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

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

Output:
Basic reporting: The authors have greatly improved their manuscript in many aspects and it reads much better than previous rounds and I would like to congratulate them for all the work they put. However, there is a couple of points regarding the niche modelling analysis that have been partially addressed.
Experimental design: The authors have improved  their niche modelling approach by downscaling some of the paleoclimate data where needed and by producing less complex models which facilitate the transferability of models in time. Also,they tested the degree of the models extrapolation over time which showed interesting results, that could be a bit more emphasised in their results and  discussion sections. Figure S3 is very nice. In this regard,they could test the degree of extrapolation of the used variables to see which aspects  of the climate differ the most over the different climate periods. Also, they could mention in the supporting information how they did the downscaling (e.g., calculated the climate anomalies and interpolated in the study area; see Patsiou et al., 2014 Global  Change Biology). However, there are a few flaws in how they select the cadidate variables:
a) The number of variables is still too high for the number of occurrences, despite they lowered the correlation coefficient threshold. A good rule of thumb for the number of variables is about 1 variable per 20 occurrences. Therefore, I would recommend that they include the test they mention on the variable values of their occurrence data, but also they carry out the same test for all variables in the whole study area. Then, based on the consensus of the two approaches select the least variables possible. Additionally,  they could consider the known ecological preferences of the species and further exclude variables if needed.
b) Lines 502-507 could go to the methods. However, why are the authors using a higher proportion of the occurrence data for validation of the models than for the model training? That should have been the other way round as has been mentioned in the  previous round of review. Please adjust your analysis accordingly.
Validity of the findings: The final results could be improved if the authors address the points mentioned in field 2 and further improve their niche modelling analysis. If they succeed to do so,  the article could eventually be published.
Additional comments: No additional comments


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

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

Output:
Basic reporting: The authors have made a good job addressing my previous concerns. Nevertheless, I still have some comments that should be addressed carefully. Please see General comments to the authors (in particular the last four comments: from lines 483 forward).
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Line 310 Three million datasets under each scenario for 5 scenarios is 15 million simulations. It this correct? Please clarify

Line 319 The meaning of “these uniform a priori can be considered non-informative” is not clear. Please clarify sentence. In additio, change a priori to priors.

Line 313-314 To avoid possible confusions please state 100 - 100 000 generations considering a 10-year generation time.

Line 314 Please change adding up to added.

Lines 315-316 Please change sentence to “For the final run, we used the following summary statistics… It is not necessary to repeat the parameters again, since their values were not modified to adjust the models.

Lines 317 and 318 Please change "segregation sites" to "segregating sites".

Line 319 Please change from "chloroplast-wide" to "choroplast".

Line 320 Please move up the information about generation time as suggested in comment for lines 313-314.

Fig S2. Please also provide the figure for the PCA (model check) for scenario 5.

Lines 483 - 488 Please remove these lines since, as I mentioned in my previous review this type of test is not valid to discriminate among scenario 2 and scenario 5. Regarding this, please acknowledge in the discussion that high type I and type II error rates make it difficult to discriminate among two scenarios and high CI for parameters suggest that scenarios for the divergence of Magnolia species might be complex and tested scenarios might not be depicting such complexity.

Lines 601 - 604 Please state that these results should be taken with caution, as the difficulty to differentiate among two scenarios and the oldest date of divergence included in the analysis was 1,000,000 years ago, you cannot rule out an oldest age of divergence and these results suggests that M. schiediana has a complex evolutionary history. Moreover, your Skyline plot analyses suggest that population expansion occurred around 250,000 and 200,000 years ago, which is older than the ~80,000 years for divergence estimated by DIYABC, providing further support to the argument of a complex evolutionary history and that the tested scenarions might not be covering the complete picture.

Lines 626-630 should be moved up (between lines 608-609), before starting the discussion about the results from the neutrality tests.

Lines 630-631. I suggest eliminating the phrase “Despite of these uncertainties, by integrating our whole results, we lean towards the dry-refugia model”. In my opinion, this sentence is inadequate as results do not provide enough power to lean towards the dry refugia hypothesis or leaning towards the moist-forest hypothesis, particularly because hypothesis testing through coalescence in DIYABC couldn’t resolve between the admixed and non-admixed models. The data presented in this manuscript show that there were changes in the distribution and demography of Magnolia schiedeana associated to Pleistocene climate change. Nevertheless, lineage divergence may pre-date the Pleistocene epoch and Pleistocene climate change might have only promoted expansion and contraction and probably some secondary contact, which may explain incomplete lineage sorting found in the genealogy estimated with Beast. Moreover, I consider that the authors conclusion at the end of the discussion that “However, as there is no conclusive evidence unambiguously supporting either of the two precipitation models, further investigations are needed by incorporating more samples (Oaxaca) and highly variable markers for testing these and other alternative hypotheses (vulcanism in the TMVB) driving lineage divergence” is adequate and cautious enough.


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: MINTIA: A METAGENOMIC INSERT INTEGRATED ASSEMBLY AND ANNOTATION TOOL
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Bardou et al. present in this manuscript a tool providing an end-to-end pipeline to assemble and analyze functional metagenomics data. The tool (MINTIA) relies on a number of established “standard” utilities, and provide a user-friendly and intuitive interface so that biology researchers can easily process their fosmid read data.
Overall, the concept of the tool is sound, and the interface well designed. My only concern is the reliance on “cross_match” from the Phrap/cross_match/swat package, which requires a specific license.  I would encourage the authors to look for open source / free-to-use alternatives to this program for future versions of their tool.
Other than that, I only have minor comments listed below:

l. 24: “easily generate and analyze large”: To my understanding, MINTIA does not provide a way to “generate” fosmid data, so this should probably be modified to e.g. “easily assemble and analyze … ” ?

l. 72: “read files are cleaned from adaptors and reads of poor quality are filtered”: Could the authors specify here whether this is done using existing tools or via an in-house script ? Same question for the read selection step (l. 73)

l. 90: “CDS and contigs are aligned using diamond”: Are the nucleotide contigs directly compared to nr and Uniprot/Swissprot ? If so, I believe this does not appear on Fig. 3, and I would encourage the authors to mention to the reader why the contigs are also used here, and not just the predicted cds.

l. 117: “generared” should be “generated”

l. 124: should “standard parameters” be “default parameters” ?

l. 135: “each of the 3 selected reference genomes”: Please specify the 3 genome/contig IDs here.

l. 166: “CDS, had” should be “CDS had”

l. 221: “we described” should be “we describe”

Figure 2: Should there be an indication (symbol ?) somewhere on this page to indicate whether a contig is circular or not ? Or maybe on the view shown in Fig. 4 ? (Apologies if it already there and I missed it).

Figure 3: The legend and figure mention “Functional classification” using MEGAN, however the main text indicates instead “MEGAN5 ( Huson DH (2007)) in order to obtain taxonomic affiliations” (l. 95), and to my knowledge MEGAN is indeed a tool for taxonomic, not functional, annotation. Please clarify

Figure 5: “Figure A” should be “Panel A”, and “Figure B” should be “Panel B”


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: MINTIA: A METAGENOMIC INSERT INTEGRATED ASSEMBLY AND ANNOTATION TOOL
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1. The study suffers greatly from the use of English. I cannot make a final assessment of the study unless English is proficient.

2. The reference of “Tauzin et al. 2020” is missing and format is wrong (Page 1, line 42-43).  And literature references is not sufficient. Please check all references and add references in introduction and discussion sections. For example, RAST server has no reference (Page 7, line 191).

3. Some results in this manuscript are just brief description. It has no figures or tables to support author’s opinions.

For example, “Moreover MINTIA …” (Page 5, line 152-156). In the paragraph “The lowest precision…” (Page 6, line 156-162)，please add figures or tables to exhibit these results.

In result sections, most of sentences describe data results, but lacking summarized sentences to exhibit the meaning of these results.
Experimental design: There are two main flaws in the current version of this manuscript .

The first one is lacking of comparisons with already available assembly pipelines, fabFos and shims2, in coverage, length and other results using the same data, In the same, lacking of comparison with orient tools, QIAGEN CLC genomics workbench, in annotated data and other results. Which step is the difference between MINTIA and these tools, and improve what? What is the difference in sensitivity and precision between MINTIA and these tools?

The second one is that, except friendly reports and files ready for submission, MINTIA have other advantages or not. If have, please add them in abstract and introduction sections. If not, it is not enough to exhibit the advantages of MINTIA.
Validity of the findings: In Figure 2 legend, the scatter plot “Scaffold coverage VS length” (not show) should add in supplementary figure.
Additional comments: 1. The first letter of each word in the current title “MINTIA: a Metagenomic INserT Integrated Assembly and annotation tool” should be unified. For example, “MINTIA: A Metagenomic INserT Integrated Assembly and Annotation Tool” or “MINTIA: a metagenomic insert integrated assembly and annotation tool”.

2.Don’t use oral words or words with emotion. For example, “thanks to” (Page 1, Line 31), “Everyday” (Page 1, Line 34), “Careful analysis” (Page 2, line 53-54), Please check them in all manuscript.

3. “Its throughput, cost and versatility have been continuously improved in the last decade, in particular thanks to droplet microfluidics (Tauzin et al. 2020).” Its refer what? Cost improving is good thing or bad thing? (Page 1, Line 41-43)

4. How to transform a microbial expression host, please describe clearly. (Page 2, Line 45)

5. “NGS technologies…”, add complete spellings on first occurrence. Please check all manuscript. (Page 2, Line 49)

6. “Genes, their genomic context …”, it is too long to understand this sentence. (Page 2, Line50)

7. Read files are cleaned after filtering adapter and reads of poor quality. (Page 2, Line 72)

8. “Align with blast versus an in-house database provided …”, software can’t add behind “align with”. Moreover, please add the version of the software you used. (Page 2, Line 94)

9. “When the vector …”, this sentence is ungrammatical, please revise it. (Page 4, line 115-116)

10. “Sensitivity corresponds …”, these sentences are too hard to understand. Please revise them. (Page 4 ,line 124-127)

11. “17 had a difference …”, what is the subject，“17”and “3”? (Page 5, line 141-142)

12. Please add specific results in comparing MINTIA and the existing tools and exhibit them using figures and tables. (Page 6-7, Line 180-198)


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: MINTIA: A METAGENOMIC INSERT INTEGRATED ASSEMBLY AND ANNOTATION TOOL
Review round: 1
Reviewer: 3

Output:
Basic reporting: For context, it might be helpful to cite the work of Lam et al. https://doi.org/10.1371/journal.pone.0098968 who addressed challenges in the sequencing of cosmid clones by using a pooled strategy.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Several places where the word "chains" could be replaced with the word "links"
Line 49: change "accessed" to "assessed"
Line 117: change "generared" to "generated"
Line 129: Unclear what the meaning of "expertized" is
Line 131: A brief description of the sequencing parameters would be helpful
Line 222: Change "Unix" to "*nix"


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: MINTIA: A METAGENOMIC INSERT INTEGRATED ASSEMBLY AND ANNOTATION TOOL
Review round: 2
Reviewer: 1

Output:
Basic reporting: N/A
Experimental design: N/A
Validity of the findings: N/A
Additional comments: I thank the authors for addressing the different comments, and have no further question or suggestion at this point.


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: MINTIA: A METAGENOMIC INSERT INTEGRATED ASSEMBLY AND ANNOTATION TOOL
Review round: 2
Reviewer: 2

Output:
Basic reporting: N/A
Experimental design: N/A
Validity of the findings: N/A
Additional comments: The authors have addressed my concerns to my satisfaction.


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: EVOLUTIONARY DRIVERS OF THE HUMP-SHAPED LATITUDINAL GRADIENT OF BENTHIC POLYCHAETE SPECIES RICHNESS ALONG THE SOUTHEASTERN PACIFIC COAST
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In this paper the authors aim to contrast different ecological hypothesis underlying a latitudinal pattern of marine benthic polychaetes diversity. The authors argue that they are testing five ecological hypothesis: species energy, species-area, Rapopport`s rule, habitat heterogeneity and geometric constraints. In addition the authors argue they are testing two evolutionary hypothesis “diversification rates” and biogeographic conservatism. I recognize the importance and relevance of this study and I believe it has potential, but I believe that at this point, the manuscript is not ready for publication. A series of improvements and modifications are necessary before the manuscript is ready for publication.

## Major points:.

Data and code availability: Before diving into the major points, I would like to point out that the authors decided to submit their paper to a journal that has a very clear polity about data sharing. In their statement, the main author affirm : "I am not submitting raw data or code - Raw data can be found on referenced literature and museum catalogs”. I understand that many of us still have an ancient urge of being the keepers of our own data, or "great collectors”, but that’s not how science advances. I would like to point out that what guarantees that this paper is reproducible is the availability of data and code. In addition, making the data available also guarantees that any researcher trying to investigate these questions in a broader taxonomical context could use the data and even fill many sampling bias for this region without the unnecessary visits to museum catalogs and dozens of papers. Please, make sure that any data and the code used for the analysis are available as supplementary material.

Analysis - Here the authors used OLS and contrast models with Akaike criteria. Although citing Burnham and Anderson’s book, I’m not sure the authors are indeed familiar with multi-model inference as there are two main problem here: a) this inferential framework do not fit the aim of this study and b) the authors use significance tests and model selection at the same time, which comes from two different inferential frameworks that should not be mixed. Model selection is designed for predictive purposes. The best model is the one that maximizes the expected predictive accuracy (i.e. the ability to fit future data). Because the authors are not searching for a model to perform predictions, this inferential framework is wrongly applied here. In addition, even if that was the case, the authors only present the AIC weights in their results, which alone does not mean anything. The authors also tested the significance of each OLS and inform significant models, but model selection and hypothesis testing are different frameworks of statistical analysis with completely different aims and should never be mixed, as pointed out by the book they are citing. To solve all of this problems, I suggest removing model selection from the study and maintaining only the frequentist portion of the analysis - OLS with significance tests. However, in order to do so, the authors should not only exclude model selection from their study but also improve how they are presenting the results. For each OLS it is necessary to present all the statistics for all variables that were used in each model, including the eigenvectors that were used to remove spatial autocorrelation from models residuals. In addition to presenting all the statistics, it is also important to present, as supplementary material, the Moran’s I correlogram in order to evaluate if the spatial autocorrelation on model’s residuals were indeed removed. Also, it is important to be aware about all the assumptions of linear models used here and perform any necessary transformation in predictor variables.

Hypothesis are not independent - The authors separated their hypothesis and even variables that are part of the same hypothesis in different linear models. But, why should energy hypothesis be analysed independent from spatial heterogeneity? In fact it sounds strange to have several independent linear models when only one model with several variables can be easily defined. In fact, when doing so the authors will have access to all statistics and significance test for all variables. Thus, I suggest analyzing as one OLS and discussing those variables that show significant effect. In this case, please make sure to use standardized coefficients in order to compare which variables strongly affects the LGD and which do not. In the current version, it is not possible to compare the different variables because they are tested in different OLS and contrasted with model selection, which informs the best model for prediction. There is one additional problem here regarding the different hypothesis. The authors are testing at the same time hypothesis that were formulated to explain the LDG, a biogeographical effect (Rapoport’s rule) and a null model (Mid domain effect) and contrasting them in order to find the best hypothesis. Rapopports’s effect is a pattern, not an explanation for LDG. Thus, it should not be compared with other hypothesis that propose explanations. In addition the goodness-of-fit of other explanatory hypothesis should be compared with the goodness-of-fit from the mid-domain model. The mid-domain effect is a null model for LDG, not a causal explanation.

Evolutionary hypothesis - I’m not sure how robust it is to infer diversification rates and ‘conservatism’ from taxonomic relationships. I am supposing that phylogenetic information for the studied group is not available. Is that indeed the case? If so, I suggest not using the term diversification, but only using what the authors are indeed calculating - taxonomic distinctness. When using the term biogeographic conservatism, I suggest using biogeographic taxonomic signal. As the authors are aware, what they do when they compute the Moran’s I is to test a signal of a trait in the taxonomy. It is not possible to safely infer 'conservatism' from these signals because there is no evolutionary model being contrasted with the observed data. In addition the authors should clarify if they are testing the Moran’s I only for the first class of distance of the taxonomy, or for the entire taxonomic distance matrix. Finally, the values of Moran’s I observed are very low, which might not be sufficient to even consider that a positive signal exists.

Finally, as I detail in some of my minor points, the authors should revise their introduction pointing out to recent updates in the LDG literature. It is very important to change how they classify the different hypothesis in the introduction and solve some minor problems in few specific paragraphs that are not consistent with recent literature.

#Minor points

Line 62 - 64 - “Latitudinal gradients of species richness (LGRs) and their explaining factors are key topics in macroecology and biogeography, providing a critical framework for ecology, evolution and conservation” - What exactly provides a critical framework for ecology, evolution and conservation ? LGD and their explaining factors ? I am not sure about that. I recommend being more precise here. Maybe saying that  that LGD is the oldest pattern in ecology and that understanding its underlying causes is still one the most challenging tasks in ecology and evolution.

Lines 70-85 - More recent classifications exists and should be used here to avoid any confusion (see Pontarp et al. 2019 - The latitudinal Diversity Gradient: Novel Understanding through Mechanistic Eco-evolutionary Models - Trends in Ecology and Evolution). Note that the energy hypothesis is not, in any sense, separated from evolutionary hypothesis, as energy itself might affect diversification rates. In addition, the authors should consider revising hypothesis for marine biodiversity (e.g. the book from Worm and Tittensor - A theory of Global Biodiversity).

Lines 95 - 97 - “Recent works indicate that these inverse trends along the SEP are robust to sampling artifacts and are not the product of statistical artifacts due to a reduced spatial scale (see Valdovinos et al. 2003, Rivadeneira et al. 2011)”. - The most recent study cited here is from nine years ago...Recent studies, at global scale, shows exactly the contrary from what has been affirmed here (see Menegotto & Rangel 2018 - Mapping knowledge gaps in marine diversity reveals a latitudinal gradient of missing species richness - Nature communications).

Lines 100 - 102 -  “...as well as the geometric
constraint-mid domain effect hypothesis (MDE hereafter) (if species ranges are random, they will tend to accumulate towards the middle of a bounded domain)...” - Species range are not random in MDE. Please clarify.

Lines 110 - 112 - “However, recently Hernández et al. (2005) and Moreno et al. (2006) evaluated the latitudinal change in species richness of benthic polychaetes along the coast of Chile” - Are these the most recent studies? Although the authors use recently, it has been at least fifteen years since that publication.

Lines 118-126 - Although the authors criticize studies conducted in other resolution, using one single finer resolution does not solve the problem criticized here as we know many ecological processes and patterns are scale dependent. Did the authors test whether the results they observe are consistent across different resolutions? If not, why not ? In addition, why would 0.5 be the best resolution for the studies group?

Lines 136 - 137 - “Filling a gap in knowledge, which will contribute to put in perspective the generality of well-known macroecological hypotheses”. As I pointed out before there is one biogeographical pattern mixtured with ecological hypothesis. In addition, I suggest changing the last phrase and discuss the novelty of this study. In theory, all macroecological studies does what the authors affirm here, thus, what is the novelty about their study?

Line 255 - “tbiogeographic” - Correct typo.

Line 327 - “ might could” - correct phrase.


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: EVOLUTIONARY DRIVERS OF THE HUMP-SHAPED LATITUDINAL GRADIENT OF BENTHIC POLYCHAETE SPECIES RICHNESS ALONG THE SOUTHEASTERN PACIFIC COAST
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this manuscript the authors revisited the latitudinal diversity gradient (LDG) of polychaetes in the southeastern Pacific coast, reanalyzing the diversity pattern described in previous studies and testing a set of underlying mechanisms that could explain it. The text is, overall, well written. I have only minor suggestions to clarify some sentences, which I highlighted in the minor comments below. Literature is well referenced, especially regarding previous studies in the study area. However, it seems that many relevant and recent discussions about the marine LDG are missing. The most recent citation about the marine LDG was published in 2015. Many papers have been published since then, using massive datasets, showing groups that follow the general LDG expectation, groups that have a peak at mid-latitudes, differences regarding the scale of analysis, the limitation of sample bias, evolutionary discussions, etc. Some critiques and suggestion below could be avoided by a revision of the most recent literature. Figures are relevant and clear. Raw data was not supplied (or at least I could not find it).
Experimental design: The research question is well defined, reinforcing previous ecological patterns and providing new hypotheses to explain the sometimes inverse LDG observed in the southeastern Pacific coast. I think that some methods need some clarification, which I highlighted in the minor comments below. The authors carefully considered the sampling bias limitation. One solution adopted here was to use the rarefaction techniques, that have been constantly used in marine studies to account for spatial variations in sampling effort. However, it is interesting to note that the number of benthic assemblages investigated (i.e. re-sampled) also increases toward high latitudes (Fig. 2). I am wondering how much is this efficient to investigate spatial variation in sampling bias. Would it be possible to apply the estimation using the same number of samples or individuals by latitudinal band? Still related to this topic, I am not sure if I agree with the solution of using the year in which the species was described as a measure of robustness to sampling artefact. I understand that this solution seems appropriated to estimate the inventory completeness of the whole study area, but I am not convinced about its efficiency regarding the latitudinal variation in sampling effort. Assuming a hypothetical scenario of historical undersampling at lower latitudes, couldn’t this method simply reflect the historical sampling bias through time (since most of the species would not be recorded or even scientifically described at these regions)? It would be interesting to hear the opinion of the authors about these concerns.
Validity of the findings: I think that some conclusions are contradictory, or at least not so robust. First, it does not make sense to conclude that the mid-domain effect is driven by evolutionary process (lines 317-319). The mid-domain effect provides a null hypothesis in macroecology, where species’ range is distributed at random. Therefore, the results provide both support for a null hypothesis and support for the historical/evolutionary hypothesis. In this case, can we assume an evolutionary process when the resulting pattern does not differ from the null expectation? I think that it is important to think about this question, especially when the evolutionary process identified here were not properly based on phylogenetic analyses, and the taxonomic distinctiveness results does not seem so robust (only one or two bands showed significant results and were highly close to the confidence interval; Fig. 6).
Regarding the biogeographic conservatism result (that species in the Northern limit present more taxonomic conservatism than those at the Southern limit), I am wondering if the simple migration process couldn’t also generate the same result instead of latitudinal differences in diversification or evolutionary restrictions (lines 337-340). Considering that the biota at the Southern part of the study area is closest to the Atlantic ocean, lineages with a completely different evolutionary history could have migrated to the Pacific coast and colonized the Southern limit (I am not sure, just wondering here). It would be interesting to hear from the authors of this scenario is possible and if it could affect the interpretation of these results.
Lastly, if I am not mistaken, spatial autocorrelation should affect the p-value of the regression, not the r-squared. However, all r-squared that you present after including spatial filters in the model are strangely high. Are these r-squared referent to the full model (predictor + spatial filters)?
Additional comments: Minor comments:

Lines 65-67: The statement is correct, but the references are not totally accurate. The sentence informs about “several meta-analyses” while only one actual meta-analysis is cited. I suggest either change the term “meta-analyses” here or to cite proper meta-analyses to be consistent. There are recent publications revisiting this topic in both terrestrial and marine realms.

Line 113: I suggest to include the latitude of the Chiloé Island to facilitate the comprehension of the described pattern.

Lines 136-137: Please, check this sentence and rewrite if necessary.

Lines 146-148: Mixing literature/museum records with field work to fill historical knowledge gaps is a very constructive practice. Well done!

Lines 162-164: I am not sure if I understood your rarefaction method. What are these 71 benthic assemblages? Are they specific locals identified in your dataset? How they are distributed? And why re-sampling only 15 individuals in your dataset? Do you have information in the individual level (maybe only in these 71 assemblages)? Please, clarify.

Lines 165-166: Note that the shape of the LDG may change drastically regarding local and regional scales (see this study of Edgar et al., 2011 [doi 10.1126/sciadv.1700419] and the meta-analyses of Hillebrand).

Line 192: Since you are dealing with benthic species, would not be more appropriated to use sea bottom temperature instead of sea surface temperature?

Lines 205-206: I am not sure of I understood. Did you run a mid-domain model previously to set the number of species in another mid-domain (what I think that does not make sense), or did you run a mid-domain model using the median number of expected species in the whole study area? Please, clarify.

Lines 215-217: I liked the methodological rigor you had here. Well done!

Line 220: Moran Eigenvector Maps (MEM) approach usually return the MEMs where the spatial autocorrelation was statistically identified. Why use the first 10 instead of using only those that may be, in fact, necessary?

Lines 224-226: Have you considered to conduct a multiple regression analysis, considering then the interaction of the predictor variables instead of using individual OLS regressions (i.e. reducing the origin of the LDG to only one single explanation)?

Line 237: “Values below delta+ indicate…”. Do you mean “low values of delta+ indicate”? Since delta+ is an index, it does not make sense to describe a value below the index, right? Please, verify and correct if necessary.

Line 255: Replace “tbiogeographic” by “biogeographic”.

Lines 377-378: I did not understand the importance of nutrient contribution here since your results suggest that primary productivity is not a predictor of species richness.

Line 381: “...there could be global effects that leave…”. What global effects? Please, be more specific here.

Lines 509-510: The link provided in this reference is not working.


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: EVOLUTIONARY DRIVERS OF THE HUMP-SHAPED LATITUDINAL GRADIENT OF BENTHIC POLYCHAETE SPECIES RICHNESS ALONG THE SOUTHEASTERN PACIFIC COAST
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript "Mid-domain effect, biogeographic conservatism and in situ diversification explain the hump-shaped latitudinal gradient of benthic polychaete species richness along the Southeastern Pacific coast," shows new and relevant results for annelids and are written in a rational hypothesis-drive context. The quality of the figures and tables are excellent.
I am positive about the manuscript, but it needs a careful upgrade in the background/context. The literature about the Latitudinal diversity gradient (LDG*) for marine species needs to be updated.
There is a good theoretical introduction about mid-domain effect, LDG, biogeography, ecological, historical and evolutionary hypothesis, but needs updated references about the LDG debate as (among several others):
- Chaudhary et al. (2016, 2017, Trends Ecol & Evol)
- Costello et al. (2017, Nat Commun 8, 1057)
- Kinlock et al. (2018, Global Ecol & Evol 27, 125-141)
- Menegotto & Rangel (2018, Nat Commun 9, 4713)
- Menegotto et al. (2019, Global Ecol & Evol 28(11), 1712-1717)

*Latitudinal diversity gradient (LDG) has been used more often in the literature than Latitudinal gradients of species richness (LGRs)
Experimental design: Two major concerns in the experimental design:
1- The first goal is (1) to re-evaluate the existence of a hump-shaped LGR (or LDG), as know as the constraint-mid domain effect hypothesis (MDE). There are enormous debates about this hypothesis, analytical methods, and explanations. However, I am skeptical about the power of the MS's analyses to address such a hypothesis with just one tail (Southeastern Pacific) of the hump-shaped curve and one taxonomic group (annelids). Also, recent studies have proposed that the latitudinal gradient
of species richness in the marine environment is bimodal (See Chaudhary, C., Saeedi, H. & Costello, M. J. Bimodality of latitudinal gradients in marine species richness. Trends Ecol. Evol. 31, 670–676, 2016; Woolley, S. N. C. et al. Deep-sea diversity patterns are shaped by energy availability. Nature 533, 393–396, 2016; among others cited above). It should be considered in the context of the first hypothesis.
2- Indeed, the taxonomic distinctness index seems an excellent approach as a surrogate of phylogenetic diversity, but the Linnaean classification tree is not an easy task for Annelids. First, since Polychaeta is a paraphyletic class of Annelida, avoid using this terminology (polychaetes) in an ms trying to elucidate the latitudinal gradient of this group. It is common this terminology in an informal conversation with colleagues, without any restriction, but scientifically is recommend to avoiding the use of polychaete/polychaetes/Polychaeta. Instead, use annelids or marine annelids. Also, I could not track precisely which Linnaean classification for annelids was used. A validation matching your species name data in the World Register of Marine Species (WORMs) is essential for using the same Linnaean classification, which is trackable and reproducible.
Validity of the findings: The conclusions are well stated and there impact and novelty, but a literature update  in the introduction and the first hypothesis is essential before to review the findings carefull
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: EVOLUTIONARY DRIVERS OF THE HUMP-SHAPED LATITUDINAL GRADIENT OF BENTHIC POLYCHAETE SPECIES RICHNESS ALONG THE SOUTHEASTERN PACIFIC COAST
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I am happy to have the chance to review this manuscript again. I was ‘reviewer #1’ from the first round of reviews and it is a pleasure to observe how this study improved in quality and clarity. Before the manuscript is ready for final publication I have two additional methodological comments regarding how the authors dealt with spatial autocorrelation and  collinearity in their modeling approach.

--Spatial autocorrelation
The authors present a Moran’s I correlogram which shows a Moran’s I of  ~0.20  in the first class of distance (Fig 2). When dealing with spatial or phylogenetic autocorrelation this amount of autocorrelation is a considerable autocorrelation structure in model’s residuals that should be removed if the author's desire to discuss the significance of their predictors effects, which seems to be the case here. Thus, because there is spatial autocorrelation in the first class of distance, the replicates are not independent and the degrees of freedom are lower than what is considered when computing the significance of the predictors. Thus, calculations of p-values might be biased. Usually, when Random Rorest (used in this study) is applied in ecology the buffer distances from all variables records are included as covariates in the model which ‘teaches’ the model the first law of geography: "Everything is related to everything else. But near things are more related than distant things." These covariates act as statistical ‘band Aids’ that deal with the spatial autocorrelation structure in the residuals. The authors might want to do something similar or just include PCNM axis, built with a distance matrix, as covariates of their model.

--Model collinearity
I understand that it is a cultural aspect of science to use “what other people did in their papers'' and that is one of the reasons why VIF thresholds >10  are still used as an indicator of multicollinearity. However, over the decades, there have been intense debates in statistics about this threshold which has been shown as a very problematic threshold allowing the inclusion of serious problems of collinearity in model building. Below the authors will find references that show that VIF > 5 are a cause of concern and >10 indicates serious collinearity problems. Some more conservative, which I am particularly more familiar with, use a threshold of 2.5. I suspect the authors are using a threshold of 10 because SST has a VIF of 8.5, which is red flag of the model in my opinion. Thus, my suggestion here is to remove SST from the model.

Menard S. Applied Logistic Regression Analysis. 2nd edition. SAGE Publications, Inc; 2001.

James G, Witten D, Hastie T, Tibshirani R. An Introduction to Statistical Learning: With Applications in R. 1st ed. 2013, Corr. 7th printing 2017 edition. Springer; 2013.

Johnston R, Jones K, Manley D. Confounding and collinearity in regression analysis: a cautionary tale and an alternative procedure, illustrated by studies of British voting behaviour. Qual Quant. 2018;52(4):1957-1976. doi:10.1007/s11135-017-0584-6

I would like to congratulate the authors for their intense work in this revision and I wish you all the best.


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: EVOLUTIONARY DRIVERS OF THE HUMP-SHAPED LATITUDINAL GRADIENT OF BENTHIC POLYCHAETE SPECIES RICHNESS ALONG THE SOUTHEASTERN PACIFIC COAST
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In this new version of the manuscript the authors really improved the data analysis and addressed satisfactorily all the questions raised in my previous review. However, verifying the dataset used to conduct the analyses (only provided in this round) and the interpretation of the new results, I see two major red flags that need to be solved by the authors before publication. These two red flags, which are both methodological and conceptual, reduce the consistency of the results and, more important, the conclusion about the main drivers of the LDG in the SEP. Below I explain in detail all my major and minor points to the authors.

MAJOR POINTS:
If I understand it right, here you use the same hypotheses used for explaining the canonical LDG. In the text you state the you relax some assumptions of the hypotheses (L139), but which assumptions of which hypotheses specifically? They seem all the same to me. Using the same hypotheses is not a problem (I actually think this is more appropriated), what I do not understand is why you do not assume previously that some hypotheses are better than others. For example, why should speciation- temperature relationship explain the higher species richness at 42°S when the SST increases toward the equator? If you are revisiting the same hypotheses used to explain the canonical LDG, you could list the main expected explanations for this situation in which the hypotheses were not proposed. Moreover, you should also discuss these hypotheses in the context of your results (see details in the last major comment).

You affirm that you have a dataset with 600 species (L189) and that the taxonomy was cross-validated using WoRMS (L198). However, checking the Dataset S1 I saw that many species still have unaccepted names (e.g. Ampharete elongata) or more than one entry point due to synonyms (e.g. Hemipodia simplex x Hemipodus simplex), misspelling names (e.g. Aglaophamus heteroserrata x Aglaophamus heterosecirrata) and subspecies (e.g. Abarenicola affinis x Abarenicola affinis chiliensis). According to the R script provided, you used this dataset without taxonomy correction to conduct the analyses. The problem here is that this absence of taxonomic correction may affect the number of species and, more important, the estimated range of the species. See, for example, the latitudinal range of Abarenicola affinis (-9.23 to -13.29) and Abarenicola affinis chiliensis (-32.58 to -33.45) or Aglaophamus polyphara (-25.42 only) and Aglaophamus polypharus (-14.23 to -15.34). I strongly recommend correcting the scientific names, merge the records when necessary and repeat the analyses to guarantee more reliable results. Check also the taxonomy of the species in the Dataset S2.

The first red flag. I understand the decision of excluding from the range size calculation those species occurring at the boundary of the SEP because your data search was focused on this biogeographic region and, in this case, the latitudinal range of these species would remain underestimated (please, feel free to correct me if my point is not correct). However, checking now the Dataset S1 I realize that you could have verified the latitudinal distribution of the species based on records from public global databases such as OBIS and GBIF. I think that this is important not only for those species at the boundary of the SEP but especially for the other species because their latitudinal range can be strongly underestimated. By quickly checking the Dataset S1 and searching for the distribution of the species in global databases we can find species that in your dataset are considered restricted to the SEP but that actually extends to the northern hemisphere (e.g. Alitta succinea, Acromegalomma pigmentum), to the Antarctica (e.g. Aglaophamus trissophyllus, Amage sculpta), or just have a distribution in the SEP wider than you found (e.g. Aricidea pigmentata, Boccardia tricuspa). Despite the impressive effort to assemble species records from the entire SEP, ignoring the occurrence of these species out the SEP region may be affecting your richness estimate and, most probably, the estimated range size of the species. The exclusion or underestimation of range size for species in the southern latitudes decreases the median range size at this region, which may bias some results. In addition the underestimated range will also affect the analyses of niche conservatism.

Please, check carefully the Fig. 3, Fig. 4 and Fig. 5 because some distributions are inverted. For example, in Fig. 3 the plot “b” seems ok (SST) but species richness is peaking in lower latitudes (plot “a”) and median range size is peaking in the higher latitudes (plot “c”), contrary to the description. I added other questions about the Fig. 4 in the minor comments below. Check also if this latitudinal inversion occurs only in the figure or if it is affecting the analyses.

The second red flag. The results do not seem robust to support the conclusion. You claim that evolutionary processes drive the hump-shaped LDG in the SEP based on the importance of three environmental variables, median range size, and results from phylogenetic diversity. First, the important environmental variables to the model were SST, Salinity and SST range. Here, only SST is a proxy of diversification dynamics. However, the relationship between SST and species richness is quadratic (Fig. 4A, peaking at 14° C), contrary to the theoretical assumption regarding the effects of temperature on increasing speciation rates. Note that you use the same hypotheses used to explain the canonical LDG (Table 2), but do not create previous expectations based on the already known hump-shaped diversity distribution in the SEP. For example, why should temperature explain a higher diversity in the mid-latitudes according to the temperature-dependence speciation hypothesis? This is not clear in the introduction and it is completely ignored in the discussion. Salinity (average) does not even appear in the Table 2 or in the introduction (L142-159), it is only used to evaluate niche conservatism. So we (the readers) were not informed about what would be the expected effects of salinity on increasing species richness and how it supports the conclusion. SST range is an hypothesis related to the “ecological limits” category, not “diversification dynamics”. Second, the results of the median range size may change since many species have their latitudinal limits underestimated (as explained above). The increasing range size in the southern region of the SEP (well possible since many species seem to be distributed on Antarctic waters) can reduce the median range size variation and maybe the importance of this predictor. Finally, the phylogenetic diversity indices have contrasting interpretations across the text. In the results section it is shown that PD and MPD have values lower than expected from the null model most in the north (lower latitudes, though the Fig. 5 seems inverted), indicating reduced phylogenetic distance among the species (L314-315). In the discussion section, the low values of MPD are used to reinforce the idea of high speciation rates in the mid latitudes (L352-354), contrasting the results. Although there are some low values around 40°S, why is not the result of the MPD indicating higher speciation rates in the lower latitudes (according to the assumptions present in the text)? Why the low values of MPD in mid-latitudes would indicate speciation while the low values in lower latitudes would indicate species sorting (L379-380)? This change of interpretation is really confusing. Moreover, automatically assuming that low values of PD and MPD directly indicate higher speciation rates is seriously misleading since they may also indicate lower speciation rates in different contexts (see Eme et al. 2020. Ecography, 43, 689-702). Altogether, I cannot see robust evidences of high speciation rates in the Chiloé region explaining the hump-shaped LDG along the SEP as the study proposes.

MINOR POINTS:

L42: I think that the acronym should be consistent with the original expression. I agree with the other reviewers that “latitudinal diversity gradient” is more common and, therefore, LDG may be used, but I do not understand why using LDG after latitudinal gradients of species richness. Why do not use “latitudinal diversity gradient” and be consistent with the LDG acronym? Same for line 73.

L83: Plural sentence?

L106-108: I think this sentence needs some clarification. The inverse trend is not a product of statistical artifacts because the spatial scale is reduced? Which scale are you talking about here? Please, clarify.

L111: I suggest remove “However” here because, if I got this right, this sentence is not contrasting your previous statements. In the previous paragraph you affirm that many taxa have non-canonical LDG and now you are detailing the known pattern for polychaetes, which is also non-canonical.

L118-120: I did not understand if these studies tested some of the hypotheses and their main limitation is only the reduced spatial resolution. If they tested some mechanistic hypotheses so these studies are not descriptive as you stated before (L109-110).

L127-129: One-sentence paragraph?

L133: Do you mean “One approach”?

L150-151: I suggest being clearer here. Many readers may not be aware about how range size may be related to species accumulation. You could be more explicit about the mechanism linking the proxy and the expected result.

L159: Which tuning? Did you do that? This sentence seems out of context to me. Please, clarify.

L217: Do you mean “range-through approach”?

L238-239: Please, check the grammar of this sentence.

L256-257: You consider here that the investigated relationships may be monotonic or non-linear, but a monotonic relationships already include both linear and non-linear distributions, right? I suggest clarify these expected relationships (e.g. quadratic, etc) to avoid misinterpretation.

L286/288: Here you use “traits” referring to the investigated environmental predictors. Is that really appropriated?

L299: Please, check if this values are correct. I found some values slightly different running the script (e.g. n = 28).

L306: Here you call the Fig. 2b and 2c to show results regarding the effect of the predictors in the species richness, but I did not understand what we should be seeing here since these figures only show the residual and the Moran’s correlogram. Please, clarify.

L308: Peak at ca. 12-14° C. In the Fig. 4a the peak seems to occur after the 15° C. Is this x axis also inverted?

L309-310: Are you sure that the Fig. 4b (SST range) shows a hump-shaped relationship?

L310-311: Are you sure that the Fig. 4c (Salinity) shows a negative relationship?

L313-315: This description apparently includes both Fig. 5a and 5b, but the representation of which values were different from the null model or not is only available to Fig. 5b. Why the p-values of the Fig. 5a are not available?

L316-317: Please, check the grammar of this sentence.

L319: Do you mean -0.81 (negative relationship)?

L322: What about the phylogenetic signal in those variables that do not reach the statistical significance? What that means?

L365: Check the grammar in “area are where”.

L383: The influence of El Niño and the bidirectional currents (371) on species distribution along the SEP are very interesting ideas.

L711: It is difficult to read a dataset with comma-separated values when one variable also have comma inside (author, year). I recommend using another separator.


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: EVOLUTIONARY DRIVERS OF THE HUMP-SHAPED LATITUDINAL GRADIENT OF BENTHIC POLYCHAETE SPECIES RICHNESS ALONG THE SOUTHEASTERN PACIFIC COAST
Review round: 2
Reviewer: 3

Output:
Basic reporting: The ms has a significant improvement. The authors addressed all the comments made by our revision and can be acceptable in this current format.
Experimental design: The research questions are more suitable in its current state and fit the reproducibility criterium
Validity of the findings: There are several intersting novelts, rational, and with the literature clear stated. It is a bit sad the authors kept their argumentation to use the term "polychaete." They are entirely right in their argumentation/answer. Polychaeta is still a valid taxon in WORMs, but it is a clear example when Linnean nomenclature rules are ambiguous with the phylogenetic hypothesis. This priority nomenclature rule makes these tasks even more complicated. Anyway, we will ensure survival; among the steps that science needs to advance in our society, this one is a minor concern.
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: EVOLUTIONARY DRIVERS OF THE HUMP-SHAPED LATITUDINAL GRADIENT OF BENTHIC POLYCHAETE SPECIES RICHNESS ALONG THE SOUTHEASTERN PACIFIC COAST
Review round: 3
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This is the third time I am reviewing this paper. It is a pleasure to see how the paper evolved in quality since the first round of revisions. I have no more major comments for this manuscript and I think the authors did a good job on responding and incorporating the reviewer’s comments. Thus, I think this paper is ready for it’s final publication. I would like to congratulate the authors for their work and I wish you all the best!

#Minor comment

I understood the authors points about the high VIF values but I think it is important to explain in the results or in the results table why high values of VIF are not a problem given the methods used. It is something that calls the attention of anyone who will read this paper and it might sound like a major error in methodology if the reader skips directly to the tables.


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: EVOLUTIONARY DRIVERS OF THE HUMP-SHAPED LATITUDINAL GRADIENT OF BENTHIC POLYCHAETE SPECIES RICHNESS ALONG THE SOUTHEASTERN PACIFIC COAST
Review round: 3
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I am glad to see how this manuscript have been improved. The authors made a major work reinforcing the data quality, data analysis and text clarity. The study seems much more robust now and I believe it brings a solid contribution to the marine ecology literature. I am satisfied with basically all modifications and responses provided by the authors.

There is only one last commentary that I believe was not totally solved at this round. The authors informed that all scientific names have been checked on WoRMS. However, there is still a few subspecies in the dataset. This means data some species are counted twice in a latitudinal bin (e.g. Maldane sarsi), or their latitudinal extent is splitted in different bins (e.g. Capitella capitata). Since the study was conducted at the species level, these subspecies should be renamed and the latitudinal extent of the species should be revised. I sincerely believe that this correction won’t change the results, neither will need major changes in the text, but I strongly suggest dedicate one more day of revision to correct the dataset and re-run the analyses, just for conscience’ sake.

To accelerate the process, I took the liberty of checking the names using an algorithm to inform the authors all species/subspecies that need some review. Here are the subspecies, and their accepted species name: Capitella capitata capitata [Capitella capitata], Dodecaceria laddi oculata [Dodecaceria laddi], Euphrosine cirrata magellanica [Euphrosine magellanica], Lepidonotus crosslandi peruana [Lepidonotus crosslandi], Maldane sarsi antarctica [Maldane sarsi], Melinna cristata australis [Melinna cristata], Neoamphitrite affinis antarctica [Neoamphitrite affinis], Nereis pelagica lunulata [Nereis pelagica], Notoproctus oculatus antarcticus [Notoproctus oculatus], Exogone obtusa tasmanica [Parexogone minuscula], Sphaerosyllis capensis chilensis [Sphaerosyllis capensis], Terebella lapidaria juanensis [Terebella lapidaria]. This species name is incorrect: Exogone lourei [Exogone (Exogone) lourei]. This species name is invalid and should probably be removed from the dataset: Mediomastus branchiferus [taxon inquirendum]. Check also the dataset 2, some of the names are also present there.

Minor comments:

L44: 651 species. This number must be revised because there are subspecies in the dataset. Same to L203, L744.

L261: “used on previous in studies”. Revise sentence.

L269: “showed a variance inflation factor”. Do you mean a “high variance inflation factor”? The previous sentence does not make sense without a context (e.g. high, above, between, etc.).

L278: I am not sure that median latitudinal range may be considered an environmental predictor. I think that using SST here, as in the previous version, would be more appropriate.

L304: “The script to run all analyses and to create each figure is provided in the file Dataset S4”. I would change it to “is provided in the supplementary material”, since the script is not a dataset.

L309: “than in the southern Ecuador (3°S) were richness”. Please, correct typo in “where”.

L319: According to the text, and Table 2, four (not five) predictors were significant. Also, there is a comma missing after “medial latitudinal range”.

L320: Unnecessary commas after “see”.

L321: Fig. 3b-c. There is no plot 3d.

L334: Remove extra dot.

L368: “Southern” Chile?

L375: Remove extra comma after “probably”.


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: LONG DISTANCE (>20 KM) DOWNSTREAM DETECTION OF ENDANGERED STREAM FROGS SUGGESTS AN IMPORTANT ROLE FOR EDNA IN SURVEYING FOR REMNANT AMPHIBIAN POPULATIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is an important paper, eDNA is clearly revolutionising how we detected and discover diversity that is otherwise hard to detect. Nowhere is this more important than with critically endangered species amphibians, which, because of their natural history are very hard to detect in the wild with traditional survey protocols (e.g. line transects, spotlighting).
The language, literature reviewed and used to support arguments,ents, the structure and findings based on previously stated hypothesis have no flaws.
Experimental design: Given the set up, of one large population and a much smaller population this presents an ideal natural setting for testing the sensitivity of the used eDNA protocol. In future it would be great to work on trying to correlate the signal detected in the PCR with the abundance of frogs with more than two populations, probably Litoria nannotis would be the ideal candidate, and see if you could link abundance with qPCR scores and then take this a step further, use eDNA to monitor population rather than detect it.

I really have no comments beyond this in terms of experimental design. The protocol has been spelled out with enough detail  could replicate it in the lab, thanks for writing simply and plainly.
Validity of the findings: This is a solid contribution, the data are very telling, eDNA in this context does exactly what it is supposed to.
Additional comments: An important contribution, especially in the context of so many stream dwelling populations of frogs that have been lost and are starting to recover. Urgent to run this in amphibian hotspots like Monteverde (Golden Toad) or Eungella National Park (Rheobatrachus) are still holding some of these extinct species alive.


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: LONG DISTANCE (>20 KM) DOWNSTREAM DETECTION OF ENDANGERED STREAM FROGS SUGGESTS AN IMPORTANT ROLE FOR EDNA IN SURVEYING FOR REMNANT AMPHIBIAN POPULATIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: I have included all comments in my attachment.

The manuscript is well written and researched.
Experimental design: I have included all comments in my attachment.

The study is well thought out and experimental design is adequate. The research question is defined, relevant and meaningful.
Validity of the findings: I have included all comments in my attachment.

This study will have high impact and is a novel use of eDNA on a well studied amphibian population.
Additional comments: Villacorta-Rath et al. have produced an excellent manuscript which describes the application of eDNA to identify a well-studied amphibian population. The in-depth knowledge including downstream limits and population abundances of L. lorica and L. nannotis have provided a unique system to test multiple eDNA collection methods for downstream detection of amphibians.

The introduction provided key information and was written to a high standard. The importance and novelty of the work was made very clear by the authors. The research is relevant to a variety of scientists across a number of fields including; eDNA, population genetics and herpetology. The research question and reason for undertaking the study was made clear. The methods included a number of site and technical replicates, there was also thoughtful consideration made to DNA inhibitors. It is an excellent use of eDNA methodologies and has been a delight to review.

I have included all comments requiring attention in my attachment.


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: SELF-REPORTED BODY WEIGHT AND WEIGHT-RELATED STIGMATIZATION EXPERIENCES AMONG YOUNG ADULT WOMEN—TWO CONTEXTS, BUT SIMILAR ATTITUDES RELATED TO BODY IMAGE, MENTAL SELF-SCHEMAS, SELF-ESTEEM, AND STEREOTYPES OF PEOPLE WITH OBESITY
Review round: 1
Reviewer: 1

Output:
Basic reporting: a.	In opening paragraph of intro (Lines 52-63), you should provide a basic definition of what you mean by weight stigmatizing experiences. People in higher body weights can experience in a variety of settings (medical, relationships, weight related teasing, etc)
b.	Some inconsistencies in terminology (noticed especially in paragraph lines 84-97). You use “higher body weight” and “obese or overweight.” There is not consensus on which term to use. The medical community leans towards “obese,” and yet many higher body weight people find that language stigmatizing. Research what term you would like to use and stay constant.
c.	Overall, authors have provided a well-researched background for the topic. However, the overall structure and order of the paragraphs was slightly difficult to follow at times.
d.     Raw data shared
Experimental design: a.	Curious as to why you used BMI above 25 as your cutoff. You may see different results if you raised your cutoff to 30 or higher. I think this cutoff needs to be supported further. You comment on this a bit in discussion, but I am not convinced this was the correct cutoff
Validity of the findings: a.	Line 566 – You make a conclusion that getting rid of weight stigma is not tantamount to positive outcomes. I am not sure you can draw this conclusion from this type of study design.
b.	You may find it beneficial to your argument to reference the weight misperception literature. That is, the literature that shows women who are higher weight but perceive their weight has normal have better health outcomes. (Sonneville, KR)
Additional comments: a.	Overall, adequate review of literature, interesting study questions, clear methods. I would like to see some restructuring of background for clarity, and other comments – but interesting addition to the weight stigma literature


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: SELF-REPORTED BODY WEIGHT AND WEIGHT-RELATED STIGMATIZATION EXPERIENCES AMONG YOUNG ADULT WOMEN—TWO CONTEXTS, BUT SIMILAR ATTITUDES RELATED TO BODY IMAGE, MENTAL SELF-SCHEMAS, SELF-ESTEEM, AND STEREOTYPES OF PEOPLE WITH OBESITY
Review round: 1
Reviewer: 2

Output:
Basic reporting: (a) Abstract:
* The comma is missing between "mental self-schemas" and "self-esteem":
“The paper compares body image, mental self-schemas self-esteem and the obese person stereotype among groups (…)”.
* I do not understand this sentence “Importantly, the studied women indicated that the ought body image from the point of view of other women should be slimmer compared to the male point of view.”
* As for the conclusion, do not these parallels apply to women with excessive body weight and stigmatized women?

(b) Introduction:
* What do "higher body weight" and “higher-than-normative body weight” mean? It should be clearly defined what these terms mean for the authors.
* The Introduction section and the presentation of the aims and hypotheses takes up 6 pages. In my opinion, this part is way too long. Authors should try to present this information in a more synthetic way - without duplicating the same information, focusing on the results of research related to their research and selecting the latest research results.
Experimental design: (a) The purpose described in the Abstract and the Method section is not consistent. Moreover, “Aims of study and research hypotheses” should be presented at the end of the Introduction, not in the Method section.

(b) Unfortunately, it is not entirely clear to me into how many groups were the women ultimately divided? Were women divided taking into account both their body weight (normal body weight or excessive body weight) and whether they felt stigmatized (yes or no) (i.e. ANOVA 2 x 2)?

(c) The manuscript should provide specific BMI ranges from which the division into "normal" and "higher" has been made with reference to the source (WHO?). Moreover, I would suggest changing the concept of "higher" to "excessive".

(d) Have other researchers used such a procedure before? I am not entirely sure whether the answer to the question "Do you think you are currently fat" clearly indicates that someone feels stigmatized.
“The following questions were asked: “Do you currently happen to hear anyone say you are fat?”; “Do you think you are currently fat?”; and “Are you currently ashamed of how much you weigh?” If an affirmative answer was given to any of these questions, the studied women were assigned to the group characterised by weight- related stigmatization experiences."

(e) It is not clear to me how this study fills the knowledge gap
Validity of the findings: (a) Abstract:
“Higher-weight women and women with weight related stigmatization experiences were characterized by greater divergences between the actual body image and the ideal, reflected and ought body image, lower self-esteem and more negative beliefs about their mental actual and reflected self”…. compared to?

(b) Method:
* There is no "Data analysis" section in which the authors will present what statistical analyses they used.
* If I understand correctly, the authors assumed that both body weight and the experience of stigmatization are important factors for the variables they analyse. So, why was two-way ANOVA not used and all 4 groups not compared (this remark obviously applies to quantitative variables)?
Additional comments: Thank you for the opportunity to read your work. This is an interesting topic that can be considered by readers. Nevertheless, there are some concerns with the present write-up that would need to be addressed for the paper to be able to achieve its potential.
Though the paper is properly organized, it is not and easy to follow. Some issues are not clearly defined (e.g. group division), which makes it difficult to understand the various parts of the manuscript.


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

Input:
Title: SELF-REPORTED BODY WEIGHT AND WEIGHT-RELATED STIGMATIZATION EXPERIENCES AMONG YOUNG ADULT WOMEN—TWO CONTEXTS, BUT SIMILAR ATTITUDES RELATED TO BODY IMAGE, MENTAL SELF-SCHEMAS, SELF-ESTEEM, AND STEREOTYPES OF PEOPLE WITH OBESITY
Review round: 2
Reviewer: 1

Output:
Basic reporting: 1. The introduction is still too extensive.
Experimental design: 2. Of course, I understand that it may be the first time that we use a given measurement method in a given study. However, I still doubt whether this is a question can measure the variable that the authors wanted to evaluate.

3. It is still not clear to me how this study fills the knowledge gap.
Validity of the findings: 4. Incorrect markings appear in the tables (e.g.!). Most often, we use * to describe p.

5. If variables are measured on quantitative scales, why are mean ranks calculated and reported for them?
Additional comments: Thank you for the opportunity to review a revised manuscript. I appreciate the authors' effort in responding to all comments. However, I still have some concerns.


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: SELF-REPORTED BODY WEIGHT AND WEIGHT-RELATED STIGMATIZATION EXPERIENCES AMONG YOUNG ADULT WOMEN—TWO CONTEXTS, BUT SIMILAR ATTITUDES RELATED TO BODY IMAGE, MENTAL SELF-SCHEMAS, SELF-ESTEEM, AND STEREOTYPES OF PEOPLE WITH OBESITY
Review round: 3
Reviewer: 1

Output:
Basic reporting: Overall, background is sufficient and clear. I do have one comment about lines 64-68. I believe the authors have excellent intentions with this paper and I want to commend them on this paper, but I want to point out that there is underlying stigma about weight in this section. 1) While weight stigma is associated with additional weight gain, we want to be really careful of how we frame this argument. It perpetuates the idea that weight gain is inherently bad. I would agree that additional weight gain has the potential to be problematic, but its still important to carefully craft that argument. I think the next sentence should be reworded as well as saying that someone feels inferior despite the weight loss makes it sound like they should no longer feel inferior based solely off of the weight loss.
Experimental design: a.	Be clear on your inclusion/exclusion criteria.
b.	I have doubts about the question “Are you fat now,” as an indicator of weight stigma. You are making an assumption that an individual experiences dissatisfaction about their weight status. The other question seems adequate. I do think it may be worthwhile to analytically look at whether or not to include this question as a measure of weight stigma. (I did see that there is a section in the discussion section about the negative stereotypes held by your respondents regarding excess weight. If you choose to keep both questions, I think you could and should highlight this data as it does appear to support your assumption.)
Validity of the findings: a.	Line 377 minor typo with p- value missing decimal point
b.	I thought the edits that were added to the discussion were excellent and greatly improved your discussion.
Additional comments: Thank you for contributing this paper to the weight stigma literature.


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: SELF-REPORTED BODY WEIGHT AND WEIGHT-RELATED STIGMATIZATION EXPERIENCES AMONG YOUNG ADULT WOMEN—TWO CONTEXTS, BUT SIMILAR ATTITUDES RELATED TO BODY IMAGE, MENTAL SELF-SCHEMAS, SELF-ESTEEM, AND STEREOTYPES OF PEOPLE WITH OBESITY
Review round: 3
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Thank you for the opportunity to review a revised manuscript. I appreciate the authors' effort in responding to all comments, and I believe that most of the issues have been appropriately addressed. Well done!


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

Input:
Title: EVOLUTION OF INBREEDING: A GAZE INTO FIVE ITALIAN BEEF CATTLE BREEDS HISTORY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The research presented is interesting, well written and correctly performed.
Experimental design: N/A
Validity of the findings: Conclusions directly derive from results. In turn, results are consistent with expectations and data available.
Additional comments: Manuscript PeerJ #61227 titled “Inbreeding trends in five Italian beef cattle breeds: a perspective of almost two decades (2002-2020)” by Rovelli et al.
I enjoyed reading this paper. The research presented is interesting, well written and correctly performed. I have no doubts in recommending the publication of this paper in PeerJ as-is.
However, with the aim of improving the interpretation of the research presented, I would like to raise a few comments that can be considered or not by the authors.
L80-81: you stated that “Our goal was to test whether intensive selection performed in the last twenty years has resulted in a significant increase of inbreeding levels in these five populations”. However, you do not present examples illustrating selection programmes involving the cattle breeds analysed (e.g. Sarti et al., J Anim Sci., 2013, 91; Sbarra et al., Ital. J. Anim. Sci. 2009,8; Fioretti et al., 2020, Livest. Sci., 232; just examples). Probably, the intensity of selection in the five breeds is not comparable and it may be lower in Maremmana and Podolica cattle (not sure). Perhaps a wider explanation of the goal (selection intensity and, e.g., temporal trends) could be advisable.
L200-209: yes, I absolutely agree. This is a clear case of population structuring due to multiple (within herd) founder effects causing that, overall, inbreeding exceeds coancestry. If between-lines (herds) gene flow is promoted this would cause a quick drop of overall inbreeding and, at the molecular level, a heterozygote excess in subsequent few generations. However, the discrepancies between Fhat and Fped may deserve an additional (indeed short) comment. Fhat is closely related to Fis and (also in the case of pedigree-computed Fis) can be interpreted in breeding policy terms: positive and high values mean that mating between close relative are not –or cannot be- avoided). Perhaps, in the smaller populations breeders are performing a more strict breeding policy to limit within-herd inbreeding.


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

Input:
Title: EVOLUTION OF INBREEDING: A GAZE INTO FIVE ITALIAN BEEF CATTLE BREEDS HISTORY
Review round: 1
Reviewer: 2

Output:
Basic reporting: I enjoyed reading the present paper and suggestions enclosed below are only suggestion as they may confer the paper with additional interesting information. However, I truly think the paper is well written and already provides a good quality material that is definitely worth being published.

Line 52 move from the same population before extracted at random.

Line 53 remove in order.

Line 59 to 61. Try not to make this expression this sharp as the topic raises controversy. The truth is that some recent papers have revealed the distortion caused by ancient contributions to inbreeding dilutes up to a degree in which pedigree-based analyses and genomic analyses may not differ that much. This should be acknowledged.

Line 68 do you mean effective population size?

Line 92. How many generations were presumably tested? Please clarify. Completeness index level (5th first generations) of the pedigree used should be provided if it is available. Endog calculates it.

M&M is well defined and clear enough as to ensure the replicability of this study. I particularly enjoyed reading the statistical approach used for the data.

Endog also permit to calculate Ne via different methods, such as individual increase in inbreeding, coancestry as the most accurate. Have the authors tried to calculate it and compare the values with those derive from genomic analyses?
Experimental design: Appropriate, see comments above
Validity of the findings: Appropriate, see comments above
Additional comments: I enjoyed reading the present paper and suggestions enclosed below are only suggestion as they may confer the paper with additional interesting information. However, I truly think the paper is well written and already provides a good quality material that is definitely worth being published.


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

Input:
Title: EVOLUTION OF INBREEDING: A GAZE INTO FIVE ITALIAN BEEF CATTLE BREEDS HISTORY
Review round: 1
Reviewer: 3

Output:
Basic reporting: The authors analyzed the inbreeding and diversity parameters in Italian dairy cattle, for four decades.
Experimental design: scientifically sound
Validity of the findings: Findings have great validity.
Additional comments: none


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

Input:
Title: EVOLUTION OF INBREEDING: A GAZE INTO FIVE ITALIAN BEEF CATTLE BREEDS HISTORY
Review round: 2
Reviewer: 1

Output:
Basic reporting: All my concerns have been correctly addressed and, therefore, I'm happy to recommend the acceptation of this paper for publication in PeerJ.
Experimental design: N/A
Validity of the findings: N/A
Additional comments: I'm happy with the revision presented.


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: EFFECT OF CONTROL MEASURES ON THE PATTERN OF COVID-19 EPIDEMICS IN JAPAN
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: The author attempted to examine the pattern of the pandemic in Japan. However, he has achieved only partial success in achieving his objective. In fact, I have some comments, all of them major.

1.- Although the author indicates in the title 'influenced by control measures' I do not see anywhere that it evaluates or, nor even that it controls by those measures.
The author should either change the title or add sections (in methods, in results and in discussion) where he evaluates these control measures in detail.

2.- The method section is very poorly explained and is very difficult to reproduce because it is not known how he applies the methods he says it uses. Among others:
2.1.- Explain DECIPHER in some detail and not just reference.
2.2.- How did it converted to a Boolean vector?
2.3.- What role do the variables confirmed cases, PCR tests and number of foreign visitors play? Did the author include them directly along with the nucleotid sequences in the PCA?

3.- Why were those the conditions for finding variants from each country? What is this range of values based on for each of the components?
Validity of the findings: The results section is also very incomplete.

1.- The author should provide a descriptive analysis of all the variables, distinguishing between Japan and each of the countries involved in his analysis.

2.- What is the variance collected by the components? How many components were chosen? The same for Japan as for other countries?

3.- In the Discussion section, the results are only compared with Johansson et al., 2021 and with a previous work by the same author.
He should compare his findings in detail with those of other studies indicating their advantages and disadvantages.

4.- It should include a paragraph, at least, of limitations, explaining how these have affected your results and what was done to solve them or, in any case, why they could not be solved.
Additional comments: The author attempted to examine the pattern of the pandemic in Japan. However, he has achieved only partial success in achieving his objective. In fact, I have some comments, all of them major.

1.- Although the author indicates in the title 'influenced by control measures' I do not see anywhere that it evaluates or, nor even that it controls by those measures.
The author should either change the title or add sections (in methods, in results and in discussion) where he evaluates these control measures in detail.

2.- The method section is very poorly explained and is very difficult to reproduce because it is not known how he applies the methods he says it uses. Among others:
2.1.- Explain DECIPHER in some detail and not just reference.
2.2.- How did it converted to a Boolean vector?
2.3.- What role do the variables confirmed cases, PCR tests and number of foreign visitors play? Did the author include them directly along with the nucleotid sequences in the PCA?

3.- Why were those the conditions for finding variants from each country? What is this range of values based on for each of the components?

The results section is also very incomplete.
4.- The author should provide a descriptive analysis of all the variables, distinguishing between Japan and each of the countries involved in his analysis.
5.- What is the variance collected by the components? How many components were chosen? The same for Japan as for other countries?

6.- In the Discussion section, the results are only compared with Johansson et al., 2021 and with a previous work by the same author.
He should compare his findings in detail with those of other studies indicating their advantages and disadvantages.

7.- It should include a paragraph, at least, of limitations, explaining how these have affected your results and what was done to solve them or, in any case, why they could not be solved.


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: EFFECT OF CONTROL MEASURES ON THE PATTERN OF COVID-19 EPIDEMICS IN JAPAN
Review round: 1
Reviewer: 2

Output:
Basic reporting: See below
Experimental design: See below
Validity of the findings: See below
Additional comments: The work is average but may be improved by the inclusion of the following suggestions.

1.	English should be improved throughout the manuscript.
2.	Quantitative information should be provided in the abstract.
3.	The concussion should be concise and to the points indicating the application of the work.
4.	The novelty of the work should be established.
5.	Refs are not updated and the following ref. The addition of this may improve the quality of this manuscript.
Sci. Total Environ., 728, 138861 (2020).


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: EFFECT OF CONTROL MEASURES ON THE PATTERN OF COVID-19 EPIDEMICS IN JAPAN
Review round: 1
Reviewer: 3

Output:
Basic reporting: A background on Covid-19 in Japan is covered in the Introduction. Part of the Introduction should be written clearly and concisely on what is the problem the paper would like to address and why it is an important problem to tackle. The Introduction contains the description of the approach, however, the discussion on the justification to support the approach taken. The findings of the approach are not highlighted from the Introduction as well as the contributions of the paper are omitted. The findings by the authors have practical value that merits sharing with the wider academic community, but more work needs to be done to emphasize their technical and applicability aspects as well as to more convincingly demonstrate the original contribution that this work makes to the scholarly knowledge base. Both findings and contributions should be clearly stated in the introduction part of the paper.

In terms of related work, a list of COVID-related studies and basically the related work in coronavirus invariants studies in other countries are not discussed in the paper. An important first step that will need to be taken to address this shortcoming is the inclusion of a comprehensive literature review. In its present form of the manuscript, there is no attempt to present a comparison of the related work features, strengths, and weaknesses, and more importantly, to show how the present work builds upon and extends what has already been done. Also conspicuously missing from the literature review is coverage of the relevant scientific literature on the control measures, the disease spread patterns, the mutation within the virus variants, and the intersection between these areas, especially as they relate to surveillance and prediction of risk within both infectious and non-infectious diseases.

In addition to performing the analysis with the confirmed number of cases, providing information such as the number of confirmed cases per population or the reproduction rate could enhance the interpretability of the content regarding the severity of the disease spread and the effect of the control measures at the national scale.
Experimental design: The author described the definition of PCA at the beginning of the paragraph. While cursory mention is made in the earlier section “phylogenetic trees“ and the fact that they require unverifiable assumptions, however, there is no attempt to make a discussion on the use of PCA in solving the problem at hand (among other possible methods) is not clearly justified. Background on PCA is extensively presented with the details of the method presumably coming from the earlier work.
Validity of the findings: Coronavirus is an ongoing pandemic and comparing the results with the information from one specific point in time (such as from a news website, the report from other countries figures need or from the relevant ministries website, it is important to report when the snapshot was taken precisely for validity purposes throughout the manuscript. Many factors may shape the response strategies of each country and the failure to contain the virus could be contributed by several factors other than the partial lockdown measure, insufficient PCR tests, and the relaxed border control protocol.

The findings on the changes in variant patterns and the timing should corroborate, triangulate and further confirm with the mobility patterns of visitors, and the civilians, as well as the temporal and spatial distribution of the cases in addition to the number of cases, or the number of visitors.

To make a real contribution to the field, the Discussion and conclusion will need to be substantially improved to (a) situate the scientific outcomes, findings, and lessons learned from the study in the wider context of the literature surveyed in the (expanded) literature review; (b) offer evidence-based practical recommendations for researchers, policy planners and system developers that are grounded in the researchers’ findings and experiences/observations; and (c) consider how the present work might apply to or otherwise have a value that transcends the discipline of epidemiology.
Additional comments: Line 71 - 73: “..converted to a Boolean vector, and subjected to PCA (Konishi et al. 2019).  Sample principal components (PCs) were scaled based on the length of the sequence (Konishi 2015).”
The same information is duplicated in describing the PCA in the following paragraph.

Line 53: At present, over 500 victims with 54 mild symptoms are waiting at home without medication in Tokyo (Bureau of Social Walfare and  Public Health 2021).
A vague word “At present” should be clarified.

Line 53: At present, over 500 victims with 54 mild symptoms are waiting at home without medication in Tokyo (Bureau of Social Walfare and  Public Health 2021).
The word “patients” would be preferable to “victims”.

Line 75: “...The number of confirmed cases was obtained from the WHO...”
For the first appearance WHO should be written as “World Health Organization”.

Line 142-145: “Australia has 39 estimated cases and 34,800 PCR tests per day. For the last 30 days, New Zealand had 802 positive responses against 194,233 negatives. Singapore had 196 positives, performing 32,100 PCR tests per day. Iceland had only 145 one domestic infection within seven days, but still performed a thousand tests per day.“

The numbers of cases in Australia, New Zealand, Singapore, and Iceland are made without proper references.

Line 194: “Repeating incomplete lockdown is an error that corresponds to a piecemeal force attack.”
The phrase “piecemeal force attack” in the sentence is not easily understandable for the reader who is new to the field.

Line 214: “If the borders are loosened again..
Do you mean “If the borders are relaxed ?”

Line #2 Figure 1 caption: “Four groups are obvious; this framework is common to other countries”..
Which framework the author is referring to?

Line #2 Figure 1 caption:“Four groups are obvious; this framework is common to other countries 8  ”
Footnote 8 could not be found.

Line 243 “Ministry of Health LaW”
The reference is not cited in the main text.

Line 247 - 248: R_Core_Team. 2020. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
R Core Team is not a hyphenated word and the website needs to be provided. The reference in APA style is
R Core Team. (2016). R: A Language and Environment for Statistical Computing. Vienna, Austria. Retrieved from https://www.R-project.org/

Several references to the online resources under the References sections are not presented in a systematic way.


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: EFFECT OF CONTROL MEASURES ON THE PATTERN OF COVID-19 EPIDEMICS IN JAPAN
Review round: 2
Reviewer: 1

Output:
Basic reporting: Revision is complete and accepted.
Experimental design: Revision is complete and accepted.
Validity of the findings: Revision is complete and accepted.
Additional comments: Revision is complete and accepted.


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: EFFECT OF CONTROL MEASURES ON THE PATTERN OF COVID-19 EPIDEMICS IN JAPAN
Review round: 2
Reviewer: 2

Output:
Basic reporting: -
Experimental design: -
Validity of the findings: -
Additional comments: The author(s) has addressed the reviewer's suggestions. Overall, the manuscript has been improved but the discussion section is still needs improvement.

Here are a few more detailed comments on the manuscript.
Line 53: Upon immigration -> is it upon arrival?
Line 169: Why eight groups? The author should provide justification.
Line 174: (shown in tangerine)-> missing reference Table/Fig
Line 201: (The slopes of the lines indicate the changes per day) -> missing reference Table/Fig
Line 318: customs inspection system -> immigration policies?
Line 353-356: Should not deviate from the main content of the paper. These sentences are not relevant. "This was one of the well-known mistakes that led to Japan's defeat in World War II, when fragmented forces were destroyed one after another, resulting in heavy losses (Saito 2013). Japan is again setting a bad example using the same approach."
Line 337: Each ascent of K was caused by a new variant. -> Reference to fig/Table.

The discussion section could be improved by writing succinctly in a more organized flow. Similar topics could arrange together. At present, the discussion on a topic is covered in multiple portions of the Discussion.

For example, the discussion on vaccination in this section is covered in

Line 356:  Vaccination is another promising strategy, but Japan is
lagging behind, and the program remains undecided (Ministry of Health Labour and Welfare,
Japan 2021).
Line 417 - 422 Vaccination is lagging, with only 4% of the population vaccinated as of May 25, 2021 (Prime Minister's Office of Japan 2021). The rate of vaccination is around 400,000 vaccines per day; as
Japan has a population of 120 million, this situation (the outbreak of new variants, resulting
peaks in the number of patients and the chronic overflow of medical institutions) will continue
for several more years if the current measures continue. Furthermore, this prediction is only valid
if the vaccine alone is effective in preventing the disease.


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: EFFECT OF CONTROL MEASURES ON THE PATTERN OF COVID-19 EPIDEMICS IN JAPAN
Review round: 3
Reviewer: 1

Output:
Basic reporting: Thank you for addressing the reviewer's suggestions. Overall, the manuscript has been improved,  a few places that need to be addressed are provided below.

Line 64 - "Immigrants" -> Do you mean visitors?
Line 242 - Fig 2A - C shows -> show

Line 363 - 'To maintain cleanliness, it is necessary to identify 364 and isolate virus carriers' ->  What do you mean by cleanliness?

Line 372 - 373 -> a single sentence should not be a paragraph

In the Results section, Reference figures should be added whenever the content of the figure is under discussion. The following sentences are a few examples of them.
Line 298 - "Even when the light blue variant increased to form the second peak" needs a reference figure
Line 309 - "blue-green variant R.1"
Line 310 - "Another blue variant"

Throughout the paper, the author is recommended to avoid using "very" in a sentence such as "very small" or "very difficult" and suggested using alternatives.
Experimental design: -
Validity of the findings: -
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: EFFECT OF CONTROL MEASURES ON THE PATTERN OF COVID-19 EPIDEMICS IN JAPAN
Review round: 4
Reviewer: 1

Output:
Basic reporting: The author(s) has addressed the reviewer's suggestions. However, it is important to note that the submitted pdf file in the manuscript folder doesn't reflect the word file in the response folder. It can be easily  checked with the line number 363 in pdf and 366 in the word file.
Experimental design: -
Validity of the findings: -
Additional comments: -