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 DYNAMICS OF CIRCULATING SARS-COV-2 LINEAGES IN BOGOR AND SURROUNDING AREAS REFLECT VARIANT SHIFTING DURING THE FIRST AND SECOND WAVES OF COVID-19 IN INDONESIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this study, Prasetyoputri et al. present genomic surveillance data for SARS-CoV-2 sequences selected from regions in Indonesia. They show that the virus lineage composition changed from the first to second infection wave based on this data set and they describe the virus lineages and mutation profiles detected.

I have some technical questions, suggestions for improvements and also further remarks that should be considered before publication that I mainly list in the “General comments” section.

Sequencing data was uploaded to GISAID. Figures should be provided in higher quality/ resolution for the final publication.
Experimental design: The experimental design is sound. The data set is quite small (202 sequences) but this is also mentioned as a limitation in the paper and it is surely difficult to get samples and perform sequencing in certain areas.
Validity of the findings: The authors present a basic study of SARS-CoV-2 sequencing data that is especially interesting due to the not so well described B.1.466.2 lineage that dominated the first wave. Interestingly, B.1.466.2 also shows the amino acid change P681R in the spike protein which is nowadays also known from overtaking Delta lineages (convergent evolution). Besides, the findings are not surprising in international comparison with Delta dominating in most countries nowadays. However, I really appreciate the effort of the authors because I can imagine that taking samples and establishing such sequencing and analyses systems is not easy in certain areas. Thus, the authors provide insights into the lineage compositions during the two waves in Indonesia, however, their results are also clearly limited by the low sample size of 202 sequences (which is also discussed as a limitation).

On a side note, I checked our German database for SARS-CoV-2 sequences for B.1.466.2 out of curiosity: I can find three sequences of this lineage that were obtained via random sampling in March 2021. All three have the S:P681R and S:N439K changes you also describe. They should also be on GISAID.
Additional comments: [1]
Background: Second sentence, “various”, “variants”, “varying”. You could rewrite this sentence a bit to avoid usage of similar wording

[2]
Objectives: This is not a complete sentence. Maybe “We investigate the ...:”

[3]
I think it is more common to write “S D614G” or “S:D614G” instead of “S_D614G”. However, this might also be a personal preference. Most importantly, it should be consistent throughout the manuscript which it is as far as I checked.

[4]
In this context, it is also not super accurate to write about a “mutation” when actually referring to an amino acid change. For example: “In the spike protein gene, S_D614G and S_P681R mutations ...”. It is more accurate to write “changes” or at least “non-synonymous mutations”. This is also a minor point, because all readers will understand what is meant here by “mutation”. However, you might want to go through the text once more carefully in this context.

[5]
Results: You write that “Most notably, S_T19R, … , and S_D950N mutations were only observed in Delta variants” Why is this so important? These are characteristic changes of Delta and so for me it is not so surprising that they are, for example, not in B.1.466.2.

[6]
Do you have any idea about the importation of Delta to Indonesia? Did they check GISAID sequences in addition to sequences you obtained? Do you have travel metadata associated with your sequenced cases?

[9]
Line 83: “nine large clades” I think you are referring here to the Nextstrain lineages? Or GISAID nomenclature? If so, this should be mentioned.

[10]
Besides the publication about the Pangolin nomenclature system, there is also now a publication about the tool itself which is worth citing.: https://academic.oup.com/ve/article/7/2/veab064/6315289

[11]
Line114: you used Ct already before, consider moving the abbreviation explanation “cycle threshold” some sentences above (Line 109)

[12]
Thanks for the already detailed description of used bioinformatics software and tools. Can you also provide some information on the version of the used ARTIC pipeline? I’m not entirely sure but I think they provide release versions of the pipeline via their GitHub repo. Line 138… “and classified the basecalled reads based on the respective barcodes.” Can you add information if the demultiplexing was done based on single or both barcodes? Demux via both barcodes at the end of an amplicon read is recommended to avoid “barcode bleeding”, however, you will lose some coverage. The option can be set in MinKnow and I’m not sure what the default is in case you used that.

[13]
Methods “Assembly Quality”: What do you mean by “calculated the total raw output base” or “calculate the total raw base”? Do you mean that you calculated the per-base raw-read coverage based on mapping to the Wuhan reference genome? Please be precise. Did you perform any quality-control of the resulting SARS-CoV-2 consensus genome sequences? For example, did you check for the N content? It’s possible that you have some amplicon drop outs which will cause longer N stretches in your consensus sequences. When the N content is high or occurs in important regions like the Spike gene, it gets difficult to reliably call the correct lineage.

[14]
Line 149: “SAM tools” → “SAMtools”

[15]
Line 151: Can you add which version of PangoLEARN you used within PANGOLIN v3.1? Actually, that’s important because the version of PangoLEARN defines which models you used for the machine learning task in lineage assignment. When you re-annotate the lineages of your 202 sequences with the most recent versions of PANGOLIN/PangoLEARN: do the assignments change a lot? I dont’ expect you to redo the whole analyses then, it’s more important to know that your annotations were done with certain models that were up-to-date at the time of analyses but now might have changed.

[16]
Results, Line 158: Can you add here again in which time period these 202 samples were taken?

[17]
Line 160: “A. Patients were male ...” ? is there a number missing here? Something like “160 patients were male ...” Ah, now I see: you refer to Figure 1A and 1B (please remove the dot between “1. A” and “1. B”). However, the Figure 1 in the manuscript does not have subfigures A and B. You mean Figure 2?

[18]
Line 164: “In total, we obtained a complete genome with 20% of total samples were categorized as low coverage by GISAID” Sorry, I can't follow this sentence. Do you mean something like “ Only 20% of our reconstructed genomes were classified as low coverage by GISAID” Although, I’m not convinced that 20% is a low amount here. This also brings me again to my question about the N content of your reconstructed genomes. I think GISAID uses something like a 10% N content cutoff, while others are even more restrictive with e.g. only allowing 5% Ns in the genome.

[19]
Line 167: “Larger coverage depths were obtained with higher total base outputs.” This is obvious, so I suggest removing this sentence.

[20]
Line 173: “B.1470” is this lineage missing a dot? → “B.1.470”

[21]
Line 186: “to the the”

[22]
Line 190: 200/202 had S:D614G, I guess the other two had low coverage in that region or an amplicon drop out? Because (almost) all B lineages should have S:D614G.

[23]
Line 194: “[A] summary of mutation spots”

[24]
You are always talking about “local variants” from the first wave (B.1.466.2, …) and Delta variants from the second wave. Although I think this is the likely scenario, you did not show that what you call “local variants” was not also some introduction from other countries. For sure, it’s likely that Delta was introduced from outside but also that is not shown. So although I get your point to distinguish the lineages of the two waves like that, I suggest rethinking the wording. Sure, the many new mutations in Delta point towards an introduction into the countries. Suggestion: consider changing the corresponding text parts to something like “We also observed that Delta variants carried various mutations that differ from variants detected during the first wave” instead of “local variants”. Or disclaim once that you are referring to variants from the first wave as “local variants” although it’s not shown how they emerged (evolved locally, introduced from outside, ..)

[25]
Line 214: I would argue that in a certain geographical area continuous evolution surely plays one role, but also the introduction from other areas (via travel, …) adds another layer. As stated before, it’s quite likely that the Delta variant was introduced and then took over your “local” variants. And did not evolve in your geographical region how the sentence could be interpreted. I just suggest rephrasing.

[26]
Line 250: I doubt that all these genetic changes are linked to increased transmissibility. Please clarify. E.g. at least weaken the sentence via “There is evidence that some of these genetic changes”

[27]
It is interesting that the local variant you describe B.1.466.2 has S:P681R which then also occurred in Delta (https://outbreak.info/compare-lineages?pango=Delta&pango=Alpha&pango=Beta&pango=Gamma&pango=B.1.466.2&gene=ORF1a&gene=ORF1b&gene=S&threshold=75&nthresh=1&sub=false&dark=true) as you describe. So this points towards convergent evolution at this specific site. I think you could emphasize this point a bit more, which could also explain why B.1.466.2 was successful during the first wave.

[28]
Is there anything known about S:N439K that you describe in B.1.466.2?

[29]
Line 261: “The mutation highly correlates with loss of smell (anosmia).” Is there a study to cite?

[30]
Lines 271-277 I think this can be shortened because information about P.1 or other lineages from Brazil does not really add value to the story.

[31]
Figure 3: It is difficult to distinguish the colors clearly from the small legend. Maybe add for the important lineages again the labels directly into the plot, at least for the higher peaks.

[32]
Figure 4: Phylogenetic tree. The tree and visualization are difficult to interpret and can lead to wrong assumptions. I don’t think that it is a good way to present a selection of lineage representatives in such a tree. For example, AY.* sublineages emerged from the parental B.1.617.2 lineage which is not visible from this tree. Also, certain B.1.* sublineages are descendants of the B.1 lineage, etc..  You only have 202 sequences so I suggest building a complete tree with all of them. It should be feasible to calculate an MSA and tree, e.g. with mafft and IQtree. You could also consider calculating a time tree to add date information from your metadata.

[33]
Please check all Figure labels in the main text. I found some mistakes where the wrong Figure is referenced, e.g. Line 194 “Summary of mutation spots is presented in Figure 4.” which is the tree.


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 DYNAMICS OF CIRCULATING SARS-COV-2 LINEAGES IN BOGOR AND SURROUNDING AREAS REFLECT VARIANT SHIFTING DURING THE FIRST AND SECOND WAVES OF COVID-19 IN INDONESIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The abstract is concise and summarizes the content of the paper effectively. Within the background portion of the abstract (line 32), specify “highest number of cases of COVID-19” as of what point in time? This will provide some context as to the time period into the pandemic.

Your introduction is very clear and concise, highlighting the advent of the emergence of SARS-CoV-2 and its impact within the population in Indonesia. Some minor grammar edits include proper capitalization in the proper names for SARS-CoV-2 (line 62-63) where it should be “Severe Acute Respiratory Syndrome Coronavirus 2, and COVID-19 (line 63-64) where it should be Coronavirus Disease 2019. For line 68, expand “WHO” into “World Health Organization (WHO)” and clarify when (date, at least month and year) that the total of 245 million cases were detected. This once again gives a concept of time within the pandemic. Minor punctuation edits on “4.7 million” (line 81) where a comma is in place of a period. The general layout of the publication is easy to follow and organized well. Figures, however, seem to be low quality (as in resolution of the images). Zooming in shows high pixilation and should be improved.

It is appreciated that the consensus sequences generated from the sequencing process was submitted into GISAID. However, the raw reads themselves (removed of any reads that align to the human genome i.e., GRCh38, should be deposited into NCBI BioProject for reproducibility of the data collected for the surveillance of COVID-19 in Indonesia.
Experimental design: The methods used are appropriate for long-read sequencing methods. This includes sequencer and bioinformatic pipelines. On line 116, it states that ARTIC v2 and v3 protocols were used “with some modifications” and I would request the direct changes be mentioned immediately followed this statement to be unambiguous and for what reason these modifications were made.

As mentioned before, the sequencing and bioinformatics methods (lines 132-142) are clear with steps and software noted with their associated versions. However, Nanostat (line 148) and “SAMtools” (line 149; correct spelling) are missing their corresponding version numbers. Additional parameters should be included for software analysis for reproducibility. For plots constructed in R (line 154), it would be worthwhile to have the corresponding R code including any preprocessing of data deposited within a Git repository (i.e., GitHub).

Line 164 in your Results section describe a “custom set of multiple primers” whereas in the methods it states “nCoV-2019/V3 primers” (line 119) for SARS-CoV-2 genome amplification. Some clarification is needed here in either the results or methods. If a custom set of primers were used, then a list of sequences should be provided as part of the supplemental information.
Validity of the findings: I appreciate the thorough breakdown of the data, namely examining the lineage distribution across different parameters of the population, even looking variants and sex differences, i.e., which variants infect different sexes more. The general size of the data is sufficient is dependent on both case load and sample quality. It is addressed as a limitation with a note describing population density (line 290-291If you used the ARTICv3 primers on your high Ct samples, was it insufficient to properly recover the genome? Prior evidence suggests it may work even in low virus titer (as seen in Nasir, J.A., et al Viruses 2020;12(8):895.).

Minor edits:
-	Line 160 and 162: fix spacing for Figure 1.A and 1.B; perhaps remove the period between them (i.e., Figure 1A and 1B)
-	Line 186-187: Wuhan-Hu-1 reference sequence can be replaced with “MN908947.3” as you already referred to this strain (unless you refer to a different accession, in which case please specify)
-	Line 191: Small syntax error where it should say “S_D614G” mutation
Additional comments: The paper is a valuable addition, highlighting surveillance of the ongoing COVID-19 pandemic and providing a retrospective look on COVID-19 cases within Indonesia. It is a well written paper with only minor grammatical revisions needed. However, sone clarification on the methods is needed for improved reproducibility including version numbers and namely parameters for the software. Any code used in R should be publicly viewable (this can be alongside your figures) since preprocessing is part of the toolkit. All raw data should be available in the appropriate databases, namely NCBI BioProject for raw reads. Sequences are available in GISAID and provided as supplementary material. The conclusions of the paper highlight the diversity in SARS-CoV-2 lineages and the dominance of the Delta variant over subsequent waves. The value of genome sequencing is reiterated as a continued power in detecting and later responding to the variant (be through monitoring and public health, or research).


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 DYNAMICS OF CIRCULATING SARS-COV-2 LINEAGES IN BOGOR AND SURROUNDING AREAS REFLECT VARIANT SHIFTING DURING THE FIRST AND SECOND WAVES OF COVID-19 IN INDONESIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The language is clear, literature is appropriately cited and raw data (sequence upload GISAID) are shared. Thanks also for providing the R code for plotting.
Experimental design: The experimental design is sound and the bioinformatics methods are appropriately described.
Validity of the findings: The presented findings are clear and supported by the data.
Additional comments: Thanks for the thoughtful revision. I am satisfied and my raised points were addressed. I just have two minor suggestions:

1) Please check the sentence
l314-315
"A study employing molecular dynamic simulation [study] further confirmed ... "
Should the last [study] be deleted?

2) Tree, Figure 3
Thanks, this tree is much better than the previous one! But I recommend removing the labels at the nodes. They are not readable anyway. Also, you could maybe color also the branches and not only the nodes to it's better visible which parts of the tree correspond to which lineage. I can recommend https://www.iroki.net/ if you have the newick tree file available. You can also provide a metadata file to easily color the lineages differently.

Thanks!


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 DYNAMICS OF CIRCULATING SARS-COV-2 LINEAGES IN BOGOR AND SURROUNDING AREAS REFLECT VARIANT SHIFTING DURING THE FIRST AND SECOND WAVES OF COVID-19 IN INDONESIA
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: All my previous concerns have been dealt with accordingly or explained!


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 PROGNOSTIC AND CLINICOPATHOLOGICAL SIGNIFICANCE OF DESMOGLEIN 2 IN HUMAN CANCERS: A SYSTEMATIC REVIEW AND META-ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: In the article the authors have reviewed the current literature to establish the prognostic value of DSG2. The results are interesting and is useful to understand the relationship between the level of DSG2 expression and prognosis of cancer patients.

The article is written in a simple way which is easy for the readers to understand. Spaces are missing at some sentences (such as line 31, between 'in' and 'the'; line 34, in between 'to' and 'cancer'; line 42, in between 'of' and 'DSG2'; and few other places). Please go through the manuscript once thoroughly for such minor errors.

The discussion part has enough literature survey but I would strongly recommend including a little more detail about the articles included in the review in the introduction section.

The figures and tables are useful for understanding the result. However, the table headlines are a little messy. If possible please change the font size and column width so that the words fit properly in the same line.

The review, especially the subset studies seems interesting and can lead to further useful research on this topic.
Experimental design: The selection of the articles and the filtering process has been explained in a detail and easy-to-understand way. The only thing I would suggest is adding a little detail about the 'invalid line' mentioned in line 91.
Validity of the findings: The validity of findings are interesting. Additionally, this finding can lead to clinical studies on the topic.
The discussion section is very well written with useful citations and valid points on the limitations of the current work.
Additional comments: I would strongly recommend adding a list of abbreviations used for readers' convenience.
In line 118 what do you mean by 'The included studies contained more than 40 cases'?
The reference format of Chen L, 2018 (line 243) seems a little different to me. Please cross check once.

With the above mentioned minor revisions taken care of, the manuscript has enough contents to be published in PeerJ.


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 PROGNOSTIC AND CLINICOPATHOLOGICAL SIGNIFICANCE OF DESMOGLEIN 2 IN HUMAN CANCERS: A SYSTEMATIC REVIEW AND META-ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Wang and colleagues have investigated the prognostic potential of DSG2 in different types of cancer by a systematic review and meta-analysis. Although this is an interesting topic, there are several major issues that should be taken into consideration before the paper is published.
There are several grammatical and syntax errors, and typos (e.g., “no-small” (line 149), “meat-analysis” (line 294)). The entire manuscript should undergo thorough revision. The figure captions should also be more self-explanatory; more detailed description is needed.
Experimental design: Regarding Methodology, a more adequate description is required. For example, in the keywords it is not clear the alternative wording and the combination of different words used; also, some major informative keywords are missing like “survival” or  “prognosis” or “survival”. It is not clear what the authors mean by “pathological methods”, and also whether any studies published in a non-English language were included in the analysis. The authors do not explain how they extracted data from the survival curves.
Validity of the findings: The major limitation of this study is the rather limited number of eligible studies. Therefore, any inferences or conclusions made should not be hasty. The authors could also supplement their study with relevant data/information from other sources like The Cancer Genome Atlas (TCGA).
In order to improve the accuracy of their results, the authors could have performed Sensitivity analysis of each eligible study or assessed publication bias.
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 PROGNOSTIC AND CLINICOPATHOLOGICAL SIGNIFICANCE OF DESMOGLEIN 2 IN HUMAN CANCERS: A SYSTEMATIC REVIEW AND META-ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript has been improved significantly.
Experimental design: Improved.
Validity of the findings: Improved.
Additional comments: All the suggestions have been included satisfactorily. I would recommend accepting the publication.


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

Input:
Title: THE PROGNOSTIC AND CLINICOPATHOLOGICAL SIGNIFICANCE OF DESMOGLEIN 2 IN HUMAN CANCERS: A SYSTEMATIC REVIEW AND META-ANALYSIS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The comments have been taken into consideration and addressed adequately by the authors. Yet, English language should be improved. For example, Line 50: ...as it can be functional...” could be changed to “can function as both...”; Line 80: diagnosed with cancer via pathology...” A more accurate technical term should be used to describe the method used for cancer diagnosis. Moreover, assertive language should be avoided like “Based on currently available evidence, the association of DSG2 expression with prognosis was context dependent.” Given also the relatively small number of eligible studies, this sentence could be revised “Based on the findings of this study, high DSG2 expression is associated with worse prognosis in patients with nonsmall-cell lung cancer.”
Experimental design: The methods are described quite sufficiently. However, more explanation is needed regarding the overall survival data derived from TCGA, that is, the clinical features of the selected patients (days to death?) , as well as the R package used for data processing and analysis (join.Cox package?)
Validity of the findings: All data used in the meta-analysis are provided and they are statistically sound.
The Conclusions also largely support the findings of this study.
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: BIRD PROTECTION TREATMENTS REDUCE BIRD-WINDOW COLLISION RISK AT LOW-RISE BUILDINGS WITHIN A PACIFIC COASTAL PROTECTED AREA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The writing is very clear and the literature review is comprehensive.
Experimental design: This is a very well-written paper that takes advantage of a unique field situation to implement a pre- post design to evaluate the efficacy of Feather Friendly (FF) bird protection materials again ORNILUX bird protection.  More intervention studies of bird protection are welcomed.  This one has a bit of a challenge in that the FF intervention is compared to another bird-friendly design (ORNILUX) instead of a true untreated control group, pre and post.  The choice of ORNILUX for the comparison group was really dictated by the site, which provided a spatially close building to the treatment area, which happened to have ORNILUX installed.  Ideally, the authors would have had an untreated control building as well, but that is not how the real world provides buildings.  Nevertheless, the efficacy of FF is demonstrated, despite the fact that it was competing against another efficacious treatment.  The findings are what one expects to see for a pre-post design with a comparison group.  The FF treatment shows fewer collisions than its own pretreated state and the decline in collisions for FF across time is steeper than the change in ORNILUX, which happens to show a slight increase.
Validity of the findings: There are a few concerning features that I would encourage the authors to address.  First, the fact that the authors collapsed the systematic with the incidental observations could be problematic if the incidental observations were biased in favor of greater detection of carcasses for the pre-treatment areas.  That is, if everyone was concerned about the amount of the bird death at the Science Complex and they really paid attention to carcasses between systematic observation days there, but not at the comparison building, then results could be biased by the inclusion of the incidental reports.  The only way to really tell is to redo the analyses without the incidental reports.  I suspect the pre- post significant difference at the Science complex would be sustained (the change would be 34 pre-treatment to 2 post-treatment). But I’m not sure the numbers would be sufficient for model convergence for the comparison site, which changed from 3 to 4 collisions across the two periods.  The reason one adopts a systematic observation schedule is to avoid these kinds of challenges to claims of internal validity.  The fact that incidental reports were treated as if they were systematic,  and that there were so many of them, despite the fairly frequent systematic observation time interval, was concerning.  Anything the authors can provide to assure the reader that this potential bias did not alter the results would be welcomed.  Had those incidentals been left on the ground, most would have been detected at the next systematic observation time, I suspect, given how persistent carcasses were when left out for scavengers.
Second, it is not clear how the authors included “feather smears on windows” (line 188) as data, or if they just used these smears as motivations to look especially carefully for carcass evidence.  If the smears were in fact used as data, it would be useful minimally to indicate how often that happened.  In addition, it would be useful to state how you kept smears from being repeatedly counted.  Many window collision studies do not include smears as data.  I have not used it because the smears often cannot be removed after observation, because the windows are too high.  The concern would be that it can be difficult to note the location of smears to assure that observers only count the smear the first time it is observed.  Please comment about whether this could be a problem in this study.  I wondered if counting smears as data also explained the unusually large number of unknown species (37 I believe).  This may be useful to comment on as well.
Third, I found it difficult to match up what was described in the data file compared to the text.  The text mentioned 364 surveys during pre-treatment and 362 post-treatment.  I assumed this would mean researchers observed building 1 and 2 364 times during pre-treatment, but this is clearly not the case.  There are 1,451 lines of data instead of the larger number that would be required by my reading (i.e. 13 facades X 364 observations = 4,732 lines of data in the Excel file, just for the pre-test, without including separate lines of incidental observations).  It would help the reader if you can clarify several things here, in case other readers want to replicate your findings.  Please clarify whether, during systematic observation, all facades were observed once and each observation led to an entry in the Excel file.  I notice that "building.side" is not evenly distributed, so there are clearly not an equal number of observations across facades.  The data show 693 occurrences of something labeled b1.1, which I believe should be building 1, façade 1.  But then there is only 1 for b1.10?  and 2 for b1.11?  In general, the excel file needs more information to help the reader identify the variables.  I would recommend simply adding a tab where you define each variable.  Also, it would help to create a text box that contains the commands that were actually run for the models tested.  I am assuming, for example, that your dependent or outcome variable is "count.area", based on what I read in the text, but it would be good to see the actual commands to confirm this guess.
One not-so-common innovation in the study was useful, and I would encourage the authors to bring more attention to it.  The authors used façade as their unit of analysis, not building.  This was a smart choice, in that facades on the same building often radically differ in their collision numbers, so it makes sense to focus on facades to understand variability.  This could make targeting of treatment areas more efficient and cost-effective. It also supplies the data analyst with more “level 2” units (using HLM terms) within studies that contain small-scale interventions. This can help with model convergence in small studies.  I wish I had realized this opportunity when conducting my own studies, but I was influence by what was standard practice back then of treating each building separately.  The authors noted that façade 8 had a high number of collisions, but it would be useful to give a sense of the numbers of collisions across other facades as well.
Additional comments: The rest of my comments are minor matters that can be addressed with word changes, sentence editing, or minor additions.

Minor points  (identified by line number)
52, 56, and 61:  There is a tendency to rely on the term “urbanization” to define risky areas for birds.  I would encourage use of the term “developed” instead.  Otherwise, readers might think the authors believe only urban centers pose risks.  Some spectacular risks, like at the world trade center, have been linked to urban areas, but other research shows how risks are especially high for one- and two-story buildings, which can be found in abundance in suburban and rural areas.  In fact, some have found rural areas more risky than urban (Kummer et al. 2016) and that large buildings in low-urbanized areas may be especially risky (Hager et al. 2017).  No building with windows is off the hook for responsibility for bird collisions, so it is useful to use words that blame buildings, not necessarily the urban location of the building.  If the authors have data suggesting we should assign more responsibility to urban locations, then please share it.

107 and elsewhere:  ORNILUX is described as not visible to humans, when the application is visible if one gets close to an ORNILUX window.  Or, if the building used a truly invisible ORNILUX fabrication, it would be useful to describe the particular name or model number that is invisible.

135:  I recommend ending the sentence with:  “, based on tunnel testing.”  This helps underscore your point that current recommendations for bird-friendly glass treatments are seldom tested in the field.

172:  As noted above, it was difficult to figure out how many observations of each façade of the building occurred.  It would be useful if you could say “all study facades of both buildings” were systematically observed on the same day, between 2 and 5 times per week” or something to that effect.
162:  I recommend here or elsewhere that you report on the cost and funder for the intervention.  Lots of people who read bird collisions studies ask me how to get these interventions funded and I have no good answer, except to encourage other researchers to include these details.
207:  Thanks for including all your software choices.  For clarity, I recommend pulling out the one that did the heavy lifting on the mixed model.  Something like:  “The generalized linear mixed model utilized the lme4 package in R”
210: Never heard of a bobyqa optimizer, but it sounds like something that might be useful in small studies?  Can you please supply a few words of description for it?
262:  This sentence could be clearer.  Perhaps you could add but not “compared with treated glass in” 2016-2018
288:  I’m not sure if it is generally thought that ORNILUX or fritted glass would need exterior protection in addition to what they already have, if this is what the author is suggesting.  For example, fritted glass has the protection baked into the glass, not on the exterior surface, and it is still effective.  So I am not sure that every preventive measure is now thought to need exterior markings as well.  It is an interesting question, so perhaps it could be brought up as an area in need of future research.  What trade-offs exist for the less aesthetically pleasing fritted glass vs. markers on the exterior of the glass.  Which would protect better?  It is not known and would be difficult to know in a field setting with pre- and post-test.
293: Can you please provide a cite for commercially available UV markers for glass exteriors?  I know that American Bird Conservancy has listed some of the stick-on markers as effective, but it was not clear how long such temporary stickers last and how effective they are (the ABC web site does not list a threat rating for them).
298:  Again, unless the version of ORNILUX you are working with is different from the one I have seen, it would be more accurate to say they offer “relatively unobstructed views.”
301: Another limitation might be cost.  I was told that adding UV windows would add 1% to construction costs over standard windows, which is pretty costly.  I gather that the authors do not think retrofits are costly though, so maybe newer materials are cheaper.  It would be good to supply more cost details, if possible.
334:  time-consuming
348:  a citation is needed here—you could use the ABC site for model legislation or building standards.
353:  cost-effective?  My experience is very different from what is suggested here.  Only if the death of a bird can be assigned a high cost would this a fritted retrofit be considered cost-effective where I work.  A retrofit implies that clear glass windows were installed but due to bird deaths are replaced with fritted windows.  First, people object to fritted glass creating a blurry view;  if they have had a clear view that gets removed and frits installed, then the difference is really noticeable.  I imagine there would be lots of worker complaints about this solution, even if it saves birds and energy costs.  The newly constructed building I examined with fritted windows was relatively safe for birds but the frits produced lots of anecdotal complaints from building users.  Second, I was told that no windows ever would be replaced on any building unless the building itself would be renovated, in order to save costs and fit within the building renovation schedule.  If you have a more hopeful story about how the windows received frits at this site and details of the funding amount and source for the Feather Friendly intervention, it would be useful to hear.  When I was trying to fund an intervention I was cautioned that many environmental donations are less than $10,000, which means that many office buildings would be too costly to mitigate, unless fundraising is unusually good.  I would love to hear about why the authors think this is relatively easy to accomplish.  Perhaps the lawsuit in Canada makes building owners take bird deaths more seriously?
362: Again, it would be useful to flesh out the details with examples of what product would be available to protect residential windows for less than $40.00.
389 and elsewhere (e.g., 429, 457, 467, 470, 473, 489):  Citations should not have capitalized words across the title.
442  something is wrong with the repeated “preprints” in this reference.  Should not be a preprint from this date but rather a full published citation.
512  Connell should be O’Connell.
Table 1:  The text needs a closed parenthesis before the semicolon:  )); It would be useful to include what the outcome variable is.  I believe it is not the raw  number of collisions but rather collisions by glass area, yes?
Figure 1:  dikes, not dykes.  Generally, I find it useful in scientific papers to avoid identifying things by color, given that readers may print out papers on black and white.  This would be time-consuming here so I’m just leaving it as a suggestion.
Figure 4:  Requires a color print to match the wording in the text; ideally, this could be conveyed with some other graphic, such as hashed lines or dots.  I am not used to seeing non-linear graphs presenting the same spacing between .01 and .10 as between .10 and 1.0 along the bottom axis.  Is this based on a log-transform?  Could you explain that in the text that accompanies the figure?
I wonder if it would be easier to get your point across by replacing the Figure with a table that would present the raw numbers of collisions and the IRRs (95% CI).  For example, you could have one row for FF and one for ORNILUX.  The columns would contain the pre-treatment collision numbers, post-treatment collision numbers, and IRR values (95% CI).  In my minds eye, such a graphic would get across the strong results in a quicker fashion, instead of having the reader wonder about the metric along the bottom axis.  Just a suggestion; this may be the preferred style of presenting IRR data from this particular statistical package, which I do not use.

References

Hager SB, Cosentino BJ, Aguilar-Gómez MA, Anderson ML, Bakermans M, Boves TJ, Brandes D, Butler MW, Butler EM, and Cagle NL. 2017. Continent-wide analysis of how urbanization affects bird-window collision mortality in North America. Biological Conservation 212:209-215. DOI 10.1016/j.biocon.2017.06.014
Kummer JA, Bayne EM, and Machtans CS. 2016. Use of citizen science to identify factors affecting bird–window collision risk at houses. The Condor 118:624-639. 10.1650/CONDOR-16-26.1


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: BIRD PROTECTION TREATMENTS REDUCE BIRD-WINDOW COLLISION RISK AT LOW-RISE BUILDINGS WITHIN A PACIFIC COASTAL PROTECTED AREA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is well-written and clear. I have made some specific comments on how to improve it below.
Experimental design: The experimental design is appropriate and follows standards form other bird-window collision studies. For the statistical analyses, I suggest adding an additional variable, please see specific comments below.
Validity of the findings: These findings are much needed and give us hope that we can reduce collisions with the appropriate collision deterrents. The findings are sound and result from disciplined sampling and data analyses.
Additional comments: You have a really nice paper showing some great results from a longish-term dataset, cool stuff! I like how you have kept it simple and clear, and you made a real effort to report all the previous literature, excellent!

I have two major comments and revisions I would like for you to make, which I believe will make your paper stronger and even more clear to the readers:

1.	Incorporate % glass into your models. Calculate the % glass cover for each of your buildings and use that as a variable in your GLMMs. This will help you control for the differences in proportion of glass in each of the buildings, and it will help understand how this variable interacts with others. This is important because % glass has been proven to affect collisions, besides just total glass area.
2.	Re-structure and re-write discussion. Currently, your discussion and conclusions have all that is needed, but the text is rather disorganized and way too long in conclusions. In the discussion section I made a specific suggestion as to how you might structure your discussion.

One last general comment: I still have one minor confusion which is why you divided the Ornilux data in 2013-2015 and 2016-2018. Maybe you need to do a better job at explaining why these data were separated in periods because there was no before-after for this building. My understanding is that you compared the Ornilux 2013-2015 to the untreated Science building. But then what did you compare Ornilux 2016-2018 with? Perhaps this is already in the paper but it was not so clear to me, which might be similar to the readers.

Introduction

You have done a really good job at summarizing and reporting the existing literature and knowledge on bird-window collisions. This introduction is well-written, appropriately supported by literature, and adequate for your paper, well done!

Ln 95 – Maybe also mention the UV-reflective films that are available
Ln 103 – Is there a citation that could back this up? I don’t personally know of one but there might be one out there…
Ln 122 – Please also review https://peerj.com/articles/4215/
Ln 137 – Perhaps a single main objective here would be good such as “Evaluate the effectiveness of glass treatments to prevent bird-window collisions”, and then you can describe the two products and situations (before-after, only-after) that you studied.

Methods

Statistical analyses are sound and appropriate for the questions you are asking. But I suggest you add % glass as a variable to the models and re-run everything.

Ln 159 – It’d be great to have the % glass which you can get by calculating the façade area and using the glass area you have already calculated
Ln 162 (Figure 2C) – Specify which panel of the figure shows the specific thing you are mentioning, in this case the retrofit
Ln 171 – Same as above. Calculate % glass
Ln 175 – Before you say 730 surveys. Please check the numbers throughout

Results
Ln 230-240 – All this text can be summarized in a table that shows collisions per building, time period, and has columns for survey or incidental. Please provide this summary table and in the text only highlight important findings, for example the % collision reduction after retrofit.

Discussion

You have most of the important points between the discussion and the conclusion text, but it is rather disorganized currently. I suggest you write an outline of the discussion (subtitles which you could delete later) and start from local to global. So, start by talking about your results and how they relate to other studies (which you have done). Then talk about collision deterrents in general and its limitations (cost, aesthetics), and maybe close with the part about policy, public engagement, and some of that text you have in the conclusions

Ln 316 – Exactly…so you need to report this difference and maybe account for it in your models

Conclusions

Here you need to start strong and report that FF reduced collisions by 92% in a before and after study, while Ornilux only in xx% compared to an untreated similar building. That should be the very first sentence.

Your conclusions are way too long and read more like a discussion. Move some of this text to the discussion (only if really required there) and leave here just the results of your study, and perhaps a recommendation sentence for future studies. Keep it short and clear. Should not be longer than 4 short sentences. Conclusions are better off without references, keep these in 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: BIRD PROTECTION TREATMENTS REDUCE BIRD-WINDOW COLLISION RISK AT LOW-RISE BUILDINGS WITHIN A PACIFIC COASTAL PROTECTED AREA
Review round: 2
Reviewer: 1

Output:
Basic reporting: In general, this is a much clearer version of the manuscript.  It is especially reassuring to know that systematic and anecdotal observations were not  mixed together in the analyses.  The ms. was strong to begin with and a few more revisions should make it a bit more reader-friendly.
Experimental design: The design is fine.
Validity of the findings: Findings are valid but I have some suggested rewording.  I only have one area of major concern and apologize that I did not raise this earlier.  I believe it is just a clarity issue, which can be addressed with minor editing. Below I have pulled original text from the ms. and Table 1 and provided a suggested set of revisions, with my comments to explain why the revisions were needed, in my view.

Original, Line 229 -231
We evaluated support for three models as shown in Table 1. Using a base model with random-
effects (year and observer) and season, we compared a building-only effect model, season and a
treatment effects model.
Original:
Table 1
Fixed effects: treat.grp = building by year treatment Science Complex Pre-FF (2013-2015), Science Complex Post-FF (2016-2018), Annex Ornilux (2013-2015), Annex Ornilux (2016-2018); building = Science Complex or Annex; season=Winter, Fall, Spring or Summer.
Random effects: 1|year = monitoring year, 1|obs = observer. Offset = window area ΔAIC =change in AIC relative to top model, w = Akaike weight., and df = degrees freedom.

Model structure 				AIC 	ΔAIC w 	df
treat.grp + season + (1|year) + (1|obs) 	335.95 0 	1.00 	9
season + (1|year) + (1|obs) 			349.63 13.68 	0 	6
building + season + (1|year) + (1|obs) 	350.25 14.30 	0 	7
(1|year) + (1|obs) 				352.78 16.83 	0 	3

Suggested revision, line 229
We compared a baseline model, which contained only year and observer random effects, against three alternatives that added fixed effects.  These additions included tests of building and season, season only, and the full model with treatment effects, which was represented by the combination of building and time period.
 Suggested revision, Table 1: I added the “Row” column to Table 1 to ease referencing.
Row	Model structure 				AIC 	ΔAIC w 	df
A	treat.grp + season + (1|year) + (1|obs) 	335.95 0 	1.00 	9
B	season + (1|year) + (1|obs) 			349.63 13.68 	0 	6
C	building + season + (1|year) + (1|obs) 	350.25 14.30 	0 	7
D	(1|year) + (1|obs) 				352.78 16.83 	0 	3

Comments
I suggest the revisions above because it seems odd to see that Table 1 has 4 rows of effects but line 229 refers to 3 models.  Also, the sentence, “Using a base model with random-
effects (year and observer) and season, we compared a building-only effect model, season and a
treatment effects model” does not seem accurate, because the base model is row D, the random effects only, yes? Here the AIC is largest, so you are progressively accounting for more variability by adding the fixed effects for rows C, then B, then A.

Original, Lines 255-258
When competing models based on standardized survey data corrected for differences in area of
glass were compared, the best supported model for predicting collision risk was the model that
included the building's treatment group, versus the building-only or base model (year, observer
and season; Table 1).

Suggested revision, Line 255:
Competing models, based on standardized survey data corrected for differences in area of
glass, compared simpler models to the full model.  The full model, testing the combination of building and time period, demonstrated the best model fit. The full effects model provided the greatest reduction in AIC, compared to a random effects model testing year and observer only (Row D, Table 1), a model adding season alone (Row B), and a model adding building and season (Row C).

Comments
I suggested this revision because it was confusing for me to try to figure out why something called a “building-only or base model” would have a fixed effect (building) in the base model, given that you have the more basic Row D.  Also, as I read the Rows, there is not a Building-only model, which I assume would have building, year, and observer.  It was not clear to me whether your phrase “building-only or base model” was referring to one or two models (is the building-only the base model? Or are you describing a building only model in addition to a base model?).

Also, you note that I suggest you refer to the treatment effect as the combination of building by period instead of building by year (“treat.grp = building by year”), because your data (although using words, not numbers) and degrees of freedom look like you handled the three pre-treatment years and the three post-treatment years as two different periods.  That is, with numeric coding your period variable would be coded 0, 1 (for 2013-2015 and 2016-2018) not 1-6 for years 2013-2018.

I do not care that you adopt these exact wording changes, but I hope that, by bringing up these suggested changes, you can see where the reader might be confused when trying to match the table to the text.  If I were writing this I would refer to a “building by period interaction,” but I understand that phrasing derives from an old analysis of variance framework, which you did not explicitly test (i.e. by including a period-only main effect model).  So I referred instead to a combination of building and time period.
Additional comments: Minor points/suggested wording changes for clarity (by line number from revised submission)

89-90.  I’d omit “that they fail to perceive and avoid.”  You make the full point in the next sentence, which is very clear.  This sentence makes me think that birds are failing to perceive an unobstructed route, when in fact they are falsely perceiving an unobstructed route.

102: by “static object” I think you are referring to the markers but this could be clearer.  I suggest: ,and therefore the color of the visual markers  must provide …

218: Data were, not data was

286:  “recommendations that were”  change to “these recommendations were”

350:  American English would be “fueled,” not “fueled.”  Not sure which one PeerJ wants.

364:  change ; to , or perhaps make text past the semicolon into a new sentence, given how long this sentence is.

381:  change are to is


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: EVALUATION OF CHANGE IN TRABECULAR BONE STRUCTURE SURROUNDING DENTAL IMPLANTS BY FRACTAL DIMENSION ANALYSIS AND COMPARISON WITH RADIOMORPHOMETRIC INDICATORS: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: Comments are attached.
Experimental design: Comments are attached
Validity of the findings: Comments are attached
Additional comments: Comments are attached


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: EVALUATION OF CHANGE IN TRABECULAR BONE STRUCTURE SURROUNDING DENTAL IMPLANTS BY FRACTAL DIMENSION ANALYSIS AND COMPARISON WITH RADIOMORPHOMETRIC INDICATORS: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this study, Karadag et al. aim to investigate the correlation of fractal dimension change with morphometric indices, mandibular cortical index, and mandibular cortical width and their correlation pre-and post-operatively in a retrospective study. Based on the collected data, they found, as expected, FD values were increased in the mesial, distal, and apical regions at the 3rd-month measurements. However, no relationship between FD and MCI or MCW was observed. Although the experimental design is easy to follow and the results are scientifically fair, the study failed to show a robust, innovative approach.
Experimental design: Although many studies in the literature have extensively investigated the same area, the presented methodology is acceptable for answering the research question.

Suggestions:

The author listed that the systemic conditions were challenging to have ( whereas it is clinically not acceptable to miss such data), the status, e.g., fully dentate or partially dentate edentulous, is critical to include.

Importantly, the Manufacturers of included implants are critical to list.

Authors are encouraged to use a Full PANORAMIC X-Ray in addition to the magnified ones in FIG. 1
Validity of the findings: Findings and conclusion are fair and clearly linked to the original question.
Additional comments: 1.	Proofreading for the English language is suggested.

2.	The limitation of the study should specify those panoramic radiographs represent a two-dimensional image of a three-dimensional structure. Although CBCT is not routinely used in every patient who presents to a dentist, the volumetric analysis provides valuable data. Three-dimensional analysis performed with CBCT will undoubtedly give more valuable volumetric 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: EVALUATION OF CHANGE IN TRABECULAR BONE STRUCTURE SURROUNDING DENTAL IMPLANTS BY FRACTAL DIMENSION ANALYSIS AND COMPARISON WITH RADIOMORPHOMETRIC INDICATORS: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 3

Output:
Basic reporting: The text is written in correct English.
The selection of literature items is appropriate, and these are relatively new items.
Figure 1 regarding the Klemetti method is probably redundant unless the authors indicate or draw on  the figure which criteria they used to assign to each category
Table 1 and Figure 2 should be adjusted to be more understandable.
Experimental design: The authors used the Klemetti method, which was originally used to evaluate 77 postmenopausal women. Therefore, they should indicate this fact as a limitation of this method.  Alternatively, authors can refer to other studies in which the age and gender factors have been verified.
The structure of the study group, demographic data and gender should be placed in the material and methods section.
The description of the test group is superficial. Factors such as general health, comorbidities and habits, including smoking, were not considered.
In the beginning, the authors distinguish 3 ROIs: mesial, distal and apical, for which they define the fractal dimension. However, for comparative studies, they calculate the arithmetic mean from all three regions. It isn't easy to understand the basics of doing this. While the mesial and distal regions have similar characteristics and their connection makes sense, the apical region is different.
The criteria for the location of the ROIs on both sides of the implant are unclear. What if the area includes compacted and spongy bone? What if the bone level around the implant has lowered after a healing period of 3 months?
Validity of the findings: Table 1 is hardly readable, the position of column “total” in the table is illogically located.
Figure 2 does not explain the doubts about the precise location of the areas, aROI-2 contains a small fragment of the implant in its region - this is probably an unintended situation and should be adjusted correctly
The authors report that the study included implants of various sizes. Was this factor statistically insignificant in the evaluation of the results?
Additional comments: In the abstract section, I suggest that you omit the part about the discussion. Moreover, the last sentence of the discussion is a re-description of the result described in the results section.
Authors should speculate more about why MCI and MCW parameters correlate with the FD dimension change. Is the attempt to link the mean FD dimension with MCI and MCW not the weak point of this study?


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

Input:
Title: EVALUATION OF CHANGE IN TRABECULAR BONE STRUCTURE SURROUNDING DENTAL IMPLANTS BY FRACTAL DIMENSION ANALYSIS AND COMPARISON WITH RADIOMORPHOMETRIC INDICATORS: A RETROSPECTIVE STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: Errors in the English language have been corrected
The selection of literature items is appropriate, and these are relatively new items.
Figure 1 regarding the Klemetti method was improved with the necessary details placed within the x-ray images.
Tables 1 and 2  were adjusted to be easier to understand and follow the manuscript's main text.
Experimental design: The authors used the Klemetti method and successfully clarified the intention to do so despite the different age/sex characteristics of the study group.
The structure of the study group, demographic data and gender were moved in the material and methods section.

Information about the position of ROI and the intention for separate statistical calculations was explained.
Validity of the findings: Table 1 and Figure 2 were corrected according to suggestions
Additional comments: Suggestions from the initial review are now included in the manuscript; I also welcome the changes suggested by other reviewers


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: TRANSCRIPTION FACTOR 7-LIKE 2 SINGLE NUCLEOTIDE POLYMORPHISMS RS290487 AND RS290481 ARE ASSOCIATED WITH DYSLIPIDEMIA IN THE BALINESE POPULATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article was written by Safarina G Malik, et al is a valuable article and provides useful information, However, there are some issues that can help improve the work and can be accepted after solving these issues.
This study aimed to investigate the association of TCF7L2 intronic SNPs rs290487 and rs290481 with dyslipidemia in the Balinese population. The SNPs’ influence on metabolic abnormalities in selected Indonesian population. The findings support the notion that TCF7L2 SNPs have a significant impact on lipid metabolism.
a.	Should mention about the genetic model in result/discussion part whether how related to dyslipidemia
b.	Subgroup Analysis of dyslipidemia with or without diabetes and obesity as TCF7L2 SNPs associated with metabolic diseases.
Experimental design: The manuscript is well written and technically sound. However, there are some points to be considered in the revision of the manuscript:
a.	The rationale of SNP selection would be elaborated.
b.	Define the metabolic disease (diabetes/obesity) in section subject and as in table 1.
c.	% Error of ARMS-PCR method and mention how random genotyping confirmed by Sanger DNA sequencing.
Validity of the findings: In this study, the author reported the impacts of individual genotypes and a haplotype of the rs290487 and rs290481 SNPs on dyslipidemia and individual lipid profile in the Balinese. This population has been exposed to westernization and urbanization brought by rapid tourism development.

It would be more interesting if the authors mention the genotype/haplotype comparing other populations especially in the Asian population and related to tourism as mentioned in the conclusion part.
Additional comments: To make this manuscript much readable, some key data from the experiment could be considered to reorganize as graphics in Figure 3, such as rs290481 genotype and lipid profile level and some proposed mechanisms.


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: TRANSCRIPTION FACTOR 7-LIKE 2 SINGLE NUCLEOTIDE POLYMORPHISMS RS290487 AND RS290481 ARE ASSOCIATED WITH DYSLIPIDEMIA IN THE BALINESE POPULATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: This clinical study has investigated the associations two SNPs of transcription factor 7-like 2 (TCF7L2) gene viz. rs290487 and rs290481 with altered lipid profile in the Balinese population. The authors have done SNP genotyping and serum lipid profile analysis from 565 subjects from four locations in Bali province. They report existence of significant associations of these TCF7L2 polymorphisms with dyslipidemia and altered lipid profile in these individuals. Although the study appears simplistic and lacks translational value, the clinical findings reported appear to be novel and have the merit for publication. There are several concerns that need to be addressed before the study can be considered for publication in its current form.
Experimental design: One of the major shortcomings of the publication is that the SNPs are associated with dyslipidemia in general which can be broad and cover a number of diseases. The authors are recommended to use clinically used Frederickson classification of dyslipidemias and associate each of these SNPs to the specific type of dyslipidemia. This will greatly add to the value of this publication and shed more light on the specificity of the genetics involved.
Validity of the findings: No comments
Additional comments: Major comments:
•	The authors have reported no significant association of SNP rs290487 with dyslipidemia. Hence, the title appears to be misleading for the future readers and should be revised accordingly to include either only rs290481 or change to specific significant associations.
•	Table 1: n(%) for Sex must be reported separately as %of total Males and %of total females separately for two reasons: 1) Total number of Males used in the study is much higher 2) Percentage of dyslipidemic subjects compared to percentage of non-dyslipidemic subjects appears to be lower in both males and females. This will add clarity for future readers.
•	Looking at the baseline characteristics, it appears that TG levels are the most altered (over 2-fold increase) in dyslipidemic individuals studied compared to levels of other lipids. This underscores the importance of studying the mechanistic role of these TCF7L2 SNPs in triglyceride metabolism and/or storage. Are there any prior studies where these SNPs or other mutations in TCF7L2 gene have been shown to play a role in the pathogenesis of hypertriglyceridemia? If yes, the authors are encouraged to cite them. If not, the authors are encouraged to expand on this interesting observation and comment in the discussion section.
•	The authors do mention a limitation of being unable to measure HOMA-IR index. However, if the authors have access to blood samples they are encouraged to measure and report HOMA-IR index in the revised submission. It would address a very critical question of the involvement of the degree of insulin resistance in these individuals.
Minor comments:
•	Table 1: Please report Age for Males and Females separately
•	Line 224: Please change ‘specific adipocyte’ to ‘adipocyte-specific’
•	The paper can use a thorough revision of grammatical errors throughout the discussion text
•	Table 2: The authors are recommended to present significant associations in the forms of Manhattan plots, this will give a better idea of the variability in the 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: TRANSCRIPTION FACTOR 7-LIKE 2 SINGLE NUCLEOTIDE POLYMORPHISMS RS290487 AND RS290481 ARE ASSOCIATED WITH DYSLIPIDEMIA IN THE BALINESE POPULATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: No further comments
Experimental design: No further comments
Validity of the findings: No further comments
Additional comments: No additional comments


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

Input:
Title: THE BIOGEOGRAPHY OF BENT-TOED GECKOS, CYRTODACTYLUS (SQUAMATA: GEKKONIDAE)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The figures are excellent and the reconstructions of biogeographic history are also very good. There is an important missing reference - Xu et al. 2020 - see my comments further in the article.
Experimental design: Most of my review will be contained in the 'Validity of the findings' section - In terms of experimental design, the paper lacks explicit comparisons to past work with the purpose of providing a hypothesis that will likely be robust to future additions and improvements in sampling and methodologies.
Validity of the findings: In my opinion, in order to publish a paper with no new data, the bar for analyses and results have to be higher in order to justify the publication. This bar was not met for this paper for a number of reasons. I think that the paper is worthy of publication, but only after addressing a number of issues and improving the paper substantially.
Here is an overview of the issues needed to make the paper acceptable for publication:

1. The biggest thing missing from this paper are quantitative and qualitative comparisons to previous work which, if completed, would allow a prediction about how robust the biogeographic conclusion are and how sensitive the conclusions are to 1. improvements in sampling 2. improvements/changes in methodology of reconstruction 3. Increased knowledge surrounding the nuclear genes and past introgression events.
By making these comparisons and addressing the issue of repeatability, this paper could be the new standard for Cyrtodactylus biogeography. Without these comparisons, it is not clear that this paper provides any unique insights into the biogeography of this group. If I had to guess, I would say that this paper is congruent with other biogeographic interpretations of the group  and will be robust to the addition of taxa and improvements in methodologies in the future, but concluding that requires careful comparisons.

2. The supplemental data is not sufficient and needs substantial editing and additions. A more complete description of the data both the text of the manuscript and in the supplemental data are needed.

Details regarding the above 2 points:
1. The following needs to be done in order to assess how different and robust this biogeographic hypothesis is:
First, to what degree is the biogeographic hypothesis in this paper different from Wood et al. 2012 and from Xu et al. 2020?
Xu et al., was not cited in the manuscript, but is important to consider - Xu, W., Dong, W.J., Fu, T.T., Gao, W., Lu, C.Q., Yan, F., Wu, Y.H., Jiang, K., Jin, J.Q., Chen, H.M. and Zhang, Y.P., 2021. Herpetological phylogeographic analyses support a Miocene focal point of Himalayan uplift and biological diversification. National science review, 8(9), p.nwaa263.
Xu et al. contains biogeographic hypotheses for both the Himalayas by itself, and an analysis that includes more categories - 6 areas for Cyrtodactylus. See the supplemental data for tree graphics and the trees with branch lengths included. Non-Cyrtodactylus geckos could be pruned out for these comparisons.
Are the trees the same? Because sampling is so complete, it would be possible to trim the number of taxa down to exactly match Wood et al. and Xu et al.
Are the topologies the same? If not, use Bayes factors to estimate how much they differ. How different are the analyses used to estimate the trees in all three cases?

Given a careful comparison of the topologies, if there are any differences in biogeographic reconstructions, do the differences in topology account for those differences? If the biogeographic hypotheses are the same, then it suggests that it may be robust to future additions of taxa and improvements in methodology.

My guess is that all three of these have congruent topologies and congruent biogeographic hypotheses. It is possible that the only difference is that the current manuscript is better resolved and included more areas than Xu et al. A quantitative proof of that guess would help to improve the importance of this paper.

Point 2 above: The supplemental data is the supplemental data from the Grismer et al. 2021 Diversity paper unchanged. The references in the supplemental table are relevant for that Diversity paper, but not for this one. The references need to be replaced with the sources for the Genbank entries for each species, Wood et al. 2012, Griser et al., etc.
For some of the species, the number entered is not a Genbank number, but is a specimen number.
Here are those entries with no genbank numbers:
C. cf. brevipalmatus	arboreal	herein	brevipalmatus	USMHC 2555
C. tibetanus	general	K. Wang. Personal communication, 2019	tibetanus	YPX1413
C. zhaoermi	general	Shi and Zhao [144]	tibetanus	YPX1433

 The Xu et al. paper has genbank numbers for the C. tibetanus, and C. zhaoermi

The supplemental data should include the nexus file with all of the sequence data for the analysis in this paper, along with the tree files with branch lengths for all of the results.

The sequence data in this paper is presented as being ND2 plus 5 tRNAs, but the sequence data presented falls into 2 categories, some of this variation in sequence completeness needs to be addressed. I don't think it will make much difference in the end, but that should be proven in the paper by either excluding incomplete sequences and showing that the results are not different, or be making an argument that the incomplete sequences are not in crucial places in the tree, or both.
Category 1, complete - Category 2, ND2 only (or less) -

If this data set is going to be reanalyzed, there are a number of newly described Indian taxa that are distinct enough to merit inclusion including - C. aaronbaueri, C. agarwali, C. bapme, and C. bengkhuaiai

The other issue that needs to be discussed if the biogeographic hypothesis is meant to be robust and long lasting is the nuclear data. Is the nuclear data presented in Wood et al. sufficient to predict future congruence of mitochondrial and nuclear data? I think a caveat needs to be made that future nuclear sequence data may prove some of the biogeographic hypotheses incorrect. For example, in Anolis, the overall biogeographic hypotheses are supported by mtDNA and are congruent with nuclear data - the anolis genome paper analyzed 96 loci and found it to be congruent with mtDNA. However, within Jamaican anoles, it was recently shown (Meyers et al., 2021 in Sys. Bio) that mitochondrial introgression has occurred making some of the previous hypotheses based only on mtDNA incorrect.
Additional comments: I have withheld from specific comments on the manuscript because the revisions are major enough, that an acceptable version would have many changes.

To summarize what would make this paper acceptable:
1) Comparisons to previous hypotheses, including Bayes factors comparing different topologies and a discussion of differences in biogeographic hypotheses.
2) An updated, revised and expanded supplemental data that includes the all the sequences, branch lengths, and appropriate references.
3) A discussion that includes speculation about the future utility of the biogeographic hypotheses presented in this paper, including the possibility of conflict or congruence of nuclear genes.


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 BIOGEOGRAPHY OF BENT-TOED GECKOS, CYRTODACTYLUS (SQUAMATA: GEKKONIDAE)
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is very well written, cites the previous literature extensively, and is structured appropriately for a study focused on presenting the results of a phylogenetic comparative method. I have only the following minor suggestions:

-there are a few places where commas are used that seem unneccessary: lines 21, 47, 248, 275, 350, 426

-the statement on lines 121-122 on region boundaries should include citations, or else state something like "see below for details" since the boundaries are discussed with citations in subsequent paragraphs.

-on line 257 "A" for the node IDs is in parentheses but that format isn't used elsewhere

-on line 306 Timor-Leste is used but from context it seems like the island of Timor is being referred to rather than the country

-there seems to be a word or words missing after "A11 diverged" on line 311. I think it is supposed to be a date or else region.

-some of the text in Figs 2 and 3, including species names, is not legible in the reviewer manuscript. This might just be because reviewers are sent lower resolution figures; if so, ignore.
Experimental design: Experimental design is straightforward. The study uses a previously published phylogeny and a new biogeographic analysis which are appropriate for the study goals. I have only a few minor comments:

-On line 123, it is noted that each species is assigned to a single geographic area. Are there any species that cross the boundaries used in this study? If there are, which species were affected and how was the "home" region defined? If not, perhaps rephrase to indicate that no species occur across the region boundaries.

-I realize the tree was already published, but it would be useful to expand slightly in a couple spots. First, was the 350 million generation length of the run just what was needed to reach sufficient ESS values, or does it have some other significance? Second, on line 204 it is noted that the backbone of the tree matches multilocus data sets, justifying use of ND2 alone. It would be worth citing the relevant studies being compared here that employed multilocus data.
Validity of the findings: In general, the conclusions are straightforward and describe the patterns observed in the timing and biogeographic analyses. I have only a few suggestions:

-Line 211 states that the best model is DEC but the table shows it to be DEC + J, and that is the model shown in Fig. 3.

-on Line 246 it is noted that the discussion uses mean dates for cladogenic events.  It would be worth stating here how broad a typical HPD range is just to provide a sense without having to refer to Fig. 3 or clutter the subsequent text.

-The introduction frames this study as an update of previous studies using a much denser phylogeny and more detailed biogeographic reconstructions. As such, it would be worth adding one sentence to the discussion describing the overall degree of agreement between these studies and the conclusions drawn here, with the caveat that only some patterns are directly comparable across studies. For example, there is one major difference with the Wood et al paper pointed out pertaining to the triedrus group, but similarities are generally not noted so a blanket statement would usefully cover this.

-Lines 338-349 posit a overland or short overwater dispersal from Indochina to the Indian Subcontinent to explain the distribution of the triedrus group. Fig. 5 shows the Indian subcontinent as adjacent to Indoburma, not Indochina, with a midsized shallow-water gap in the 35-40 million year time frame. Do the authors think that extinction in the intervening Indoburma region is a better explanation than a longer overwater dispersal that bypassed Indoburma?

-On Lines 351-353 it should be noted that the triedrus group pattern is the authors' interpretation based on the overland dispersal posited in the previous lines since there isn't direct evidence that the group formerly occupied the northern Indian subcontinent.
Additional comments: Very nice study overall. Although certainly not necessary, it would be great if some of the biological patterns were superimposed on the paleogeographic reconstructions included in Fig. 5. For example, regions inferred to be occupied by Cyrtodactylus at each time point could be more intensely colored, or arrows added to indicate dispersals similar to those used in Fig. 1.


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: COMPARATIVE TRANSCRIPTOME ANALYSIS OF COLD-TOLERANT AND -SENSITIVE ASPARAGUS BEAN UNDER CHILLING STRESS AND RECOVERY
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this study, authors have employed RNA sequencing to investigate the transcriptome dynamics of Dubai and Ningjiang 3 beans during cold stress and normal temperature recovery. The results presented show Ningjiang 3 beans have higher cold tolerance than Dubai beans at the seedling stage.

Authors should use clear and unambiguous English language across the manuscript. One such example is Abstract line 22-23 "However, the key genes and regulatory pathways that respond to low temperature in this legume are still poorly understood". These lines should be reframed. Authors should conduct thorough proofreading of the manuscript.

Line 90/Line 113 Authors should provide full forms of all the abbreviations used at the first instance of their occurrence in the manuscript for the general audience of the journal. For example SOD, DEGs

Line 180 "For genes…. stages" extra "High" should be dropped.

Line 317-319 "After low…….. Variety". This paragraph is poorly written making it hard for the reader to follow.
Experimental design: See comments below.
Validity of the findings: Line 138-140 "However, at 12h and 24h …. growth". It is not evident from Figure 1 (R12, R24 images) that there is any visual difference between the leaves of the two Cultivars. Authors should provide additional evidence supporting the claims made in lines 138-140.

Figure 2 Authors should elaborate on why the leaf fresh weight is lower for Dubai beans whereas the SOD and proline content is matched between the two bean varieties at time 0?

Figure 3 A Is there a statistically significant difference in the number of genes expressed by Dubai beans compared to Ningjiang 3 beans for the R24 time point? Line 175 of the results section authors claimed the number to be higher but there is no statistical evidence provided for the same.

Line 223-225 "Besides…. Respectively" the statement is vague and should be rewritten for the readers to follow. Zf-HD1 is upregulated as shown in Figure 5B.

 Line 317 "Some reports …. results". Please provide relevant references to support this statement.

 Tan et al. employed RNA-Seq to explore the gene expression differences between the same asparagus bean varieties with different cold tolerance under 0 and 24 hrs stress. How are the findings in the current study any different from those already reported in the literature? What is the value-add of having more time points? Authors should discuss the differences/ new findings if any between their results to those previously reported in the literature.
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: COMPARATIVE TRANSCRIPTOME ANALYSIS OF COLD-TOLERANT AND -SENSITIVE ASPARAGUS BEAN UNDER CHILLING STRESS AND RECOVERY
Review round: 1
Reviewer: 2

Output:
Basic reporting: Writeup needs a lot of edits.
Professional English edit is needed before any acceptance can be ma
Experimental design: pathetic
Validity of the findings: Invalidated results and conclusions.
Additional comments: Introduction is trash, there is no new method description in the Introduction section, what the authors want to do ? The introduction is definitely loosely written and is important relevant work in the field.
Why the two beans were selected? What is the logic behind the selection? No reference given appropriately.
Result section is definitely incomplete and data is missing and experiments have not been well thought of.
The authors say they calculated SOD content and proline content.. but why was no experiments done to probe CAT assays and APX enzyme based assays? More background information on probing proline content should be explicitly mentioned.
This paper needs  a major revamp.


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: COMPARATIVE TRANSCRIPTOME ANALYSIS OF COLD-TOLERANT AND -SENSITIVE ASPARAGUS BEAN UNDER CHILLING STRESS AND RECOVERY
Review round: 1
Reviewer: 3

Output:
Basic reporting: In this study, Miao et al. evaluated the cold tolerance of two asparagus bean varieties at the seedling stage by using phenotype, physiological indexes, and transcriptome comparison. They found some major transcription factor families and cold-responsive genes may play roles in the cold tolerance of Ningjiang 3. This research is interesting and provides a better understating of the cold stress mechanism for the two asparagus bean varieties. The manuscript is well written and easy to read. I recommend doing major revision.
Experimental design: 1. For the cold stress treatment of two seedlings, the authors changed temperatures between 25℃/5℃and  light intensity between 30,000 lx/6000 lx. And all the experiments the authors did later were based on this cold stress treatment. If the authors need to focus on the effect of cold stress on the seedling growth,  why did the authors change the light intensity? If so, all the conclusions authors obtained in this study not only resulted from cold stress but also from light density stress.
2. In figure 1, the seedlings of Ningjiang3 and Dubai bean showed different growing statuses at the beginning of cold stress (C0): Ningjiang3 looks much taller and stronger than Dubai bean, which may cause Ningjiang3 to show better cold tolerance. Thus the authors should use two seedlings with similar growth statuses in height, size, and age. If it is hard to get similar seedlings, at least the author should repeat this study with taller/bigger Dubai bean and shorter/smaller Ningjiang3 to see whether the author can obtain similar results and conclusions.
3. In this study, the author mentioned “the cold tolerance of Dubai bean at adult stage is higher than that of Ningjiang 3. This indicated that the molecular mechanisms at seedling stage and adult stage were quite different between the two asparagus bean varieties (lines 284-287).” If drew the conclusion that the molecular mechanisms at the seedling stage and adult stage were quite different, the authors should provide some evidence, did the authors check the changes of transcription factor genes and cold-responsive genes by using the qRT-PCR experiments in Figure 8 for the two adult asparagus beans after cold stress-recovery cycle?
4. In Figure 5A and Figure 6, the authors compared the differential gene expression in Dubai bean as compared with Ningjiang 3 at different stages of cold stress and recovery. For example, in Figure 5A, DC0 vs NC0, there were 3487 gene increased and 1741 genes decreased in Dubai compared to Ningjiang3, but those gene differences are not due to cold stress, similarly, not all the gene changes for DC3 vs NC3, DC12 vs NC12, and other bars come from cold stress. If the authors want to find gene changes affected by cold stress, why not do comparisons with Dubai bean for DC0 vs DC3, DC0 vs DC12, and DC0 vs DC24, DC24 vs DR3, DC24 vs DR12, and DC24 vs DR24, as well as do a similar comparison for Ningjiang3 seedlings?
Validity of the findings: Please do statistical analysis for Figure 2.
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: COMPARATIVE TRANSCRIPTOME ANALYSIS OF COLD-TOLERANT AND -SENSITIVE ASPARAGUS BEAN UNDER CHILLING STRESS AND RECOVERY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed most of my concerns in the revised version, but I am still worried about the much big different sizes of the two seedlings used in this study, which may cause the conclusions the authors claimed in this study to be inaccurate.
Experimental design: For most models used in research, we generally allow reasonable ranges for ages, size, weight, etc. Unfortunately, the seedlings of two different varieties used in this study were obviously out of a  reasonable range of size. There are several methods to fix the defect of different seedling sizes, for example, the authors can verify and confirm their transcriptome data findings in two different seedlings with similar sizes. Actually, this verification is quite important and necessary for transcriptome data, however, the authors did not try to address the issue.
Validity of the findings: The authors need to verify and confirm their transcriptome data findings in two different seedlings with similar sizes.
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: N-MIXTURE MODELS PROVIDE INFORMATIVE CROCODILE (CROCODYLUS MORELETII) ABUNDANCE ESTIMATES IN DYNAMIC ENVIRONMENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall, the paper is well-written and clear, the results are placed in the appropriate context, the background information is thorough, and the figures and raw data pass the sniff test.
Experimental design: I find the research question to be very interesting because many crocodilian species are threatened and it’s difficult to develop appropriate management plans because getting accurate population estimates can be difficult. This paper lays out a clear road map for how to generate reliable population abundance estimates for crocodilians. The experimental design is mostly solid, but there are a couple of points that need clarification (see below). In general, a bit more detail in the survey methods would be very helpful.
Validity of the findings: The findings are valid. I also have a few minor comments that hopefully will be useful (see below).

I enjoyed reading this manuscript and I hope to see it published.
Additional comments: Line 143: How did the authors estimate total length from eyeshine? Need to explain their methods in a bit more detail here.

Lines 172-173: What statistical test are the authors reporting the results for here?

Lines 176-177: How were hydric state and vegetation cover determined?

Lines 177-179: Why was this necessary to do?

Line 189: Should be “we” instead of “we’ve”

Lines 196-198 and Lines 139-140: Seems like there’s a big assumption in this study: that the crocodiles are only found on the shoreline. Is that really true for this species? Did the authors survey open water at all? If so, please describe. Also, how big are each of the surveyed aguadas in terms of surface area and perimeter? Would be good to know the size range.

Lines 196-198: Why not just add up all the local abundance estimates for each water body? Why do the authors have to do this extrapolation at all?

Lines 327-331: The use of the terms “genetically pure” and “genetic pollution” here is a bit odd to me. It reads like these are value judgements of different crocodile populations based on their potential for hybridization. Please consider rephrasing.

Lines 377-379: What is this reference? Is this a document published by the website ResearchGate? If so, is it actually citable?


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: N-MIXTURE MODELS PROVIDE INFORMATIVE CROCODILE (CROCODYLUS MORELETII) ABUNDANCE ESTIMATES IN DYNAMIC ENVIRONMENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written, well-documented, and sufficient field background/context was provided. I have some minor recommendations to improve the clarity of the information provided in the methods section, that will help readers to follow the rationale of the manuscript. Authors must include clue information such as c-hat of every important model so readers can judge the efficiency of models. I suggest sending figure 5 to supplementary material as I don't see the relevance of it. I also suggest running some extra models to shed some clarity about the effect outliers can bring to the results presented. Authors can find detailed comments in the document attached.
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: N-MIXTURE MODELS PROVIDE INFORMATIVE CROCODILE (CROCODYLUS MORELETII) ABUNDANCE ESTIMATES IN DYNAMIC ENVIRONMENTS
Review round: 1
Reviewer: 3

Output:
Basic reporting: No captions for figures. Figures need more explanation to fully evaluate.

Several minor grammatical or word choice issues. See attached document.

Lack of consistency in using the SI abbreviation m for meters/meteres.
Experimental design: In the methods it is not clear how often each site was surveyed, but I was able to determine from the data provided in the supplement that each site was surveyed 2-7 times. What concerns me the most about this, is the fact that this takes place over several years and during different seasons within a year. One important assumption of the N-mixture model you are using is that the population at each site is closed to changes in abundance. Thus all differences in counts over time are due to changes in detection probability. However, here you are using counts spanning up to 4 years and do not have any repeat surveys within a season. This is potentially an issue and should at least be explained in the methods so that readers can understand that the assumptions of the model may be being violated.
A better way to handle the question of changes in abundance over time would be to use the dynamic version of this model (pcountOpen in unmarked). However, you would still have the issue of no repeat samples within a season.
I think it is great to compare the hierarchical model with the MPS and VFM methods, but I would like to see more detail on these. For instance, when you have 7 counts made over 4 years for a site, what value is used for the MPS? Is it the highest value during that period or the mean of the 7 values? If it is the sum across the 7 samples at a site, doesn’t that risk counting a single individual more than once? I also do not understand exactly what relative abundance is as you use it and would like to see that better defined.
When it comes to the hierarchical modeling, besides my concerns over the use of data from a long time span in a closed model, I also have concerns about the way models were compared. It is worthwhile to compare the model types (i.e. parameter distributions) but it is not appropriate to compare between them using AIC. AIC should only be used within a model type to rank models not across model types. This is because the model likelihoods are different, and there is no theoretical basis for comparing models with different likelihoods. This means that Table 1 should be re-done and any reference to comparing the models using AIC should be corrected.
In addition to providing the total estimates for each method in Table 2, I would like to see the estimates of abundance for each waterbody using the various methods. To me it would be much easier to understand the differences between the models that way. Maybe this could go in a supplement?
Validity of the findings: The findings may be valid, but the model selection method needs to be revised. Also, the fact that the models used are unlikely to meet the assumptions of the model chosen needs to be addressed. At a minimum the authors should discuss this fact. I would consider throwing out the negative binomial model all together.

We must see more details on the methods for the Generalized Linear Mixed Model and the error estimation for the estimates.
Additional comments: I found this to be an interesting manuscript with some valuable information. However, I do see some shortcomings that need to be addressed. I believe that the hierarchical modeling used in this paper is a sound approach, but the dataset used in the analysis are very sparse for to put such high confidence in these estimates. It seems that the main point of this paper is to support the use of the N-mixture model for this system, but I remain unconvinced that it is completely appropriate.
On the manuscript I have made numerous comments in specific places that should be addressed. Here I will try to relay my general concerns.