Is not clear. Some Atlantic populations are missing (e.g. Espichel, Lagos). Moreover and indication of the depth where the temperature was measured is needed. Again, to me, shallow and deep in the context of the manuscript need to be better explicated.


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: GENETIC DIVERSITY INCREASES WITH DEPTH IN RED GORGONIAN POPULATIONS OF THE MEDITERRANEAN SEA AND THE ATLANTIC OCEAN
Review round: 2
Reviewer: 1

Output:
Basic reporting: Some English mistakes have crept in throughout the new version which needs to be revised (ex. L255-6 “AS a whole”; L253 “diversity IN shallow waters”; L257-8 “the tests aiming AT size reduction” (by the way, reduction of the size of what?); etc.)
The captions of figures 3 and 4 are swapped.
Experimental design: My main criticism of this new approach is that the chosen environmental variables kind of stack the deck against finding differences in other variables and in favor of temperature. I understand the rationale for using maximum temperature as a variable. I imagine that minimum current velocity is less variable among sites and with depth than mean or maximum current velocity; and I don’t really see what physiological basis is behind this choice; minimum productivity is the same case. The authors justify their choice by citing Boavida et al (2016) who actually identify slope as the most important factor in their modelling study, followed by temperature minima and maxima, then silicate maxima. Slope was not used here. The question is then: can slope be systematically related to depth? – if so it could be confunding. I understand that it is not possible to include all variables and the study of Boavida et al (2016) points to the direction to be taken, but their main factor is ignored. The authors seem to agree (L233-240), so why not include slope in the study?
Validity of the findings: See comment above.
Additional comments: The authors should be congratulated in taking on most of the criticisms of the first draft and this paper has been substantially modified from the first version, for the better.


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: GENETIC DIVERSITY INCREASES WITH DEPTH IN RED GORGONIAN POPULATIONS OF THE MEDITERRANEAN SEA AND THE ATLANTIC OCEAN
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors made substantial improvements on the manuscript. In fact, they correctly addressed, from my point of view, two of the most problematic questions posed by me:

"Both populations are a little bit difficult to compare, due to the fact that they are sampled at different depths in the twilight zone." is now clearer; the changed text is satisfactory

"No one word about the reproductive and dispersal patterns of the species." is now substantially changed
Experimental design: They made a good job readdressing the questions made not only by myself but also by the other two referees. The Experimental design is now clearer.
Validity of the findings: I had no doubt in the previous review that the findings were relevant and valid.
Additional comments: From my side, the paper has the improvement needed to be published. The "original question" has been clarified and the robustness of the paper is now improved, with a concise target.