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: IROKI: AUTOMATIC CUSTOMIZATION AND VISUALIZATION OF PHYLOGENETIC TREES
Review round: 1
Reviewer: 1

Output:
Basic reporting: Moore et al. worked in a tool for phylogenetic tree visualization and customization. The manuscript is clearly written in professional, unambiguous language. However, there is a key point that should be considered.

In the introduction section, it is unclear why the reader should use the Iroki tool instead of the usual ones. The authors say that other tools are more “complex” (lines 49-50), but this should be clearer. I suggest you to provide a table comparing the main advantages of using Iroki over others you cite in the paper (e.g. iTOL and FigTree).
Experimental design: All raw data are supplied by the authors in an organized manner to ensure reproducibility. I tested the online tool and one thing is unclear: does the software only accept rooted trees? Is it possible for the user to specify the root after submitting? I think that this point should be discussed in the paper (if applicable).
Validity of the findings: In the results section, the authors explore data on viruses and bacteria. I have some minor questions and suggestions:

1- In 2017, Czech et al published a paper about the use of support values in phylogenetic tree viewers (Mol. Biol. Evol. 34 (6): 1535–1542 - doi: 10.1093/molbev/msx055). They discuss about ambiguous semantics in tree file formats that can lead to erroneous tree views and, therefore, to incorrect interpretations of phylogenetic analyzes. I think you should do these tests to see if Iroki is free of such errors. Maybe, citing this paper would also give more strength to your work.

2 - I think Irok could be even more interactive. Can the user modify the label name in the phylogenetic tree after submitted?

3- Line 194: Why did you chose p-value < 0.2? I suggest making it clearer in the text.
Additional comments: No comment.


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

Input:
Title: IROKI: AUTOMATIC CUSTOMIZATION AND VISUALIZATION OF PHYLOGENETIC TREES
Review round: 1
Reviewer: 2

Output:
Basic reporting: I congratulate the authors for the quality of the submitted manuscript that, in my opinion, already addresses all requirements for publication. The accompanying supplementary data and online webapps and documentation links are very good, although the online documentation could contain more rendering examples.
Experimental design: The manuscript by Moore et. al presents a flexible and simple tool for visualisation of phylogenetic trees and hierarchical data and associated metadata. It very well written, presenting in a clean and straightforward manner several features of the tool. It demonstrates the tool's usefulness with three convincing examples and covers precedentes from the literature with sufficient detail.
Validity of the findings: This tool is undoubtedly useful and can only be improved as it attracts more users. I can find no errors in the example analysis presented that need fixing.
Additional comments: If the authors are considering future development of this tool, I can suggest a few features that could be added:

1) Consider letting the user name the column with leaf names to avoid forcing users to rename columns
2) If possible, more interactive tree viewers, such as interactive components from D3 or BioJS could be considered as an option for the tree canvas in use right now. This could give the web app a more dynamic look and feel
3) As mentioned above, the documentation could have more detailed rendering examples.

Keep in mind that my comments are only suggestions for future versions of the tool and should be interpreted as impediments from publication.


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

Input:
Title: TALL PINUS LUZMARIAE TREES WITH GENES FROM P. HERRERAE
Review round: 1
Reviewer: 1

Output:
Basic reporting: See below
Experimental design: See below
Validity of the findings: See below
Additional comments: The article is interesting, important and should be published with minor changes:

1: Title, why "... - an unexpected result..."? Maybe a more neutral title is the better choice.
2: Line 98 and 106 (447): Concle & Critchfield, (1998) correct: (1988).
3: Line 100 and 333 (544): Is that Little & Francis, 1965 or Little & Righter, 1965 ?
4: Line 152: (Fig. 2) correct to (Fig. 1).
5: Line 223: Include reference to (Fig. 2).
6: Line 387 (539) Lexer et al. 2008 correct: Lexer et al. 2005.


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: TALL PINUS LUZMARIAE TREES WITH GENES FROM P. HERRERAE
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper is aimed to investigate the degree of introgressive hybridization between two pine species Pinus herrerae and P. luzmariae using a combination of phenotypic and AFLP-derived molecular data. Based on the assumption that individuals clustering with the majority of ones from another species are likely to contain a mixture of genetic information from both species, the authors identified the percentage of putative hybrids in four populations of P. herrerae and P. luzmariae. The analysis indicated that the hybridization occurred in all stands under study and that hybrids in P. luzmariae populations showed enhanced silvicultural traits compared to either parent species.

The paper provides appropriate background, describing the phenomenon of heterosis and briefly outlining the current state of affairs in studying population relationships among Mexican pine species. Previous works on using AFLP markers in detecting introgressive hybridization in plants are given, and the advantages of this method are described. However, the weaknesses of using AFLPs in population genetics are not mentioned.

The manuscript is written in clear and unambiguous language and conforms to the standards in the field. Although, there are some minor corrections that should be made in order to improve the text:
1.	In Line 157 the authors describe the location of the tree stands and mention distance between study sites but refer to Fig.2 which depicts the results of clustering based on AFLP data. The reason for such reference in section ‘Study sites’ is not clear.
2.	The term ‘Dasometric’ in Line 176 rarely occurs in literature. This word seems to be a direct translation of Spanish term ‘dasometría’ which implies the application of statistical methods for forest measurements and, to the best of my knowledge, is not used in international scholarly publishing. I would recommend that the authors consider using more common terminology to avoid confusing readers.
3.	It seems that there are missing words in Lines 200-201. Is it 16 randomly chosen individuals from each population?
4.	In Lines 279-280 PH stands are called red and PL blue, whereas in Figure 2 (which these lines are referring to) PH are blue and PL are orange.
5.	The second paragraph in the Conclusion section contains repetition of ‘essential’ in Lines 398 and 400.

Comments on Figures and Tables:
1.	There are some inconsistencies in Figures labeling. For instance, in Figure 1 populations of P. luzmariae are marked with red triangles and P. herrerae with yellow circles, while the caption says different. In Figures 2, 3, 6 and 7 there is a population marked as PH-T which is not described in Study sites section (I assume this is a typo).
2.	Additionally, Figures 3, 4, 5, 6 and 7 consist of two or more parts but do not have proper labels such as “A, B, etc.”. The authors should ensure that all the figures have the correct labeling as described in the Submission Guidelines.
3.	In my view, Figures with PCoA clustering results (Fig. 3, 6 and 7) would benefit from being colored and uniform in size and quality. As well as adding labels to the photographs of trees and cones (Fig. 4 and 5) identifying which species or hybrid they belong to would improve clarity.
4.	Finally, it seems like a good idea to represent the last paragraph in the Study sites section as a table or add this information to the one that describes the locations of the stands.
Experimental design: A great amount has been conducted by the authors to collect the specimens and morphological data across several seed stands of Sierra Madre Occidental. The methods used in the paper conform to the stated question of identifying hybrids between two close species. The authors use established a protocol for performing AFLP analysis, and traditional approaches to processing the data. However, the procedure of testing the affiliation of individuals to each species using Bayesian clustering is not clear. Particularly in Line 225 what is meant by “association between PH and PL trees”?

The use of Affinity Propagation (AP) clustering raises some questions. It is said that “AP has several advantages over related cluster techniques”, but these advantages are not listed. Furthermore, AP does not require a predefined cluster number, however, in the case of identifying hybrids between two species the number of clusters is known. Hence the advantage of using AP over k-means is not obvious. I would suggest authors including more information that clarifies their choice of this method.

Additionally, it is not stated in the text how the authors identified the hybrids with the PCoA clustering, i.e. what thresholds (if any) they use to detect hybrid individuals.
Validity of the findings: My major concern is related to the lack of the exact numbers in the description of the clusterization results. The authors present only proportions of identified hybrids (Tables 3 and 4) not providing precise numbers of putative hybrid individuals (although some numbers appear in the text) detected by processing molecular or morphological data.

Discussing the results authors indicate that “gene flow from PH to PL seems to be more effective as more hybrids were found in the PL stands”. How this can be explained (for instance, it can be noticed that stands of P. luzmariae are generally located lower compared to P. herrerae stands)? I would suggest elaborating on this a bit more.

As a minor comment regarding data representation, “apcluster” package has built-in plotting tools so the results of clusterization can be easily visualized and presented in a more reader-friendly way.
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: TALL PINUS LUZMARIAE TREES WITH GENES FROM P. HERRERAE
Review round: 1
Reviewer: 3

Output:
Basic reporting: •	Authors present the work in clear professional Engilsh
•	Introduction provides appropriate context.
•	Literature is somewhat dated – newer references would be appropriate in many places throughout the intro
•	Figures are reasonable, but some suggested changes are provided below
•	Raw data are provided, although one Table is missing (see below)
•	The Methods are lacking several critical pieces, which make it difficult to assess the validity of the Results.
Experimental design: •	This work is within the scope of the journal
•	Research question is well defined and fills a knowledge gap
•	I have identified several issues that the authors must address to ensure the validity of the work
•	Additional information and clarification is needed within the Methods

The authors did not clearly define the pure individuals that serve as references to define the hybrid nature of each individual in the study. This is a critical step for any project with this scope. I am hoping that this was an oversight.  If pure individuals do not exist, then I would consider this a fatal flaw in the design of the study.

With pure individuals it is possible to assess the power to identify hybrid individuals within the five populations examined by the authors.

I need further information to fully assess the strength and design of this study.
Validity of the findings: •	To assess the validity of the findings, there are issues that need to be addressed, in particular the presence of pure individuals to use as references for establishing the diagnostic nature of the molecular markers

•	Underlying data are provided, with the exception of one critical table (individual collection data)
Additional comments: Detailed Comments
The authors present an interesting study examining the potential impact of hybridization on pine tree growth in Mexico. My biggest concern is a lack of pure reference populations needed to define the diagnostic state of the difference AFLP fragments used to identify hybrids. I hope that this was an oversight by the authors and this can be clarified.  I outline additional issues below.

Introduction
•	Throughout, there are mostly older references  - please try to identify newer references that discuss issues such as hybridization
•	Line 74-96: This section seems out of place relative to the surrounding text. I suggest a reorganization
•	Line135: The topic sentence of this paragraph needs revision to clearly introduce this paragraph.

Methods
The authors need to provide greater information in the section for the Molecular Detection of Hybrids.  First, do they include individuals that are known pure species? This to detecting portions of the genome that are introgressed into the other species.  Inclusion of these types of samples is considered standard practice.  Second, the descriptions of the analytical methods used in this section require greater detail.  For example what were the protocols used for STRUCTURE (e.g. burnin, # generations)? Third, I am concerned about how hybrids are defined in this context.  I would strongly recommend a more quantitative approach (For example:  Cullingham et al. 2011
https://doi.org/10.1111/j.1365-294X.2011.05086.x)

I would also like to see a figure that shows the morphological measurements that were taken on the cones and needles.  While this information may be present in an earlier paper, it is important that this manuscript is able to stand independently.  Clear descriptions of the morphological traits and a figure that shows each would be needed.

•	L199: Clarify your meaning of reference samples
•	L230: What do you mean by putative pure individuals?
•	L248: What are the voucher numbers for the individuals deposited in to the collection?
•	L249: Write out the name of CIIDIR in full

Results
•	The authors need to provide a Table that includes the collection data and assignment of each individual.  It should also include the voucher number for each specimen and any other associated data (individual NewHybrid results, structure assignment).
•	L279: There is confusion here with the colours used to denote PH and PL.  Here the authors state that PH has a dominante variant (Red).  In the Structure plot, PH = blue.  Where does the red come from?
•	Line297:  What is your power to detect hybrids? See Cullingham et al. 2011 for methods to determine your  to detect hybrids
Discussion
•	Line317: The first sentence of the Discussion mentions hybrid vigour.  There were no data that measure hybrid vigour in the trees tested for introgressed alleles. There should be a section identifying traits that define hybrid vigour (tree height, straightness) for each individual tree measured for the study.
•	Line 330:  How can you be certain that these shared fragments are due to introgression rather than shared regions due to a shared anscestory?  You would need to have pure individuals of each species to define what are Ph and Pl markers prior to identifying hybrids
Table 2
•	I think it would make more sense for this table to show the differences between the two species (i.e. the species diagnostic traits) as well as the ranges for the populations that are being studies. This speaks to the larger issue of not having clearly defined pure individuals/populations.
Figure 2
•	Identify the different hybrid classes for each individual within this Structure plot
Figure 3
•	Difficult to differentiate the PH-T and PH-V triangles. Revise.

Figure 5
•	Label identity on each figure panel


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: TALL PINUS LUZMARIAE TREES WITH GENES FROM P. HERRERAE
Review round: 2
Reviewer: 1

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
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: TALL PINUS LUZMARIAE TREES WITH GENES FROM P. HERRERAE
Review round: 2
Reviewer: 2

Output:
Basic reporting: The article is written in clear language and all appropriate background is provided. The authors substantially revised the manuscript, adding more recent literature and changing some of the used methods (see comments below).
Experimental design: There are a couple of questions regarding the description of methods:
•	Was the distribution of morphological traits tested for normality before performing LDA? It may be worth explicitly specifying what methods were used (graphical or some frequentist test).
•	Did you use the training set for LDA to get LD functions? Also, was any standardization used for the variables? You may wish to clarify this in the methods section to ensure reproducibility.
Validity of the findings: See below
Additional comments: There are some minor notes on the changed parts of the manuscript:
•	Lines 237-238, the end of the sentence looks a bit strange, it might be worth revising
•	Line 300, probably a missing preposition
•	Line 404, the word “respectively” seems to be out of place
•	In Figure 6, does “the one linear discriminant” in captions mean the first discriminant function?
•	In Figure 7 the left tail (one tree with 14 m height) is not shown in the histogram, although it is mentioned in the text.


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: TALL PINUS LUZMARIAE TREES WITH GENES FROM P. HERRERAE
Review round: 2
Reviewer: 3

Output:
Basic reporting: The authors use clear language throughout the manuscript. They have updated their references to provide more current background/context.

I find no evidence that the authors have shared the raw AFLP data or morphometric data set.
Experimental design: My biggest concern in an earlier version of the manuscript was that the authors had not defined "pure" species in their data set.  They have now been clearer in their revisions about how they identify "pure" individuals. Ideally, I would prefer to have the pure individuals identified a priori, rather than analytically after the fact, but I acknowledge that this is not always feasible. As such, I am okay with the current revisions.
Validity of the findings: With the improvements on pure vs hybrid differentiation, I believe that the authors have provided evidence to support their conclusions.
Additional comments: Thank you for your attention to details and efforts to revise the manuscript in response to my earlier comments.

Please indicate where you will deposit your raw data.


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

Input:
Title: ELEMENT CONCENTRATIONS IN PELAGIC SARGASSUM ALONG THE MEXICAN CARIBBEAN COAST IN 2018-2019
Review round: 1
Reviewer: 1

Output:
Basic reporting: This submission is topical and will be of interest to all those researching and effected by Golden-tide problem in the Gulf of Mexico and the Caribbean.

It is generally well written, although there is some awkward phraseology, such as line 197.

The scientific question and experimental set up seem sound with appropriate statistical methods. The figures are clear and have sufficient captions for them to be read stand-alone.

The primary method is XRF, which, although novel, is not the standard method of  'heavy metal' analysis.; more discussion on the strengths and weaknesses of this method relative to the more usual procedures such as ICP may be of value.
Experimental design: The scientific question and experimental set up seem sound with appropriate statistical methods. The figures are clear and have sufficient captions for them to be read stand-alone.
Validity of the findings: The primary method is XRF, which, although novel, is not the standard method of  'heavy metal' analysis.; more discussion on the strengths and weaknesses of this method relative to the more usual procedures such as ICP may be of value.
Additional comments: This submission is topical and will be of interest to all those researching and effected by Golden-tide problem in the Gulf of Mexico and the Caribbean.

It is generally well written, although there is some awkward phraseology, such as line 197.

The scientific question and experimental set up seem sound with appropriate statistical methods. The figures are clear and have sufficient captions for them to be read stand-alone.

The primary method is XRF, which, although novel, is not the standard method of  'heavy metal' analysis.; more discussion on the strengths and weaknesses of this method relative to the more usual procedures such as ICP may be of value.


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: ELEMENT CONCENTRATIONS IN PELAGIC SARGASSUM ALONG THE MEXICAN CARIBBEAN COAST IN 2018-2019
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: Because the temporal variability was analyzed, the collection date of each sample should be given in Table1. I am also concerned with the very few samples in some locations. As there were so many floating Sargassum in the sea, why only one sample was collected in some places. The replication for these locations was not enough. At least the authors should describe the reason for the limited number of samples.
Validity of the findings: no comment
Additional comments: I do not agree on one point in the first paragraph of Discussion.
The authors wrote the heavy metals were unlikely adsorbed nearshore. But as I know, the adsorption process is usually very fast, so it cannot exclude this possibility.

In the method section:

Did you handle the samples before drying them? As you have discussed, epiphytes may adsorb or absorb metals. Did you remove the epiphytes before the analysis?

I am concerned with the limited sampling size in some locations. If this issue can be addressed reasonably, I recommend the acception of this MS as basically it is well organized and well written.


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: ELEMENT CONCENTRATIONS IN PELAGIC SARGASSUM ALONG THE MEXICAN CARIBBEAN COAST IN 2018-2019
Review round: 2
Reviewer: 1

Output:
Basic reporting: No further comment
Experimental design: No additional comments
Validity of the findings: No further comment
Additional comments: The authors have fully answered my queries and substantially improved grammar and phraseology.  However, please check Table 1 in the supplementary materials there are citations with superscripts, but no superscript entries in the table.


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: IMPACT OF EXAMINED LYMPH NODE COUNT ON LONG-TERM SURVIVAL OF T1-2N0M0 DOUBLE PRIMARY NSCLC PATIENTS AFTER SURGERY: A SEER STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. In Figures 1 and 2, x-tile is best used only to determine the cut-off value. Patients should be regrouped according to this cut-off value and survival analysis should be conducted by new groups. You can put the picture of the x-tile results in the supplementary picture.
2. In lines 131-132, the authors say “no significant difference was found in sex and race between two groups.” No specific p value is given here. Even if there is no significant difference between variables, the p value is best listed.
3. In lines 137-138, the authors say “Among all lesions, the median ELN count went out to be 4 but differed significantly between two groups (P=0.018) possibly due to the diverse distribution.” Only objective facts need to be stated in the results section, and the reasons for the differences in results should be discussed in the discussion section.
Experimental design: 1. Patients are included between 1988-2013; it is unclear what the average follow-up time was, what was the last date patient information was updated? How does the SEER provide an update on OS or CSS (usually once yearly?). This should be specified.
2. This is a clinical retrospective study, and given that the data are from a public database, the authors would be well advised to state that the study was exempted by the ethics review committee.
3. Since there are too many criteria for inclusion and exclusion of patients, it is better to provide a flow chart to show how many patients are included and excluded in each step.
4. As far as I know, the number of examined lymph nodes in SEER database has some unreasonable data. How do you deal with some obviously unreasonable data? This needs to be specified in the methods section. If data from other database or medical institution can be used for external verification, it will help to solve this problem.
5. The authors say “SDP-NSCLC group patients were those which second primary NSCLC was identified within 6 months after the diagnosis of first primary NSCLC.” How is the 6 months standard formulated? Why not 3 months, 4 months or 9 months? What is the effect of different time nodes on the prognosis of the two groups?
Validity of the findings: 1. In the abstract section, the authors conclude that “These findings indicated that ELN count played a vital role in the long-term survival of T1-2N0M0 double primary NSCLC patients after surgery.” In my opinion, this is not accurate. ELN count does not play an important role in prognosis, but is maybe highly correlated with prognosis. There is no causal relationship between them, so it cannot be said that ELN count plays an important role in the prognosis.
Additional comments: Lymph node dissection is an important part of tumor surgery. The pathological examination report of lymph nodes is helpful for the postoperative pathological stage of patients, which is also helpful for the clinicians to judge the prognosis of patients and the formulation of follow-up treatment strategies. The authors want to explore the relationship between the number of lymphadenectomy and the prognosis of multiple primary tumor patients. This is good, but there are still some questions confusing me and they need to be addressed furtherly.


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: IMPACT OF EXAMINED LYMPH NODE COUNT ON LONG-TERM SURVIVAL OF T1-2N0M0 DOUBLE PRIMARY NSCLC PATIENTS AFTER SURGERY: A SEER STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper needs to be check by a professional native-english speaker.
Experimental design: The design of the study is well presented into the methods; however, the results section is  confusing and the author should better explain his finding adding more tables; otherwise, it is very difficult to read and understand the finding.
Validity of the findings: the result section is confusing and difficult to read; the author should better explain the finding eventualy adding more tables to make it more clear to the reader . Also the discussion is more a review of the literature than a discussion of the results of the study and it should be re written with more discussion of their finding compare with the literature.
Additional comments: The manuscript is about a very interesting topics; however there are few issues that the author should fix before considering it for publication. In particular the result section is confusing and difficult to read; the author should better explain the finding eventualy adding more tables to make it more clear to the reader . Also the discussion is more a review of the literature than a discussion of the results of the study and it should be re written with more discussion of their finding compare with the literature.
- This sentence into the methods line 97-100 should be re written because it is not clear: "On account of the difficulty in discriminating the first and second primary cancer in SDP-NSCLC, we brought each lesion rather than patient into the statistics and set up new variables, including grade max, size max and ELN plus, in the survival analysis of SDP-NSCLC group"
- The author should better explain what the X-tile analysis is.
- Into the results section the paragraph between line 149-154 is unreadable. Please, make it more clear to the reader.
- Into the discussion the author stated: "Then, we recommended that a sum of more than 22 lymph nodes should be examined during the surgery of two lesions for SDP-NSCLC patients while over 9 lymph nodes to be examined during the surgery of the second lesion for MDP-NSCLC patients, with the purpose of achieving better survival " How many per each side? Which stations?? Hilar? Mediastinal? Considering that this sentence is the more important one of the study (see the conclusion), it should be better explained and argumented into the discussion.


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: IMPACT OF EXAMINED LYMPH NODE COUNT ON LONG-TERM SURVIVAL OF T1-2N0M0 DOUBLE PRIMARY NSCLC PATIENTS AFTER SURGERY: A SEER STUDY
Review round: 2
Reviewer: 1

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


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

Input:
Title: HOLISTIC ENVIRONMENTAL APPROACHES AND AICHI BIODIVERSITY TARGETS: ACCOMPLISHMENTS AND PERSPECTIVES FOR MARINE ECOSYSTEMS
Review round: 1
Reviewer: 1

Output:
Basic reporting: I have a very hard time to capture the scope and objectives of this paper. Nowhere in the text, “environmental assessments” are explained – but to my knowledge, this refers to “an assessment of the ecological consequences (positive and negative) of a plan, policy, program, or actual (development) projects prior to the decision to move forward with the proposed actions”. However, the only way to let this paper make somehow sense is to swap the wording by “environmental Monitoring and Evaluation”. However, there seems to be additional confusion as – in their methodology/literature review - the authors seem to lump “environmental M&E” with “ecosystem-based approaches”; the latter is actually a management approach. This very essential problem, which is not just about terminology but also about interpretation, undermines the relevance of entire study.

The main hypothesis of this paper seems to be that a more holistic environmental monitoring & evaluation can (directly) lead to better progress towards the Aichi Targets. Intermediate steps – i.e. proposition of management approaches and effectiveness of their implementation, are not discussed. Also, one of the key reasons why targets under the current Strategic Plan for Biodiversity are not met is related to the challenge of developing and using indicators to monitor progress in the targets, and the fact that the current targets are often to vague (not SMART) whereas they should be crisp and measurable (with elements that can be disaggregated) reflecting both processes as well as status outcomes. Again, this has not been considered/discussed.

Furthermore:
- Introduction: I am puzzled about the explanations for the links between the so-called "Environmental Assessments" and each of the Strategic Goals, and targets. I found the causalities rather simplistic and not always clear. An example of a confusing sentence (lines 62-64): “holistic frameworks also help in the development of ecological indices, as they integrate different ecosystem components in a coherent methodology, which is relevant for Target 17”. Also the section on Goals B, C and D (lines 67-75) seems to reflect poor understanding of these strategic goals and underlying targets.
- Research Perspectives: The so-called research priorities identified are not research priorities per se, but just proposals for improved environmental monitoring and evaluation, that are – all together – not innovative.
- The entire paper is also characterized by sloppy (e.g. lines 20-21) and weird phrasing (e.g. lines 109-110; lines 151-153; lines 156-158; 191-194; 289-291).
Experimental design: - Methodology: it is unclear what type of studies were analysed (somewhere it is stated that Ecosystem-based management studies were considered to be equivalent to Holistic Environmental Assessments??). Also, the selection of key words is not explained; the authors themselves determine what should be considered as properly ‘holistic’ (lines 93-94). Robustness of analyses is doubtful.
- The methodology used to define the so-called 'research priorities’ (“gathering input from experts”) is too vague to be meaningful
Validity of the findings: Given major flaws explained under 2. - I don't feel conclusions are sufficiently supported, nor clear.
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: HOLISTIC ENVIRONMENTAL APPROACHES AND AICHI BIODIVERSITY TARGETS: ACCOMPLISHMENTS AND PERSPECTIVES FOR MARINE ECOSYSTEMS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Please check grammar and tense throughout – e.g. line 28 “continue to provide”, e.g. 292 Management of ecosystem services categories, etc.

Please define or present your definition of environmental assessment in the Introduction, as this term is used in many different ways across different disciplines. Also, your initial definition or description of holistic (e.g line 31-32 or 36-37) should also include reference to the time/temporal component which you refer to later in the discussion.

Would the authors consider creating a conceptual diagram or figure linking the components of HEA to the different Aichi targets? This would send a more powerful and elegant message than just listing the Aichi Targets in Table 1 and then referring to each in reference to HEA in the manuscript text.
Experimental design: Is it not clear why the authors did not include “environmental assessment” in the initial terms search?

Also, in filtering the initial search results for holistic EBM, why not include other similar terms such as “comprehensive”, “multi-” or other relevant term?

Please clarify that in the end, the total number of articles included in the review of fit to the 4 categories of HEA is 77?
Validity of the findings: This manuscript reviewed 77 articles for classification of fit into 4 components of HEAs. The rest of the paper provides 5 recommendations  for conducting and improving HEA. However, either before or within each of the resulting 5 recommendations, it would be good to review or present what key documents, tools and datasets are already available to guide HEA and/or EBM studies.
Additional comments: The topic of this paper is important and timely (if not overdue) for assessing global or national progress toward the Aichi Targets. However, the methodology, article classification and resulting recommendations seem cursory and could benefit from a more in-depth analyses. Suggestions include improved definitions, expansion of search terms, a conceptual model linking HEA to the Targets, and a more thorough review of existing tools, data and guidance already available for HEA.


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: HOLISTIC ENVIRONMENTAL APPROACHES AND AICHI BIODIVERSITY TARGETS: ACCOMPLISHMENTS AND PERSPECTIVES FOR MARINE ECOSYSTEMS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The first sentence of the abstract and manuscript refers to Conference of the Parties, but fails to mention under which Convention this CoP is operating (e.g. Convention on Biological Diversity)! This is slightly worrisome!

Line 70 - as this an after the fact perspective, it makes more sense to state that you are discussing the relevance of HEAs for reaching the Targets, rather than their contribution. This should be changed throughout (e.g methodology, etc.).

There are still many grammatical and semantic errors throughout. e.g HEA in the plural should be HEAs.

The last paragraph of the introduction is very confusing. Goals A-E are introduced - followed by HEA examples. However, it is difficult to follow the logic, and as written, the HEA examples do not seem to match up to the Goals.  For example Goal E is related to enforcement of government or other conservation measures - but the corresponding HEA example is for predicting ecological consequences of mutliple drivers of change?
Experimental design: The methodology section is clearer and improved with the inclusion of Table 1. However the nested search pattern used is not very clear in the methodolgy text.  Figure 2 is a bit confusing - in the legend "each HEA" should be "each of the 9 types of HEA" for example. Do not include methods in the Figure Legend.

The study design is essentially just a key word search. No attempt is made to define the 9 HEA terms or to further analyze or categorize what the resulting articles in the search actually said or did.
Validity of the findings: Figure 2 is interesting and a good start. However, the section labels (A-D) in the legend do not appear correct. Also the stated linkages (e.g. arrows) between Aichi Goals/Targets and HEA types/Research Priorities are not intiutive or clear.  For example, how do any of listed Aichi Targets prioritize research in HEA vocabulary?

Discussion of the linkages among the 4 components of figure 2 needs to be better discussed in the text. At the moment, they are each referred to individually at convenient places in the paper, but the figure as a whole and the linkages it shows are never really discussed.

If you could find a way to strengthen these linkages (or redefine them) and give them a more thorough discussion in the text, your conclusions would have more validity, and the overall message of the paper would have more rigour, beyond a key word search.
Additional comments: This revision is much improved, but the linkages among the Aichi Goals/Targets and HEA types/ research priorities are still very weak as presented, and specifically need further thought and discussion.  Additionally, there are still many grammatical and semantic errors throughout.


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

Input:
Title: THE DETECTION OF TRANS GENE FRAGMENTS OF HEPO IN GENE DOPING MODEL MICE BY TAQMAN QPCR ASSAY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well written. Introduction covered all the content needed to understand the results with literature well referenced and current. All figures are in good quality, however, it is necessary to improve the subtitles according to the journal standard and add relevant information for the understanding of the images and graphics presented (see General comments).
Experimental design: This work is within Scope of the journal and shows a well-designed and rigorous research with coherent methods to achieve the proposed objectives. Methods were described with sufficient detail and information to replicate.
Validity of the findings: This work contributes with many information to understanding and development methods for gene doping and it has scientific relevance in the research field. My opinion is that the score assigned to the manuscript is good for publication in this jornal. My concerns and suggestions are described in General comments.
Additional comments: Line 188: The authors described "Transgene fragments were detected in all samples in TaqMan qPCR", but in results section (lines 179-180) was described "In the blood specimens, using the TaqMan probe, transgene fragments were detected at 1, 2, 3, 6, and 12 h in the IV and IM groups and at 1, 2, 3, 6, 12, and 48 h in the IP group". Why were samples at times 24 and 48 h not considered?

Line 190: Statistical analysis were presented in the tables legend 2 and 3 "**: p < 0.01 vs Pre in each group. *: p < 0.05 vs Pre in each group", but this information is nowhere in the tables.

Table 2: Why was the detection of transgene fragments in blood samples by TaqMan qPCR and SYBR Green qPCR higher in 3h than 2h? Because according to the results, the tendency of values is to decrease in blood samples. These results were obtained from how many independent experiments? This information is missing from material and methods.

In line 195 is written " Transgene fragments were detected in all samples in TaqMan qPCR" but was not in accordance with the results given in table 3 for IP samples (24 and 48 h).

Lines 208 and 210: Check and correct the figures citations.

Lines 219-220, 225-226, 236-240, and 251-255: In the figures legend (2, 3, 4, and 5) were described results, which already were presented in the images. It would be more useful to add important information to understand how that result presented in the image was obtained. This information makes reading more enjoyable and practical, as the reader does not have to go back to the material and methods to check.

Figure 2: The results presented for negative controls and specific amplification are clear, but the times of 1 and 3h inserted in the image are confusing. Was the 3h time only used for the IP sample?

Figure 4 and Figure 5: The hEPO-reference and amplicon sequences identifications are exchanged in the images.


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

Input:
Title: THE DETECTION OF TRANS GENE FRAGMENTS OF HEPO IN GENE DOPING MODEL MICE BY TAQMAN QPCR ASSAY
Review round: 1
Reviewer: 2

Output:
Basic reporting: Cited references were insufficient to provide the scientific background.
In raw date, several cells were written in Chinese and Japanese.
Experimental design: It is not suitable for animal model in this study.
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: THE DETECTION OF TRANS GENE FRAGMENTS OF HEPO IN GENE DOPING MODEL MICE BY TAQMAN QPCR ASSAY
Review round: 2
Reviewer: 1

Output:
Basic reporting: It is not problems in English.

Several references is not suitable to introduce the research background of simply injection methods of naked plasmid DNAs. For example, in "Ito T et al., Mol Pharm. 2019", they used several excipients as non-viral gene carriers, and ,in Kanemura H et al., Hepatol Res. 2008, they performed gene transfer under hypertonic stress similar to the hydrodynamic injection.

Figures, tables and raw data is enough to publish.
Experimental design: Not enough. The authors should establish gene doping mice model and investigate the effect of gene doping using that model.
Validity of the findings: The novelty of this research is poor. Because the clearance of naked plasmid DNA from the body is well-investigated since 1990s.
Additional comments: no comment


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

Input:
Title: FORELIMB MUSCULOSKELETAL-TENDINOUS GROWTH IN FROGS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Manuscript #40988 “Forelimb musculoskeletal-tendinous growth in frogs” dealing with the musculoskeletal-tendinous system variation in frogs through ontogenetic perspective while taking into account potential impact of species assignment and locomotor mode.
Manuscript is clear with technically and grammatically correct English and well structured. Introduction section is relevant to the topic with appropriate literature cited. Hypothesis is well defined and relevant as there are only few studies dealing with the ontogenetic variation of the musculotendinous system. Raw data shared.
Experimental design: Research is within aims and scope of the journal and fills knowledge gaps in the fields of anatomy, morphology, evolution and development of anurans. Analyses were done on the seventy-seven specimens belonging to seven anuran species. Sample size is rather small for some species (e.g. Xenopus laevis) with only one or two specimens from specific age category. However, robust and rigorous statistical procedures with the resampling give results that are reliable. Material and methods are clear, easy to follow and easy to replicate.
Validity of the findings: Results and conclusions contribute to the better understanding morphological variation, development and evolution of musculotendinous system in anurans.
Additional comments: Specific comments:
Lines 3, 5, and 7. Replace a,b,c with 1,2,3
Line 142. Erase “Descriptive statistics and” as in Supplementary file only individual values are given.
Line 162. Erase “)” from the end of the line
Suggestion. In order to make results more transparent add table with allometry coefficients and CI intervals as supplementary file (similar to Table 3 but with calculated numerical values instead of +,-,=).


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: FORELIMB MUSCULOSKELETAL-TENDINOUS GROWTH IN FROGS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Clear paper

References sholud be revisited

Good structure of the paper. But Figure 1 must be revisited and a Table with "ecological requirements" of the studied species should be useful

Descriptive paper. Please indicate the tested hypothesis into the last paragraph of the introduction
Experimental design: OK. But only one varialbe (length used).

The study is rigorous and stats seem to be very good.
Validity of the findings: In my opinion, this paper can be published in a more anatomical or herpetological journal. Adding Table with locomotor modes, testing the modes (indicating the results) should be useful.
Additional comments: The paper present nice results. But some points must be clarified or emphasized:
- Hypothesis
- Selection of the species and thier modes of locomotion
- Figure 1 should be revisited


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: FORELIMB MUSCULOSKELETAL-TENDINOUS GROWTH IN FROGS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Article is written in clear English language with appropriate literature referenced. Introduction section was corrected according to reviewer suggestions. Additional tables were added as a supplementary files upon reviewer request that make results more transparent. Hypothesis were clarified upon the request of reviewer which improved clarity of manuscript.
Experimental design: Experimental design is clear and all analyses are rigorously performed.
Validity of the findings: Conclusion section is corrected according to the reviewer suggestions, supports the results and its easy to follow.
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: CAMPSITES, FOREST FIRES, AND ENTRY POINT DISTANCE AFFECT EARTHWORM ABUNDANCE IN THE BOUNDARY WATERS CANOE AREA WILDERNESS
Review round: 2
Reviewer: 1

Output:
Basic reporting: I commend the authors, as this paper is well written with sufficient background, results, and discussion.  However, there are some minor edits that I recommend:

- There is inconsistency in the use of "Boundary Waters Canoe Area", "Boundary Waters", "Boundary Waters wilderness", "BWCA", etc. to refer to the study site.  I believe that the official name is Boundary Waters Canoe Area Wilderness (BWCAW).  The authors should use the full name at first mention, introducing the acronym in parentheses, and thereafter use the acronym.

- Line 68-70, This sentence is awkward, suggest rephrasing.

- Line 78, Here you use epigeic but later you use epigenic (Line 284).  Keep consistent.

- Line 119, Need to specify if this citation is 2017a or 2017b

- Line 192, Delete A and start paragraph with Structural Equation Modelling....

- Line 211, Correct Poison to Poisson

- Line 267-269, See also Shartell et al. 2015 for earthworm relationships to anthropogenic activity.

- Line 286, Missing a word?  Need to fix this sentence

- Line 290, Insert the word "on" after effects

- Line 339-342, This is the opinion of the authors and I don't believe this citation should be used. The cited paper is not on earthworm removal (see comment above, this cited paper is related to anthropogenic use and earthworms). You could search the literature for research related to removing earthworms.  For example, Madritch and Lindroth. 2009. Removal of invasive shrubs reduces exotic earthworm populations. Biological Invasions.
Experimental design: The question and methods are well defined but how it is relevant to management is not fully addressed.  Why is this information meaningful and how can the results be used to improve conservation and management of this wilderness area?
Validity of the findings: I believe the findings are valid and interesting.
Additional comments: Nice work.  I think this paper is ready for publication with the minor edits above.  I had a few thoughts that do not need to be included in this paper, but could spark future work.

What is the probability of multiple introductions on earthworm metrics.  What anthropogenic features are more likely to lead to multiple introductions, and thus effect richness, etc.

I was also curious about the understory plant spp diversity, and whether the plants were mainly native or if exotics/invasives were present.

Do these islands have a past history of fire (prior to Pagami Creek Fire)?  How might that have an effect on earthworms?  Is the reduction of earthworms after fire temporary?  How long do fire effects last?


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: CAMPSITES, FOREST FIRES, AND ENTRY POINT DISTANCE AFFECT EARTHWORM ABUNDANCE IN THE BOUNDARY WATERS CANOE AREA WILDERNESS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The paper meets all of these standards.
Experimental design: The paper meets all of these standards
Validity of the findings: The paper also meets these standards
Additional comments: This is a nicely done study with interesting results. There aren’t any major flaws in the design, data collection of analyses or interpretation. The number of samples per island, and size of each sample on the ground, the way samples were handled in the lab all seem well founded. It is good that they measured both density and biomass of earthworms. I am not surprised that islands within lakes turned out to be independent for purposes of the study—that is in agreement with what I have found in the BWCAW. Finally, explaining almost half the variance in a SEM model is quite good for this type of study. The positive campsite effect on worm biomass seems very reasonable and well supported by the data, with a p-value of 0.001 in GLM analysis. I think the explanation given in the discussion for why earthworm biomass increases further into the wilderness, is reasonable. It does relate to human behavior and use of live bait. I leave it to the authors to decide if they want to make any revisions to the discussion in response to points 1 and 2 below, and following that there are some minor editorial items numbered 3, 4, and 5:

1. The study captured some of the effects of the fire, 4.5 growing seasons after it occurred, and obviously those effects would have been more prominent 1-2 years after the fire and will gradually disappear with time since fire. However, the snapshot after 4.5 growing seasons still contains useful information given how little we know about fire and earthworm interactions.

2. Regarding the discussion about the positive effect of worms on understory plants (lines 292-299). The  the explanation might be that the study is detecting places where environment was good for both plants and worms—in other words pockets of deeper soil on this rocky landscape, and that SEM can’t really show those two-way relationships (in fact, I don’t know of any statistical methods that can do that).

Minor comments:
3. Line 130,  40% is not ‘mostly’
4. Line 192, reword, either say 'A Structural Equation Model was used...' or 'Structural Equation Modelling was used...'
5. Line 290—missing word—‘on these variables’?


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: FULL-ANNUAL DEMOGRAPHY AND SEASONAL CYCLES IN A RESIDENT VERTEBRATE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors demonstrate how cyclic variability can describe variations in monthly demographic rates for a resident tropical lizard.  The objective of identifying the advantages to full cycle demographic rate estimation is useful, however the authors overstate the novelty of this approach.  The authors examine within year variability of survival and migration rates.  It is relatively common to examine variations of within year survival rates for many species of mammals, birds, and reptiles, particularly for non-migratory species (game species in particular provide a wealth of literature on this).  That is not to say the objective is not worthwhile, but the authors repeatedly mention how very few studies examine this and that is not correct.
While there are many studies that do examine within year variations in demographic rates, the authors are correct that it is more common to examine demographic rates during a single season (usually the breeding season).  These single season assessments are useful in tracking population changes and examining how annual fluctuations in climate or habitat, etc. relate to these demographic estimates.  Since the authors are advocating for more research on the full cycle demographic variability, it would be useful to put the introduction and discussion into the context of when the different types of estimates should be used, and when a single season approach may be insufficient.  What specifically can we do with a full cycle demographic data that we could not do with a single season estimate?  When should we bother with the full season?  How would management or conservation change with that information?
If the introduction and discussion were restructured to emphasize the information gained from a full cycle approach and the implications of that information for conservation or ecology, then the discussion the species biology could be more easily incorporated into the study objectives.  Currently, the species specific information is disjointed with the rest of the paper.  But if comparisons are made back to how this additional information can be useful (and is not obtained in single season demographic assessments) it would help tie the paper together.
Experimental design: Line 144: What is the error rate on identification for this method?
The robust design approach used assumes closure within a month and allows for instantaneous transitions between months.  Describe the possible implications for this assumption and how might the results be impacted if transitions are not instantaneous.  The approach is acceptable, but you should recognize how the interpretations are impacted by this design.
Validity of the findings: Lines 203-206: The logic here was confusing.  Why did the survival drop after reproduction when the previous sentences suggest survival might be lower during reproduction?
Lines 212-214: Why is the high newborn emigration probability explaining the scarcity of juvenile demographic information?
Line 221: Authors should discuss other reasons where capture rate might increase that is not related to activity rates. Is there any reference that supports this?  Could the capture rates not vary with resource availability or predator levels that are not directly correlated with activity only?
Lines 251-253: This sentence is great and finally helps me see your argument for examining full cycle demography.  Bring information like this to the introduction and expand on it here!
Additional comments: Line 26 (and line 47). Specify wildlife demography or similar, human demography generally refers to different criteria.
Line 50: Authors state we often lack sufficient resolution in our observation.  But lack the resolution to do what?
Line 63: “represents annual events” is unclear.
Line 77: Give examples of temporal predictors.
Line 78: Avoid using ‘they’, what are you referring to here?
Line 160: Explain how 11,011 trap-days is achieved.  How many days vs how many traps.
Line 190: Be more explicit than “broaden the understanding”.  I’m still unclear on the benefit of the study from this sentence.
Line 194: The ~6500 species of lizard worldwide?


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: FULL-ANNUAL DEMOGRAPHY AND SEASONAL CYCLES IN A RESIDENT VERTEBRATE
Review round: 1
Reviewer: 2

Output:
Basic reporting: For the most part, the writing and other reporting are clear and well done.
Lines 73 – 75: I would add temperature and rainfall to the list of possible temporal drivers.
Lines 75 – 76: The paragraph this sentence is in is a bit confusing. If I’m reading it correctly, the authors could make it clearer in this sentence by confirming that “temporal drivers” and “temporal predictors” are referring to the same things in somewhat different contexts.
Study species section should make clear when hatching occurs and when newborns become adults. Can individuals transition from newborn to adult within the study year?
Line 190: Specie’s population biology should be species’ population biology, I think.
204: “but may present survival decrease due to basking activity…” should be rephrased. Something like “but may have lower survival due to basking activity…” might work.
205: “30% to 35%” should be “30% or 35%,” I think.
Line 238: See comment on line 190.
Figure 1 is compact and information-rich (only figure), and that is admirable. But it’s a bit tricky to make out many things. The symbols should be larger or in some other way clearer, as it’s hard to tell them apart. The heading should designate the period of study, in part to make the x-axis a little clearer. If I understand the figure correctly, the results from model 2 show neither uncertainty (credible intervals) around the cycles nor the monthly random effects. At least the first of these (preferably both) should be included, especially given the high uncertainty shown around the model 1 results. These changes may require splitting the results up into more panels or more figures.
Experimental design: In general, the experimental design seems sound and well described.
Lines 73 – 90: This is a key paragraph for the justification of this approach. It is true that data on relevant “temporal predictors” are often not available. Temporal drivers offer more than understanding the importance of temporal variability, however. Ideally, they indicate the proximate or ultimate drivers of it. As such, they provide a somewhat more mechanistic approach to understanding temporal variability in demography than the cyclic approach worked out here.
Line 100: May want to define SVL
Lines 109-111: Section on determining class by length doesn’t make a lot of sense. Are sizes never in between?
Lines 124-129: May want to make clear apparent survival opposite of permanent emigration, not temporary
Lines 131-133: Why is pent a nuisance parameter? Isn’t that recruitment? I think the case may be different in the Rankin paper, where dolphins must acquire marks (naturally?) before they can be entered into the CMR dataset. In addition, there was informal language in this sentence.
Line 167: This would be clearer to me if the species information had spelled out the annual cycle of this species a bit more. When in the year is the hatchling phase?
Validity of the findings: In general, the approach and the findings seem valid. However, I have one set of serious concerns, all related to the strength of inference that can be made about full-annual-cycle (FAC) population dynamics from this study.
1)	I can’t speak for my coauthors or others that have written about FAC population modeling, but for me, a key component is modeling *events* that happen within the year, or in some sense capturing dynamics with consequences beyond the year. Why do cycles in survival, emigration, or recapture probabilities within the year matter for long-term population dynamics? What would a population model parameterized with annual demographic rates get wrong in this case (assuming the population census was timed correctly within the population model)? Some speculation might be required here, of course.
2)	In general, there is a lot of inference made from one year of data (see specific comments below).
3)	FAC population modeling is about modeling both within and between years. This manuscript is about demographic estimation, not population modeling, of course. But understanding population dynamics requires understanding year-to-year variation in demography at least as much as it requires understanding within year variation in demography.
This is not to say I think this study is useless or that it requires more years of data to be published. I believe this study is valuable and the approach used is interesting and potentially useful for other studies. But I think some of the claims in the introduction and discussion about what was accomplished need to be tempered.
Was Model 2 designed before or after looking at variation in vital rates (e.g., through running Model 1)? In other words, was it developed a priori or post-hoc? Either is fine, but it’s good to be explicit, and with only one year of data, the answer affects the strength of inference for cycles in general.
Statement in lines 188 – 190 may need more than one year’s data to justify.
Lines 206 – 208: This sentence goes too far in a few ways, I think. Although carryover effects have been demonstrated in many other species, the authors have not proposed a mechanism for this one or explained why the survival cost of breeding would come a few months later. There may be many other things that differed over that period compared to the rest of the (or that) year – there’s little evidence presented that the drop in survival probability was due to reproduction.
Lines 209 – 210: Why would lower energetic reserves lead to temporary emigration?
Lines 210 – 212: This explanation makes more sense to me. I think it should be elaborated on a bit.
Lines 246 – 248: Again, what’s the justification for this claim? Why should the reader believe that the pattern over one year represents something more general?
Lines 253 – 256: I’m not sure this is a point specifically illustrated by the results.
Lines 256 – 257: Not demonstrated with only one year of data.
Additional comments: No additional comments


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

Input:
Title: THE BODY PLAN OF HALSZKARAPTOR ESCUILLIEI (DINOSAURIA, THEROPODA) IS NOT A TRANSITIONAL FORM ALONG THE EVOLUTION OF DROMAEOSAURID HYPERCARNIVORY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript fills the requirements for being considered for publication in PeerJ. It is concise and well-written, and only needs minor changes.
Experimental design: Methods are sufficient and accurate
Validity of the findings: The findings are totally supported by the evidence presented in the MS and include interesting novel data
Additional comments: I congratulate the author for suhc interesting contribution that sheds light on the poorly known and enigmatic theropod Halszkaraptor. It is a very valuable contribution