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: RELATIONSHIP BETWEEN HEMOGLOBIN GLYCATION INDEX AND EXTENT OF CORONARY HEART DISEASE IN INDIVIDUALS WITH TYPE 2 DIABETES MELLITUS: A CROSS-SECTIONAL STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: Clear and unambiguous English is used throughout the text. References are relevant, authors removed older references and added more recent ones. Corrections suggested directly into the submission .pdf file were sufficiently fullfiled. All tables are structured accordingly. Supplementary (raw) data is provided separatedly. Despite being clearly presented in Table 2, I believe that there's no need for presenting "yes" or "no" numbers for "LAD disease". By simply indicating "LAD disease" on the left colum and data related to "yes" group (presence of LAD disease) would be enough to imply that the remaining individuals from the groups did not present with the disease. It, however, is not an essential modification, and authors may opt not to make further changes in the refered table. Figures are good and improve undertanding of the data, but I'm not certain about resolution; authors should make sure to provide files with at least 600dpi resolution. If such files were already provided separately, please disregard this recommendation.
Experimental design: Experimental design is overall clear and reproducible. I have no further comments on this section.
Validity of the findings: "no comment"
Additional comments: Please verify my comments on the "Basic reporting" section. Other minor sugestions are presented at the .pdf file. New recommendations are of minor relevance and authors may or may not accept such changes, considering that they refeer only to the manuscrit, not the study itself. After that, I acept the paper with no further changes.


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: RELATIONSHIP BETWEEN HEMOGLOBIN GLYCATION INDEX AND EXTENT OF CORONARY HEART DISEASE IN INDIVIDUALS WITH TYPE 2 DIABETES MELLITUS: A CROSS-SECTIONAL STUDY
Review round: 3
Reviewer: 1

Output:
Basic reporting: The article is presented in high quality.
This reviewer has no further comments
Experimental design: Design is adequate.
This reviewer has no further comments
Validity of the findings: The authors responded to all comments and suggestions made by the reviewers.
This reviewer has no further comments
Additional comments: Thank you for addressing all comments and suggestion made by the reviewers.
This reviewer has no further 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: RELATIONSHIP BETWEEN HEMOGLOBIN GLYCATION INDEX AND EXTENT OF CORONARY HEART DISEASE IN INDIVIDUALS WITH TYPE 2 DIABETES MELLITUS: A CROSS-SECTIONAL STUDY
Review round: 3
Reviewer: 2

Output:
Basic reporting: There is a highlight mark in the word "glycation" (left and right) from figure 2 - bottom boxes, I believe it's not supposed to be there. Other than that, no comment.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: CLONE WARS: ASEXUAL REPRODUCTION DOMINATES IN THE INVASIVE RANGE OF TUBASTRAEA SPP. (ANTHOZOA: SCLERACTINIA) IN THE SOUTH-ATLANTIC OCEAN
Review round: 1
Reviewer: 1

Output:
Basic reporting: Please see General comments below.
Experimental design: Please see General comments below.
Validity of the findings: Please see General comments below.
Additional comments: In this paper, the authors examined the genetic population structure of invasive Tubastraea species in the South-Atlantic Ocean by using microsatellite markers which have been newly developed by their study. Their analyses seem good and the interpretation of the results is also valid. Thus, I recommend the publication in PeerJ. I show some comments below.

When reading the manuscript first, it seemed difficult to understand the present distribution patterns of Tubastraea species used in their study. I recommend that the authors add the information in the map (Figure 1).

In the result, the lower genetic diversity around IGB for both species seems intriguing. Is IGB the marginal area for their distributions? If some environmental data such as temperatures are available, it would be informative to interpret the results (for example, please see the paper below).

Reference:
Dimond, J. L., Kerwin, A. H., Rotjan, R., Sharp, K., Stewart, F. J., & Thornhill, D. J. (2013). A simple temperature-based model predicts the upper latitudinal limit of the temperate coral Astrangia poculata. Coral Reefs, 32(2), 401-409.

L323: About the possibility of cryptic species, more descriptions may be helpful for the discussion. Please refer to the paper below too. This paper also discusses clonal diversity and the existence of cryptic species in coral shown by microsatellite analysis.

Reference:
Nakajima, Y., Nishikawa, A., Iguchi, A., Nagata, T., Uyeno, D., Sakai, K., & Mitarai, S. (2017). Elucidating the multiple genetic lineages and population genetic structure of the brooding coral Seriatopora (Scleractinia: Pocilloporidae) in the Ryukyu Archipelago. Coral Reefs, 36(2), 415-426.

Other comments:
L130: the authors should add the citation for FASTX-Toolkit.
L139 and other lines: "uL" -> "micro-L"
L139: "10ul" -> add space
L142: "MgCl2" -> "2" should be subscript.
L144 and other lines: "52°C–62°C" -> 52–62°C
L199: "hypothesis" -> "hypotheses"
L256: "were similar" -> "were higher"?
L305: "to a thoroughly examine" -> "to thoroughly examine"
Table 2: "," -> "."


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: CLONE WARS: ASEXUAL REPRODUCTION DOMINATES IN THE INVASIVE RANGE OF TUBASTRAEA SPP. (ANTHOZOA: SCLERACTINIA) IN THE SOUTH-ATLANTIC OCEAN
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript is well written. However, there are a few things that should be revised or clarified before this manuscript is published.

Line 26: azooxanthellate
Line 87: monobuoys
Line 88: citation please
Lin 165: MLL, term needs to be specific and identical in whole manuscript
Line 298-299: this sentence is not appropriate here. It is better to cite cases from animals instead of plants. There are some other examples from animals such as cnidarians that have been reported.

Table 2.  He values of T. tagusensis should be with dot.
Experimental design: There are 4 collection sites (Buzios Island, monobuoy, Todos-os-Santos Bay (northeastern Brazil), and Ilha Grade Bay (southeastern Brazil)) as described in the Materials and Methods. Why only the result of the genetic connectivity between two localities have been shown in the study?
What are the genetic structures of samples from Buzios Island and monobuoy at Sao Sebastiao channel?

Line 193: The initial burn-in is 500,000 cycles followed by 500,000 additional cycles. How the number of burn-in cycles and run length have been determined?
Line 194: why the test of K varied from 1 to 3 only?
Validity of the findings: Since the asexual reproduction is the nature of these species which could cause the low genetic diversity overall. I would suggest the authors to increase the sample size to get more understanding regarding the origin of the invasive Tubastraea which is more relevant to the goal here. For example, if these species were transferred by the vessels, is it possible to collect some samples from the harbors and compare the data with those from the other areas, so we may see a picture of how these species migrate or spread?

Since the Tubastraea was first reported in the Caribbean and is now in Gulf of Maxico and Brazilian coast. It would be great if the authors perform the phylogeographic analyses to show the relationship of these species in the Brazilan coast and other places. By doing this, this will be clear to see how the invasion affect the local population.

The Tubastraea coccinea has been shown high dispersal potential (at least on the scale of tens of kilometers) (Mizrahi et al. 2014). Although this impact might be ruled out from the sites between TSB and IGB, can it affect the populations from the locations nearby, such as the localities in the south?
Also, I would suggest the authors to add an inset in Figure 1 to illustrate the collection sites in the south, so it could be helpful to understand the geographic distance among these sites.

The results also indicated at least two different populations of T. coccinea have been introduced to the southwestern Atlantic. Is it possible to detect the gene flow? By doing this, it will be helpful to understand where is this species from.

I also suggest authors to describe the asexual reproduction mode (s) of Tubastraea in the Introduction. Do T. coccinea and T. tagusensis have the same asexual reproduction strategies? Are these modes important for the expansion of these species?
Additional comments: The study aimed to identify the origin of the invasive Tubastraea spp. along the Brasilian coast by using microsatellite approach. The results showed the high proportions of clones at two analysed localities on Brazilian coast, indicating the dominate asexual reproduction which leads the conclusion that no significant population structures have been observed. The authors also concluded that the vector transport is the cause for spreading the species along the coast.
I appreciate that the authors share these dataset and analyses which will be important for the marine conservation management in the future.


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: CLONE WARS: ASEXUAL REPRODUCTION DOMINATES IN THE INVASIVE RANGE OF TUBASTRAEA SPP. (ANTHOZOA: SCLERACTINIA) IN THE SOUTH-ATLANTIC OCEAN
Review round: 2
Reviewer: 1

Output:
Basic reporting: 1. The authors should check the English before the publication.

Line 26: azooxanthellate

2. From the response, it seems the goal of this study is not to identify the origin of the invasive population as what is said in the manuscript. To make less confusing,  I suggest the authors should remove this sentence in the Introduction "and the origins of the invasive populations remains a mystery", or modify it to something like "dispersal of the invasive population remains unclear".
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: NEW WHAITSIOIDS (THERAPSIDA: THEROCEPHALIA) FROM THE TEEKLOOF FORMATION OF SOUTH AFRICA AND THEROCEPHALIAN DIVERSITY DURING THE END-GUADALUPIAN EXTINCTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: This paper describes two new whaitsioids, and the description is informative. I agree on the identification of new taxa, but I think it is better to compare them with relative taxon to show their autopomorphies and other diagnostic characters. This part can add after the phylogentic analysis.

Figure 5 A the light is too bright
 B The position of this one seems not match the direction of light

ONLINE SUPPLEMENTARY INFORMATION is nearly identical to 2015 JVP paper, you need adjust it for this paper. Really, only the codings of new taxa are needed here.
Experimental design: For the diversity study, my opinion is similar to that of Frobisch and Irmis. You can do it and you need think about the number of specimens as well. Your main point is the earlier appearance of Hofmeyria and other species. It is better you provide a photo of SAM-PK-K10525 and other specimens (L635-L637), because they are your key evidence.
Validity of the findings: no comment
Additional comments: You said the age of Pristerognathus Assemblage Zone is (late Capitanian–Wuchiapingian) (Table 2, L917), but your figure 1 and figure 11 it is only in Capitanian.
Also, you state Hofmeyria atavus in Pristerognathus Assemblage Zone, why do you not show it on Fig 11?

Table 3 Dalongkou fuae  We showed the age is latest Permian in Fig. 1

L130 miss a ‘.’
L172, 173 References: Broom 1905, 1903
L266, L 274  repeat ‘bars the lacrimal from contacting the nasal’
L278 Fig. 3C?
L289 bar is more so than in other?
L301  dorsalmost
L432  anterior face that (should) overlap the   It is disarticulated!
L437 enclosure forming the pineal duct??
L582  Ancestral state reconstructions of early eutherocephalian dentition
The title is too big for the following content, you only state morphology and texture, change it

L588 precanine maxillary teeth?
Figure captions: remember change the taxonomical names in italic
L603  For this kind of study, my opinion is similar to Irmis. You can do it and you need think about the number of specimens as well.
L692  Micro


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: NEW WHAITSIOIDS (THERAPSIDA: THEROCEPHALIA) FROM THE TEEKLOOF FORMATION OF SOUTH AFRICA AND THEROCEPHALIAN DIVERSITY DURING THE END-GUADALUPIAN EXTINCTION
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This manuscript names and describes for the first time two previously mentioned but unnamed whaitsioid therocephalian taxa, which were in the past years collected from the upper Permian Teekloof Formation of the South African Karoo Basin. The manuscript is well written and requires only very minor editorial corrects (see track changes in doc file). The content is clearly articulated and well structured. The illustrations are sufficient and properly referenced throughout the manuscript. Beyond the description, the authors discuss the new specimens' relationships within Therocephalia and their impact on the general phylogeny of the clade. Moreover, the Discussion includes a brief treatment of ancestral therocephalian dentition (as new anatomical information from the new material provides new insights) as well as a short review of therapsid and specifically therocephalian diversification across the end-Guadalupian Extinction. All of these aspects are well integrated and provide new insights into therocephalian evolution. The only concern that I have with regards to this contribution concerns the fact that the authors assume a mostly undistorted nature of the holotype and only specimen of the second new genus, Ophidostoma. The authors mention that the type skull is slightly crushed but on the other hand disregard the possibility that the overall unique skull proportions of being as wide as long is a result of distortion rather than genuine. I don't generally doubt the validity of this taxon or the overall anatomy as described, but the images and drawings clearly indicate that the skull is massively distorted. This should be made more clear in the text and overall proportions should be taken with caution. Other than that and the few suggestions for changes (see doc file), I strongly recommend publication of this manuscript 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 PLASMODIUM BERGHEI RC STRAIN IS HIGHLY DIVERGED AND HARBORS PUTATIVELY NOVEL DRUG RESISTANCE VARIANTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: No additional comment; the paper satisfies all the criteria.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: In this study, Songsungthong et al use whole genome sequencing to examine the P. berghei RC (PbRC) strain that in earlier work by Peters was selected to be chloroquine resistant. The RC strain is deficient in haemozoin formation, has increased levels of glutathione, and was more recently identified as resistant to artemisinin. Here, the authors start by validating the reduced susceptibility to artesunate, with the RC strain approximately 8-fold less sensitive than PbANKA. Whole genome sequencing of PbRC revealed a high level of divergence from the reference PbANKA, as well as several other sequenced P. berghei genomes. The high number of variants that are unique to PbRC, almost 10-fold higher than any other strain with unique or private variants, confounds the identification of possible resistance loci that could contribute to the observed phenotypes. The authors survey possible candidates, and report SNVs in several, including PbCRT, PbMDR1, the deubiquitinating enzyme PbUBP1, and PbPI3K, but not the P. berghei ortholog of Kelch13. None of these SNVs is an obvious smoking gun, and the inability of the RC strain to form gametocytes precludes the use of genetic crosses to further dissect the resistance phenotypes.

Overall the study by Songsungthong et al demonstrate the high level of divergence of the RC strain from other sequenced strains of P. berghei, and provide a foundation from which further genetic validation of drug resistance candidates could be based.

There are a few additional points that the authors should consider. i) For the analysis of “private” variants in PbRC, it would be informative if the authors described in more detail the proportion of SNVs that are located in coding regions, are non-synonymous, and are in the core genome. ii) Gene amplification is a common mechanism of drug resistance in Plasmodium sp. Could the authors comment on whether gene amplifications could be detected, and might be a mechanism of resistance in this strain? iii) Given the inability of the RC strain to form gametocytes, were there mutations detected in AP2-G and other candidate loci involved in gametocytogenesis?


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 PLASMODIUM BERGHEI RC STRAIN IS HIGHLY DIVERGED AND HARBORS PUTATIVELY NOVEL DRUG RESISTANCE VARIANTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Well written paper that is clear and easy to understand. All the data has been shared.
Experimental design: Antimalarial drug resistance is an emerging global health issue as malaria has become untreatable in some parts of the world due to failure of drug treatment, including the current frontline therapy, artemisinin. Recent evidence show that artemisinin resistance is multi-factorial though mutations in one gene, kelch 13, show a clear association with resistance. The authors of this study attempt to identify the genetic basis of antimalarial resistance using the murine malaria parasite, Plasmodium berghei. A specific strain of P. berghei, PbRC was known to be resistant to several antimalarial drugs, including artemisinin (ART) and chloroquine (CQ). The authors hypothesize that PbRC may share some of the resistance mechanisms with drug resistant human malaria parasites. The authors use whole genome sequencing to answer this question and compare the genome of PbRC to published genomes of several P. berghei strains to identify SNPs unique to PbRC. They use Tajima's D score to identify genes undergoing selection.  The methods are described in detail and the work is well done. The story of artemisinin resistant malaria is still evolving and we don't have the complete picture. The authors identify numerous genes that may play a role in drug resistance.
Validity of the findings: The authors show that PbRC is resistant to artesunate, a water-soluble derivative of ART, with an increased ED50. Using whole genome sequencing, the authors identify several unique SNPs in the PbRC strain and convincingly demonstrate that it is quite divergent from other sequenced P. berghei strains. Unfortunately, the SNPs identified in PbRC do not match with SNPs found in artemisinin resistant P. falciparum. This does not take away from the study though as artemisinin resistance is known to be multi-factorial and our understanding of it is incomplete. The authors are careful about using the literature to make an educated guess as to which sets of genes are likely responsible for drug resistance.
However, one issue is that the PbRC strain does not form gametocytes and strains that do not form gametocytes often have associated mutations with them. The authors do not compare PbRC genome with the genome of the ANKA 2.33 strain (gametocyte non-producer) to narrow down their targets.
Another potentially useful method to narrow down the list of candidate genes responsible for drug resistance would be to assess essentiality. The authors do that for one candidate (Pbdpap3) but not for others. As the authors may be aware, this information is available for nearly 3000 genes in the P. berghei genome (Plasmogem phenotype database: http://plasmogem.sanger.ac.uk/phenotypes).
These comparisons may help the discussion to focus on drug resistance and curate the list of candidates further.
Additional comments: Please discuss why you think that host cell invasion genes are changing due to balancing selection. Its unclear how they would help/hurt drug resistance. Why would PbRC need to evade the immune system more than other strains? Maybe it has more to do with being a gametocyte non-producer than drug resistance?
It may also be useful to compare the unique PbRC SNPs with the transcriptional dataset for ART-resistant P. falciparum (Mok et al Science 2015, 347:431-35).


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: ASSESSING THE LIVING AND DEAD PROPORTIONS OF COLD-WATER CORAL COLONIES: IMPLICATIONS FOR DEEP-WATER MARINE PROTECTED AREA MONITORING IN A CHANGING OCEAN
Review round: 1
Reviewer: 1

Output:
Basic reporting: English is not clear in some cases, I have annotated the pdf to highlight ambiguous statements and in some cases I commented or provided suggestions of how I think the English can be improved. Yet I did not revise the entire manuscript thoroughly as I believe the authors should do this before submitting a manuscript for revision.
Also the manuscript uses many acronyms and it is difficult to keep track of all of them – I suggest authors should consider spelling out as many terms as possible rather than using acronyms.Other minor suggestions are noted on the pdf.

My expertise lies with tropical corals, remote sensing and climate change, not cold water corals. I am not aware of any important references that were missed, but the manuscript seems to have many self-citations. I advise another reviewer with cold water coral expertise comments on this point.

The structure of the manuscript is good, However, several figures are sub standard they need significant improvement – please see specific comments on pdf

This is a self-contained manuscript – but hypothesis are not explicitly explained.
Experimental design: Original primary research within Aims and Scope of the journal.
Yes

Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap. The submission should clearly define the research question, which must be relevant and meaningful. The knowledge gap being investigated should be identified, and statements should be made as to how the study contributes to filling that gap.
Yes

Rigorous investigation performed to a high technical & ethical standard. The investigation must have been conducted rigorously and to a high technical standard. The research must have been conducted in conformity with the prevailing ethical standards in the field.

No – my biggest concern about this manuscript is that it is not possible to determine the precision of the measurements made. Based on both the text and the figures provided it seems to me that the lines used in Image J to measure coral size could have stopped anywhere, they do not seem to stop at the top of the coral and from previous experience with similar measurements I know it can be very tricky to do this in a standardized fashion.
Unless more detail and exact method of standardization of these measurements is provided I cannot recommend publication.

Methods described with sufficient detail & information to replicate. Methods should be described with sufficient information to be reproducible by another investigator.

See comment above
Validity of the findings: Impact and novelty not assessed. Negative/inconclusive results accepted. Meaningful replication encouraged where rationale & benefit to literature is clearly stated. Decisions are not made based on any subjective determination of impact, degree of advance, novelty, being of interest to only a niche audience, etc. Replication experiments are encouraged (provided the rationale for the replication, and how it adds value to the literature, is clearly described); however, we do not allow the ‘pointless’ repetition of well known, widely accepted results.

No, see comment under experimental design and validity of measurements.

Data is robust, statistically sound, & controlled. The data on which the conclusions are based must be provided or made available in an acceptable discipline-specific repository. The data should be robust, statistically sound, and controlled.

No, see comment under experimental design and validity of measurements.

Also, images for all 18 colonies and measurements should be provided in supplementary material – not just the table of derived values. Given the rarity of these ecosystems and data, it is essential to provide the imagery.
Conclusion are well stated, linked to original research question & limited to supporting results. The conclusions should be appropriately stated, should be connected to the original question investigated, and should be limited to those supported by the results.

NA – I did not finish reading the manuscript as I don’t think it has merit unless details are
provided regarding the methodology and measurements.

Speculation is welcome, but should be identified as such.

NA – I did not finish reading the manuscript as I don’t think it has merit unless details are provided regarding the methodology and measurements.
Additional comments: This manuscript investigates the live vs dead coral tissue of 18 coral colonies in deep cold water reefs. Cold water corals are not studied enough and it is important to improve our understanding of these systems and their related organisms.

My biggest concern about this manuscript is that it is not possible to determine the precision of the measurements made. Based on both the text and the figures provided it seems to me that the lines used in Image J to measure coral size could have stopped anywhere, they do not seem to stop at the top of the coral and from previous experience with similar measurements I know it can be very tricky to do this in a standardized fashion.

Unless more detail and exact method of standardization of these measurements is provided I cannot recommend publication.

The manuscript also needs significant improvement on its English grammar, at present it is not very clear and in some instances it is difficult to understand what the authors mean. I recommend authors ask a good scientific writer (preferably whose first language is English) to revise their manuscript prior to resubmission. I have made detailed comments on the pdf.

The manuscript figures are of low quality and need to be significantly improved as well. I have made detailed comments on the pdf.


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

Input:
Title: ASSESSING THE LIVING AND DEAD PROPORTIONS OF COLD-WATER CORAL COLONIES: IMPLICATIONS FOR DEEP-WATER MARINE PROTECTED AREA MONITORING IN A CHANGING OCEAN
Review round: 1
Reviewer: 2

Output:
Basic reporting: The structure of the paper meets required standards. The language is clear and the literature cited was fairly extensive given the relatively short paper. Figures etc were clear and of good quality.

The discussion is rather disjointed in places with statements that do not seem to have a context. A little more work is needed on the discussion

The addition of a hypothesis would improve the paper. Since the authors are comparing two different sites, it would be relatively easy to formulate a hypothesis about expected differences between the sites.
Experimental design: The survey design was unbalanced, which reduced the comparative value of the study but did not invalidate it.

The study is focused on the application of a new method for assessing coral growth, and as such is useful.

I think there needs to be more detail on the abiotic factors: what the values were and how they were derived from the model. They are superficially described but the reader has no information with which to assess the colony measurements or the discussion.

The absence of temperature as an abiotic correlate is surprising as it is one of the more important factors that influence growth. Temperature should be included in the analysis, or if the data is not available, it should be considered in the discussion.

There is no abiotic data for the Pisces sites, which is a flaw as it does not allow site comparisons. If this data is not available, the effects on the analysis should be acknowldged in the discussion
Validity of the findings: Additional information the aboitic factors is needed to determine whether the data used is robust and statistically sound. The statistical results for these analyses should be presented fully  - a table would suffice.
Additional comments: A valuable paper but needs some work on the discussion and data analysis. I have made some additional comments and suggested edits in the attached PDF file.


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

Input:
Title: ASSESSING THE LIVING AND DEAD PROPORTIONS OF COLD-WATER CORAL COLONIES: IMPLICATIONS FOR DEEP-WATER MARINE PROTECTED AREA MONITORING IN A CHANGING OCEAN
Review round: 2
Reviewer: 1

Output:
Basic reporting: This is a second review and the authors have addressed all my initial concerns appropriately. I recommend accepting the re-submitted version of this manuscript.
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: IMPACT OF LAND RECLAMATION AND AGRICULTURAL WATER REGIME ON THE DISTRIBUTION AND CONSERVATION STATUS OF THE ENDANGERED DRYOPHYTES SUWEONENSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Seems very good.  Relatively good English with a few small errors or stylistic problems as noted in the General Comments section.  Well structured in standard format.
Experimental design: Seems fine to address most of the questions asked.  Probably not adequate for some, though--extreme spatial autocorrelation of sources of water means that many other grographical variables may be confounded with water source; see comments on Figure 2 in general comments section and comment on lines 229-235 in "Validity of the Findings"
Validity of the findings: 229-235 Not sure I see the significance of this?  I assume that the percentages of sources of water just relate to the species’ geographic distribution.  Sources of floodwaters are highly spatially autocorrelated and cannot be regarded as independent for the pruposes of things like chi-squared tests.

See also Figure 2 comment in general comments section and comment on 287-297
Additional comments: Most of these are simple English comments, however a few are more substantive.

54 should either be “a species’ range and habitat preferences” or “species’ ranges and habitat preferences”

60 “The amphibia class -> “The Class Amphibia”

64 “Besides, those farmlads” -> “Farmlands”

76 “lead to expect” -> “led us to expect”  lead is a metal, or something one does to guide someone to a place (pronounced "leed"), led is the past tense of the guiding meaning. Good old English...

79 “karyotype warranting” -> “karyotype, warranting”

88 “negative” -> “negatives”

100 “absence for” -> “absence of”

110 “study for” -> “study of”

139 “presence of the” -> “presence of”

174 needs a rewrite.  Do you mean you hypothesized that it was important that water be linked to the Gxxx river?  I say Gxxx because here you refer to the Geum river and above (156) you referred to the Gum river, and I am on an aeroplane with no access to a map to check which is correct.

176-177 “We subsequently assessed the random distribution of D. suweonensis in relation of the agricultural flood water.” -> “We subsequently assessed whether
distribution of D. suweonensis was random in relation to that of agricultural flood water.”

184 “and variables such as water quality are important the” -> and because variables such as water quality are important in the”

195 “were” -> “where”

202-203 “surveyed three” -> “surveyed over three”

218 This is important—did the range decrease by 729 km2 or from 729 km2 to some lesser area?  Just a typo I’m sure

241 “temporal” -> “temporary” if that is what you mean; temporal is definitely wrong, anyway.  Dr. Who’s TARDIS is a temporal structure; I don’t know of any others.

254-255 “The known range of Dryophytes suweonensis has doubled over the three years of this study” -> “The known range of Dryophytes suweonensis was doubled by the data collected over the three years of this study”

258-259 “This new knowledge is, however, sobered down by several potential local extirpations” -> “The apparent expansion of the species’  known range is, however, countered by several potential local extirpations”

260 “”Besides, the” -> “The”

262 “Namely, because of an extent” -> “It has an extent”

265 “Besides, the” -> “At present, the”

267 “It is however” -> “This is”

272 “Accordingly” -> “Additionally”

276 “Encroachment had been” -> “Encroachment on the species’ range by development has been”

277 “carried at” -> “carried out at”

283 if there are numerous major landscape barriers within potential metapopulations, they probably are not single metapopulations, but either groupings of isolated populations or groupings of isolated metapopulations.  This needs to be revised.  Just adding the word “potential” preceding “metapopulations” would do the trick.

287-297 See my comment in the “Validity of the Findings” section about this.  If this is a real thing it needs to be explained more thoroughly and justified better.  Otherwise it may just be the result of any of the many factors that might be restricting geographic distribution of the species.

306-307 “neither than introduction at new sites” is completely wrong wording; I really am not sure what you mean; do you mean you do not recommend ex-situ conservation other than introduction at new sites outside the present range (commonly called translocation), or do you mean that you recommend neither ex-situ conservation nor translocation?

Figure 1 legend I would suggest saying
(blue dot) Dryophytes suweonensis present
(red dot) Dryophytes suweonensis absent

i.e. reverse the wording for the present and absent categories.  Not really necessary but clearer and better English

449 “was” -> “were”

Figure 2—note the extreme degree of spatial autocorrelation, i.e. each point sampled is very non-ndeendent from many others in terms of the source of water, so that regarding them as independent and conducting a chi-squared test, which assumes that, is incorrect.

452 “Bird view” -> “Bird’s-eye view” or “Overhead view”

457 “Lateral view the” -> “Lateral view of the”


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

Input:
Title: IMPACT OF LAND RECLAMATION AND AGRICULTURAL WATER REGIME ON THE DISTRIBUTION AND CONSERVATION STATUS OF THE ENDANGERED DRYOPHYTES SUWEONENSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: I found this to be a very well written paper, based on several years of survey data.  Clearly a lot of work was done to gather the data.  I make some minor suggestions below to improve the grammar.

Line 28: replace “evidences” with “evidence”

Line 30: replace “Besides,” with “In addition,”

Line 33: delete “ultimately” as this word is not needed in the sentence

Line 41: I don’t know if you mean “extinction risks” (plural) or “extinction risk”.  You should say either “extinction risks depend on” or “extinction risk depends on””

Line 44-45: Change so it reads “The lack of knowledge of the distribution of a species has already resulted in extinction that could have been easily avoided”.

Line 45: Change to “For example, the Tecopa pupfish….”.

Line 48: Change “Knowledge on” to “Knowledge of”

Line 50: Say “subspecies of Ursini’s viper”, not “subspecies of the Ursini’s viper”

Line 51: Change to “was known to occur only in Greece and at a single locality in Albania.”

Line 57: Change to “The occurrence of a species ….”

Line 58-59:  you finish the sentence with “and despite the low occurrence of endangered species within protected areas (Brooks et al. 2004).”  I don’t understand what you mean by this, in relation to the rest of the sentence.  Can you clarify?

Line 60: Change “amphibian class” to “Class Amphibia”

Line 64: Change “Besides” to “Furthermore”

Line 66: Say “where rice production has decreased …”

Line 72: Change “occur on” to “occur in”

Line 76-77: Change to “lead to the expectation of a broader distribution for the species”

Line 79: Change “enterprised” to “aimed”

Line 99: this is the first time you mention D. japonicus.  You should say something about why this species is important to your study.

Line 110: Change to “occurrence of this species”

Line 116: Change “before” to “adjacent to”

Line 125-126: Do you mean you had previously measured the detection range of frog calls, or you did this at the end of each site survey.  I suspect the former, but please clarify.

Line 160: Change “traceability in the origin” to “traceability of the origin”

Line 171: Insert a comma after “species”

Line 177: Change “in relation of” to “in relation to”

Line 179: Change “From presence data from the surveys” to “From survey presence data”

Line 182: Say either “the species’ preferences” or delete “the” and just say “species preferences”

Line 184: Change “the ecological preferences” to “ecological preferences”

Line 191 to 193: I would make this sentence more concise by saying something like “That is, the sites were beyond the ecological requirements of the species as there
was no standing water; instead the sites were mostly greenhouses, apartment complexes or dry crops.”  If that is what you mean.

Line 195-196: Change “from 94 of the 100 sites were the species was detected” to “from 94 of the 100 sites where the species was detected”

Line 198: delete the comma in the sentence as it is not necessary.

Line 204” I’m not sure “aggravated threats” is the best phrase.  Perhaps change to “significant threats” or similar.

Line 215: Change “Besides” to “In addition”

Line 218: you say “the species decreased by from 729 km”.  It should either be “by 729 km” if that is what you mean, or “from 729 km to XXXX” if that is what you mean.  But don’t say “by from” in the same sentence.

Line 247: I would change “bird-eye view” to “aerial view”

Line 258: Change “sobered down” to “tempered by” or similar

Line 260: Replace “Besides” with “Furthermore”

Line 262-265: The sentence “Namely, because of an extent of occurrence < 5000 km2, a severely fragmented population, with a continuing decline observed, estimated, inferred or projected for extent of occurrence; area of occupancy; area, extent and/or quality of habitat; and the number of locations or subpopulations” is a bit confusing.  I am not sure exactly what you mean, but this should be clarified.  For example, what does “and the number of locations or subpopulations” refer to?  Is that referring to a previous part of the sentence regarding continuing declines (observed, estimated, inferred, projected), or are you just talking about the actual number of locations and subpopulations being the issue?

Line 270: Change “strive” to “exist”

Line 271: Change “knowledge on” to “knowledge of”

Line 277: Change “carried at” to “implemented at”

Line 302: Change “southern part on” to “southern part of”

Line 306: Change “neither than” to “nor”

Line 447: You need a better Figure heading.  Keep what you have, but start with something like “Relationship between water type and species presence”.
Experimental design: My main question relates to the use of a single 5 minute survey each year to assess presence or absence of the frog species at a site.  This may be justifiable - I just don't know.  See my comments below in the Validity of the Findings Section.
Validity of the findings: I have some questions about the data analysis.  The authors detected frogs at 114 sites, and never found frogs at something like another 250 sites.  Each site was surveyed during a single 5 minute survey (listening for frog calls) during the breeding period.  My first question relates to detection probability.  How confident are the authors that a single 5 minute survey is sufficient to detect the presence of the species at a site?  There is a large literature on this for amphibians in general.  For some species, detection probability is quite high (close to 1; thus a single survey is an adequate sampling period), but for other species it is low and so multiple surveys in a  short time frame are required to be confident of species presence or absence.  This obviously can have significant implications for identifying the distribution range of the species, as well as identifying habitat correlates.  Do the authors have any data on the detection probability of their target frog species?  If so, and it is high, that would help justify the use of a single 5 minute survey at a site once a year. I agree that the authors have expanded the range of the species, I’m just not sure if the actual range is even larger than they suspect – if the species has low detection probability.

As I understand it, to identify important habitat variables for species presence, the authors focused on the 114 sites where the species was present, and did not include data from the other 250 sites (approximately) where the species was never detected.  Is that correct?  If yes, I don’t understand why the authors didn’t use the data for all 350+ sites (species detected or not detected) in an analysis like logistic regression to see which of the habitat variables was significant in explaining the detection or non-detection of the species at sites?  Unless you think detection probability is low, and therefore sites where the species was not detected are too questionable to use to identify habitat correlates.  Or there were other reasons to not expect the presence of frogs at some sites independent of local habitat conditions. There may be a reason for their approach to analysis, but the authors should clarify their decision.  Or if I have misunderstood the analysis, the authors should be more explicit in describing the analysis they used.
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: IMPACT OF LAND RECLAMATION AND AGRICULTURAL WATER REGIME ON THE DISTRIBUTION AND CONSERVATION STATUS OF THE ENDANGERED DRYOPHYTES SUWEONENSIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Nicely conceived maps and figure. I would like to see a few clarifications of them as specified in the manuscript enclosed. I was confused by your use of ancestral and current distribution and your suggestion that rice seedlings are necessary for the species. If this is true ancestral has a very restricted meaning.
Experimental design: I think your a priori selection of field sites to survey is excellent, but you need to highlight how excellent it is by telling us more about how you went about drawing the boundaries on the original area that you are focused on and how you the selected the individual sites within this larger area.
Validity of the findings: I suggest you develop your figure 3 more clearly. It is based on other work in large part (e.g. vegetation characteristics) so it kind of drops out of the blue. But, it is a beautiful figure.
Additional comments: This is an important study that has many good features associated with it. Primarily the extensive field survey work which documents the occurrence of this endangered species and data associated with positive impacts of both rice paddy development and negative impacts of urban encroachment. A particularly strong component of the study is the large effort that went into gathering presence absence data and correlating this with human land use modifications. The paper is difficult to read and I have made many suggestions, corrections, and comments on the enclosed manuscript. I edited in MSword so the track change comments came across with MOU and REV associated with them. They have not meaning. They are all my 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: EXCEPTIONAL SOFT TISSUES PRESERVATION IN A MUMMIFIED FROG-EATING EOCENE SALAMANDER
Review round: 1
Reviewer: 1

Output:
Basic reporting: The report is written mainly clear English, but see below.
Literature is appropriate.
Figs are excellent.
No clear hypotheses but not necessary in this report.  Considerable speculation but generally ok with me.
Experimental design: Not relevant
Validity of the findings: I think the descriptive information and especially the visuals are of high quality.
Additional comments: I would tuck the information gathered from this manuscript in that part of my brain labeled “Cabinet of Curiosities”.  The phosphorized fossil is remarkably well preserved and the authors have derived a lot of information from the scans.  I am interested in salamander anatomy, and accordingly enjoyed reading about there methods and interpretations.
What I take home from this manuscript is that under certain circumstances, not well understood, amazing preservation of anatomical detail is possible in fossils.  That is it.  It is not known exactly where the fossil was found and so taphonomic details are lacking and speculation results.
Line 69 is an incomplete sentence and the entire complex sentence would be better as several sentences. Technical English is best in short declarative sentences.
I think the anatomical inferences are generally good and justified.  I think the authors are correct regarding muscles, lung, cloacal glands and even the partial frog in the gut.
The frog in the gut of a relatively small salamander is a surprise.  Salamanders generally do not eat frogs or even tadpoles (I can add Ambystoma gracile to the short list of salamanders known to eat metamorphosing frogs).  In this instance the frog seems to be partially dismembered, or has been digested in a peculiarly selective manner).
Even without the lung evidence, this is not a plethodontid on the basis of vertebral anatomy and especially the very long and well-developed ribs.


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: EXCEPTIONAL SOFT TISSUES PRESERVATION IN A MUMMIFIED FROG-EATING EOCENE SALAMANDER
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comments
Experimental design: No comments
Validity of the findings: The paper is a valuable contribution and I strongly support its publication in the PeerJ (after very minor revision).
Additional comments: I have no major suggestions on the paper. I enjoyed the opportunity to read this MS and I look forward to see it published. My minor suggestions for the improvement of the MS are listed below:
“Abstract”, line 26, I recommend to add “juvenile” before “frog”. It is important to provide a characteristic of a prey (= the swallowed frog was juvenile).

“Introduction”, line 47. Please, clarify why “external features” are “notable” (e.g. notable for taxonomic identification?)

“Results”, “Lung”, line 156. I recommend to remove the phrase “(i.e. within the rib cage)” because salamanders do not have a rib cage (this structure is typical for amniotes)

“Discussion”, “Exceptional preservation”, line 193, I recommend to use the name Vertebrata (Latin) or vertebrates (English), but not Vertebrates.

I waive all anonymity for my review. The authors are welcome to contact me directly should they have questions or anything they wish to discuss.

Pavel Skutschas


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: PERCH, PERCA FLUVIATILIS SHOW A DIRECTIONAL PREFERENCE FOR, BUT DO NOT INCREASE ATTACKS TOWARD, PREY IN RESPONSE TO WATER-BORNE CORTISOL
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is largely well-written, with sufficient references and background in most places. The raw data are available. I do not think that, given the controls in the experiment, that the hypotheses are truly being addressed as they are currently worded.
Experimental design: The research aims are within the scope of the journal. The research question is well defined, although I think more motivation is needed. I think that additional controls, such as behavior of a non-predatory fish, would have been useful. The ethics and methodological details are sufficient, though there are some things that should be clarified with the statistics.
Validity of the findings: There are some major statistical concerns (see general comments) that should be addressed. I think that, given that more or different controls would be useful for identifying if the change in behavior is indeed predatory, the discussion should be more speculative.
Additional comments: General comments

The manuscript is generally well written and clear. I think that it presents an interesting and relevant topic, as the idea that reduced stress responses may have evolved as a mechanism to avoid predators is an intriguing idea and worth exploring. However, I have some major concerns about the manuscript in its current state:

1.	I have some major statistical concerns that I think need to be addressed to make the results more convincing.
a.	You found that perch tended to show increased lunges toward stickleback during the cortisol treatment, but the majority of trials that were removed because the perch did not move or lunge at all were cortisol trials. It seems likely to me that removal of those cortisol trials (with zero lunges) may have biased the dataset, and it would be useful to run the stats with and without those trials. I understand that using those trials for proportion of time oriented or spent in a zone is biased by including them, but I don’t think that the same is true for the lunges.
b.	I am somewhat confused by your statistical methods. I assume you ran 4 separate models, each with one fixed effect (treatment) and one random effect (perch ID)? If so, you should specify that in the table legend and replace “fixed effects” in the top row to “treatment”. Additionally, because the proportion of time spent in the chemical stimulus zone, proportion of time oriented in the chemical stimulus zone, and proportion of lunges are likely not independent, it would be more statistically rigorous to control for multiple tests.
c.	I don’t understand why you used the proportion of lunges and not the total number of lunges. It seems to me that the total number of lunges would be a more accurate reflection of predatory behavior, and it would be useful to justify why proportions were used in this case. Further, how often did the perch lunge in the opposite stimulus zone and do you know what was the purpose of that behavior is?

2.	Since you used stressed levels of cortisol (0.20), you need to justify why you used acclimated sticklebacks in your experiment or reframe your question. It seems to me that, to understand if cortisol itself is responsible for giving cues of prey vulnerability, a better control would be to compare cortisol alone (at stress induced levels) to visual cues of stressed prey and/or natural chemical cues of prey that are stressed.

3.	Given that, as you state in the introduction, prey can respond to the cortisol emitted by conspecifics, how do you know that predators interpreted the cortisol as cues of prey and not as a signal of danger to themselves? Given that some predators froze, which is an antipredator behavior in many species, is it possible that this is the case? On the other hand, predators might be less willing to stay in the area with the cortisol if it was a cue for danger (the lunging results would also provide further proof of prey cues if the results still hold after redoing the statistics). I think it would have been extremely useful to have additional controls- to understand if a non-predatory fish reacts to the cortisol release in a different way or is this behavior specific to predators. I think that further discussion of this is necessary (and additional tests with this control, if possible, would definitely improve the manuscript). Suggestions for other possible controls are given below.

4.	Clarification on what type of cortisol (free or conjugated) is dropped into the water would be useful, as receptors for conjugated steroids tend to be much more prevalent than receptors for free steroids and therefore, perch would have different abilities to detect free versus conjugated steroids.

Specific comments

Lines 30-32: Here and elsewhere, it feels like there are more commas than are needed in the text. Reducing the number of commas would improve the readability in sections.

Line 32: relative to presentations of natural chemical cues…

Line 33: In addition, perch tended to show increased…

Line 52: If you bring up the life and dinner principle, it would be useful to readers to define it here.

Line 74: Citation?

Lines 70-76: Here and elsewhere (e.g. lines 82-84), you repeatedly motivate the study by stating that we do not know that much about responses of predators to prey. There should be more motivation to do the study than the fact that it merely has not been done before, and indeed, I do think that it is an important topic of interest. I would remove these statements and instead be more specific in how “predators respond to the chemical cues released by prey would provide insight into the selective forces that shape the chemical ecology of predator-prey interactions”. For example, you allude generally to something in lines 371-372 of the discussion that is worth expanding on in the introduction.

Line 79: Such as? And given that there are lots of potential predatory cues, is it possible that putting any of them into the water at high concentrations would produce the same results? As in, I think it is worth discussing (and further investigating for someone) whether or not these results are associated with cortisol alone or if these results can be replicated by having high concentrations of any alarm pheromone in the water.

Line 98: influence

Line 112-113: I think part of this sentence is missing?

Line 113: Or cortisol might just provide information about location of prey, not necessarily vulnerability. I think a control where you run cortisol plus natural cues on one side, with just natural cues on the other, would differentiate between these.

Line 143: Did you reuse sticklebacks? If so, were there any notable changes in stickleback behavior over time? As in, sticklebacks could be responding behaviorally different to perch the first versus third time they see the predator.

Line 158: Again, what type of cortisol is important information.

Lines 160: Since that is not natural levels, but stressed levels of cortisol, I don’t understand why you used acclimated sticklebacks in your experiment, rather than stressed sticklebacks who would give visual cues of vulnerability and natural chemical cues of vulnerability. It seems to me that, to understand if cortisol itself is responsible for giving cues of prey vulnerability, that a better control would be to compare cortisol alone (at stress induced levels) to natural cues of prey that are stressed.

Lines 216-221: Again, why proportions? How often did they lunge not at stickleback?

Lines 224: Again, I assume that these are not independent. If they are not independent, controlling for multiple tests would be beneficial.

Line 228: Degrees of freedom are needed here and throughout

Line 234: Package?

Lines 251: Final sample sizes for each treatment after removals would be useful. Also, I think removing 12 tests from models looking at lunging behavior likely biases the results.

Lines 260: Including the statistics here and in the table is redundant- please choose one.

Lines 264-265: I’m not quite sure what you mean by “the chemical stimulus was dripped in the cortisol test relative to the water control”.

Lines 265-267: I may have missed this, but how did you measure movement? Just movement between zones?

Line 270: Range or standard error?

Lines 270-271: Again, this is a large difference, which makes me question why comparing unstressed visual and chemical cues to stressed cortisol levels helps you test “the hypothesis that the disturbance cue cortisol informs predatory behaviour when presented with prey.” I think you need to reframe and/or clarify your question, making it clear that you aren’t testing visual versus chemical cues of stress.

Lines 276-285: See my general comments- I think that alternative explanations for altered behavior should be considered here.

Lines 298-305: It is a little unclear how these sentences connect to the rest of the discussion- transitions would be useful

Line 307-308: But prey who have been repeatedly exposed to predators may have dampened cortisol responses

Line 316-317: I think that you can really only say this if you look at whether or not non-predatory fish behave in the same way.

Line 333-334: Affect behavior in what way? Also, “but” at the beginning of the next sentence might be replaced by “however”.

Line 335: that were elevated

Lines 337: What do you mean by undirected changes?

References: Make sure you italicize scientific names

Figure 2: I don’t understand what the numbers in the bars are- please include that in the figure legend. Also, it would be useful to see both sides of the standard error bars, especially since the data are not normally distributed and therefore, the error bars should not be symmetrical. 2C should have letter b instead of c over the cortisol treatment.


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: PERCH, PERCA FLUVIATILIS SHOW A DIRECTIONAL PREFERENCE FOR, BUT DO NOT INCREASE ATTACKS TOWARD, PREY IN RESPONSE TO WATER-BORNE CORTISOL
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is, in its majority, a very well written manuscript. It flows well and everything is backed up with what seems to be a very comprehensive literature review. The results obtained are relevant to the hypothesis and interpreted in a rigorous and informed way. In L335: change 'we elevated' to 'were elevated'.

I would encourage the authors to avoid using bar graphs and replace them with boxplots. This is because boxplots show the distribution of the raw data and, thus, are more informative.
Experimental design: The design is simple and well thought through. It is clear that the research question(s) fills a knowledge gap. Methods are described in detail. The passage were the hypotheses are stated, however, needs to re-worded. Paradoxically, this is the least clear paragraph in the whole manuscript.
Validity of the findings: Data analysis is mostly appropriate. Taking into account the 'repeated measures' nature of the experiment, the authors rightly included predator id as a random factor in their statistical models. However, I'd suggest they reanalyse their data regarding number of movements and number of attacks with a GLMM with a Poisson distribution, which tends to be the distribution that fits counts best.

The authors acknowledge the limitations of their study, and state the conclusions that derive strictly from the data presented.
Additional comments: I enjoyed reading the manuscript!


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

Input:
Title: PERCH, PERCA FLUVIATILIS SHOW A DIRECTIONAL PREFERENCE FOR, BUT DO NOT INCREASE ATTACKS TOWARD, PREY IN RESPONSE TO WATER-BORNE CORTISOL
Review round: 2
Reviewer: 1

Output:
Basic reporting: It is well-written and clear, sufficient background and literature review.
Experimental design: Well-designed, research question clear and relevant, methods are sufficiently detailed.
Validity of the findings: Some minor statistical changes would be useful, but generally, the data are sound.
Additional comments: This version of the manuscript is greatly improved over the last version, both in terms of readability and in terms of robustness of the data. The abstract, introduction, and discussion all read very well, although some minor changes to the introduction and discussion (see below) would clear up a few remaining ambiguities. The additions to the methods were useful, although I still have some remaining statistical concerns.

Specific comments
Lines 60-62: It would be useful to give an example here of how this is the case.

Lines 67: information regarding the presence of predators?

Lines 81-82: Additional fitness benefits of releasing alarm cues? This paragraph is a bit unclear to me, as it starts with saying the predators use alarm cues to locate prey (which seems bad for the prey), but you then say that it is beneficial because it attracts more predators. Expanding and clarifying this paragraph would improve the readability.

Lines 83: Remove the comma between injury and attract

Lines 89-90: It would be useful to define disturbance cues here.

Lines 135-141: You make predictions here with respect to visual cues versus cortisol, but it would be useful to understand what differences you expect to see (if any) in natural cues versus cortisol.

Lines 263-264: I think it would be useful to clarify that these are (as I interpret it) lunges toward the stickleback on the side of the chemical stimulus versus lunges to sticklebacks on the visual cue only side.

Lines 276: Did you check to see if your data were overdispersed (i.e. if you should use Poisson or negative binomial distribution)?

Lines 272-275, 328-332: Does the total number of lunges and movements include the trials in which perch did not lunge? I agree that, in some cases, excluding individuals who do not react to the stimulus presented by the researchers is appropriate. For example, removing the samples in which the perch were immobile when trying to evaluate proportion of time spent in the chemical stimulus zone seems appropriate because, as you say, it is possible that they spent 100% in the chemical stimulus zone merely because they never moved. With the proportion of lunges, it is also appropriate. However, I do think that it is important to include those zeros in the trials examining total numbers of lunges/movements- if you remove them, you effectively remove many more zeros from the cortisol treatment group than you did from the other two treatment groups and this almost certainly biases the data.

As it is written, it is unclear if you did or did not include the trials with immobile perch in your current analysis, and you should show your data with and without those trials removed. In the minimum, you should show the additional analyses that you put in your letter “we do not think this is the case for our data because when we re-analyse the perch behaviour including only those perch who are active in all three conditions (9 perch, and 27 trials) our result is the same: Proportions: Duration, GLMM t = 3.62, P = 0.002; Orienting, GLMM t = 3.91, P < 0.001, Lunges, GLMM t = 4.34, P = 0.08. Total lunges: GLMM z = 4.50, P < 0.001.” I think this does provide support for the robustness of your results.

Lines 354-357- I would expand this a bit, or at least cite studies showing that immobility is a deterrent behavior.

Lines 360: Instead of “reduced predator avoidance”, I would say “a reduced ability to avoid predators”.

Line 366: I think a more specific transition here would make this a bit more readable. Instead of “Context can influence the behavioral response of fish to chemical cues”, it would be useful to say something along the lines of “Predators may respond differently to chemical cues of prey depending on the social or ecological context or depending on their own attributes” as the example you use primarily refers to differences in size/age in how perch respond to cues.

Lines 433-434: It would be useful to explain this. E.g. further tests with a  non-predatory fish would be needed to confirm that changes in behavior are specific to predatory fish and not a general response to cortisol. I think that this would be interesting because it would likely confirm that this is indeed something specific to predator-prey interactions.


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: PERCH, PERCA FLUVIATILIS SHOW A DIRECTIONAL PREFERENCE FOR, BUT DO NOT INCREASE ATTACKS TOWARD, PREY IN RESPONSE TO WATER-BORNE CORTISOL
Review round: 2
Reviewer: 2

Output:
Basic reporting: I have had a look at the response letter and the amended manuscript and I am happy to say that the authors did a great job with their revisions in agreement with my, and the other reviewer's, suggestions. Thus, I am happy for this MS to be accepted.
Experimental design: As I said in the previous review, I think the experimental design is well thought through.
Validity of the findings: Conclusions are backed up by the results of the experiment
Additional comments: The authors did a serious and thorough job with the revisions!


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: A PRELIMINARY SURVEY OF ZOANTHARIAN ENDOSYMBIONTS SHOWS HIGH GENETIC VARIATION OVER SMALL GEOGRAPHIC SCALES ON OKINAWA-JIMA ISLAND, JAPAN
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1- Line 28: The verb “prefer” is not only too anthropomorphic, but also implies experimental manipulations were performed to investigate shifts in Symbiodinium communities. I strongly recommend that it be revised to “be associated with” as their study is purely one of associations between diversity and the environment.

2- Line 29: “slight” is awkward. Suggest “less than those usually investigated….”

3- Line 32: Suggest “accurately determine species diversity and their distributions.”

4- Intro, paragraph 2: Microsatellite markers have also been develop to investigate fine-scale diversity in Symbiodinium (see, Pettay & LaJeunesse 2007 [Molecular Ecology Notes], Grupstra et al. 2017 [Coral Reefs]).

5- Line 58: Suggest specifying “this work,” perhaps as “As a result of the development and implementation of finer resolution molecular markers…”

6- Line 65, for consistency, revise “reexamine” to “re-examine.”

7- Line 92: Another crucial aim was to explore potential associations between diversity and the environment, and is equally important to include at the end of the Introduction.

8- Line 122: Revise “Nucleic acids were extracted” to “DNA was extracted.”

9- Line 139: The psbA *gene* was not sequenced; the non-coding region was.

10- Line 142: Which previously reported sequences? Provide accession # for these here (as well as later in the Results as has been done).

11- Line 197: First sentence is awkward. Suggest, “We next examined the distribution of Symbiodinium lineages across locations.”
Experimental design: 1- Line 86-87: Clarification is needed here (as well as later in the Methods for PCR and sequencing ITS2). If ITS2 sequences were already obtained for Symbiodinium within P. tuberculosa in southern Japan (*including Okinawa*), what was acquired in this study? New samples?

2- Line 124: According to TableS1, not all samples have a pending accession # for ITS2, implying that only a subset of samples were PCRed and sequenced for ITS2? Please clarify.

3- Line 131: Primer concentrations are needed.

4- Environmental data results: Were there any significant differences in temperature and chl-a between sites, for example, were southern sites *significantly* warmer than northern sites? A simple statistical test to test for significance between sites could add a great deal to explaining how/why the environment could shape the diversity observed. In contrast, if the sites are not significantly different, more caution should be made in declaring that the environment shapes diversity. Alternatively, address whether these environmental differences (whether significant or not) are biologically meaningful to the coral/symbiont relationship? Does a 0.95°C difference in temperature make a big difference in the coral/symbiont world?

Furthermore, “Yearly average chl-a concentration values were generally low” (Line 172 and later in Discussion), but no mention of whether there are apparent differences between sites to consider.

Finally, are there available software that could be used in this study to better test for diversity/environmental data associations? The program Geste and R ‘vegan’ package come to mind in using generalized linear modeling to investigate whether genetic structure relates to environmental factors. However, I am unsure whether the sample sizes in this study are sufficient or whether sequence data are able to be analyzed by these programs. Worth looking into these and perhaps other options.

5- Why the ITS2 marker was used at all needs additional justification (in addition to Line 277- the end of the paper). Its results are hardly ever mentioned/discussed in the discussion and understandably so; however, it needs to be made more clear why this marker was used in the first place (in Methods), and why the results from psbA noncoding region were the focus of the conclusions and discussion.
Validity of the findings: Overall, the findings and conclusions drawn are sound. I appreciate their recognition of the limitations of their study Lines 252-260. As pointed out in this paragraph, host variation could explain Symbiodinium diversity. While they cite cases of mismatch between host and symbiont, they should also reference studies that have found a match suggesting Symbiodinium diversity/distribution is simply due to host-specificity (examples include Bongaerts et al. 2010 [PLoS One], Prada et al. 2014 [Mol Eco]).
Additional comments: Noda et al. use a faster evolving gene to elucidate the diversity of Symbiodinium within Palythoa tuberculosa in Japan, and combine it with fine-scale environmental data to explore any associations between this diversity and the environment. This work is crucial to the field in joining a few other recent papers that advocate for such a finer-scale approach to better understand the biogeography of Symbiodinium. Overall, the study is sound and robust. The paper is overall well written and this review presents minor comments and revision suggestions.


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

Input:
Title: A PRELIMINARY SURVEY OF ZOANTHARIAN ENDOSYMBIONTS SHOWS HIGH GENETIC VARIATION OVER SMALL GEOGRAPHIC SCALES ON OKINAWA-JIMA ISLAND, JAPAN
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors present a clear and unambiguous analysis of Symbiodinium diversity in Palythoa tuberculosis using a highly resolving genetic marker. Using satellite derived environmental data, the authors discuss the fine-scale zonation of different zoox haplotypes and discuss this in the context of the importance of fine-scale surveys to accurately capture Symbiodinium diversity in corals. I am glad to see more manuscripts moving away from the classical single-marker ITS2 approach and towards a multiple-marker approach. Based on the improvements made to this version of the manuscript (I reviewed a previous version), I am happy to recommend this manuscript for publication in PeerJ. The next obvious question that arrises from this work is what are the functional differences between psba haplotypes?
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: ELEVATED SERUM OSTEOPROTEGERIN MAY PREDICT PERIPHERAL ARTERIAL DISEASE AFTER KIDNEY TRANSPLANTATION: A SINGLE-CENTER PROSPECTIVE CROSS-SECTIONAL STUDY IN TAIWAN
Review round: 1
Reviewer: 1

Output:
Basic reporting: the article is written in a clear way
 references  are sufficient (but could be improved)
the structure is acceptable
the results  are clearly  expressed, though they do not fully support the hypothesis
Experimental design: the research is within the aims of the Journal
as reported in the comments to the AA, the methods are  not fully adeguate to  add knowledge to  the topic
No problem by the ethical point of view, but there are some   methodological inconsistencies
the description of the methods should be improved
Validity of the findings: no particular novelty
The Data and their statistical  handling are  far from being satisfying
the conclusions should be resized on the basis of the limited information given by the presented data
Additional comments: This is a prospective observational study intended to evaluate the relationship of osteoprotegerin (OPG) serum levels and peripheral arterial disease (PAD) in a cohort of kidney transplanted (KT) patients (n. 74). The main conclusion was that higher OPG levels are associated with the presence of PAD in KT patients.

There are some critical points which should be better addressed:
-	The first point to be faced is to better explain which could be the possible pathogenic link between high OPG levels and vascular calcifications, given that all the experimental data indicate that OPG mainly acts as an inhibitor of the calcification process. Is OPG simply a marker of VC or a counteracting compensatory response?
-	A second point which deserves a more in-depth   discussion is the assumption that  an elevated ankle-brachial index (ABI)  is sufficient  to make a diagnosis of PAD. In fact, though I can easily agree that ABI is highly related to the vascular calcification process, it cannot be assumed that all patients with higher ABI have for sure a PAD, given that  no other clinical and instrumental tool have been used for a specific diagnosis of PAD. It could be more appropriate to talk of a relationship between OPG and arterial stiffness and not PAD.
-	It is not clear whether  the KT patients included in the study were all the  patients followed in the medical center in Hualien or only part of the whole cohort. If the latter was the case, it could be worth describing the criteria for choosing the studied cohort.
-	The authors should describe more in detail the methods used for the measurement of OPG and PTH, giving the normal values for their laboratory, the coefficient of variation, the intra- and interassay CV.


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: ELEVATED SERUM OSTEOPROTEGERIN MAY PREDICT PERIPHERAL ARTERIAL DISEASE AFTER KIDNEY TRANSPLANTATION: A SINGLE-CENTER PROSPECTIVE CROSS-SECTIONAL STUDY IN TAIWAN
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript would benefit from professional editing. In particular, a few sentences are really ambiguous and rather difficult to read. Examples: line 66 "the arterial-venous shunt preservation on the limb for prior renal replacement therapy", lines 82-84 "the ABI is the ratio of the systolic blood pressure of the ankle divided by the systolic blood pressure of the arm with lower one of ankle systolic blood pressure value to calculate ABI. As previous our study we set...", lines 170-171 "OPG plays a protective role in term of vascular calcification of animal studies but also being detrimental effect on the progression of atherosclerosis in clinical consideration". Additionally, there are several typos and syntax and grammar mistakes (e.g. line 72, "The informed consent" rather than "Informed consent"; line 86, "part of sample" rather than "part of the samples" etc.)

Table 3 does not show (or mention) the different variables included in the model, apart from the variables which reached statistical significance.
Experimental design: The research question is well defined and potentially meaningful. Methods are reproducible with any statistical software. Ethical standards were respected.
Validity of the findings: The Authors should have compared the sensitivity and specifity of osteoprotegerin with the sensitivity and specificity of ankle-brachial index, in order to emphasize the potential relevance of the new essay. For example, a recent review from the Cochrane collaboration (Crawford F et al. Cochrane Database Syst Rev. 2016. 9:CD010680 showed that only one study out of 49 met the eligibility criteria, thus underscoring that evidence about the accuracy of ankle brachial index is sparse, as also highlighted by other Authors (sensitivity 15-79%; Xu D et al. Vasc Med. 2010. 15: 361-369.
Additional comments: At the moment, the discussion is excessively focused on evidence from animal models. The Authors should make an effort to try to reconcile evidence from experimental studies (protective role of OPG) and evidence from human studies (detrimental role of OPG). Although they acknowledge that the observational nature of the study does not allow to establish a causal relationship, they should try to discuss possible explanations of this discrepancy. Is OPG an "innocent bystander", rather than the cause of peripheral arterial disease? Is it possible that the increased level of OPG triggered by inflammation is actually a compensatory mechanisms that tries to limit the harmful effects of endothelial dysfunction? This is a crucial point, as inflammation markers have not been tested in the study. Finally, are the different actions of OPG potentially mediated by different receptors, like in the case of AT1 and AT2 receptors in the renin-angiotensin system?

Also, there is an apparent contradiction between the statement (lines 144-145) that "the renal function of patients who undergo KT unfortunately remains within the range of chronic kidney disease (which is often true, but not always) and the subsequent statement (line 197) that "the KT patients in the present study had relatively good renal function". Also, how would an average eGFR of 42 (stabe 3b CKD, moderate CKD) represent a "relatively good renal function"?

Line 143: please substitute "multivariable" with "multivariate" (Am J Public Health. 2013 January; 103(1): 39–40)

Line 92: please provide a reference for the MDRD formula; did you use the 4-variable MDRD or the 6-variable MDRD?

Line 53: please substitute "PAD is not an uncommon manifestation" with "PAD is relatively common"

Line 54. please substitute "was shown to significantly associate" with "has been associated with"

Conclusions (line 208). The statement "Management of biological markers of vascular risk" should be substituted with "Timely detection of biological markers of vascular risk"


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: ELEVATED SERUM OSTEOPROTEGERIN MAY PREDICT PERIPHERAL ARTERIAL DISEASE AFTER KIDNEY TRANSPLANTATION: A SINGLE-CENTER PROSPECTIVE CROSS-SECTIONAL STUDY IN TAIWAN
Review round: 2
Reviewer: 1

Output:
Basic reporting: all the four issues are satisfied
Experimental design: all the four issues are satisfied
Validity of the findings: all the four issues are satisfied
Additional comments: the authors fully answered the raised questions


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: ELEVATED SERUM OSTEOPROTEGERIN MAY PREDICT PERIPHERAL ARTERIAL DISEASE AFTER KIDNEY TRANSPLANTATION: A SINGLE-CENTER PROSPECTIVE CROSS-SECTIONAL STUDY IN TAIWAN
Review round: 2
Reviewer: 2

Output:
Basic reporting: No concerns
Experimental design: No concerns
Validity of the findings: No concerns
Additional comments: Please modify the sentence : “Fourth, lack of study concerned of sensitivity and specificity of ABI for diagnosis PAD in KT patients and no angiographic image was also applied in this study” with "Fourth, the lack of data on the sensitivity and specificity of ABI for the diagnosis of PAD in KT patients and the absence of any angiographic images may pose additional limitations to our 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: DIVERSE RESPONSES OF SYMBIODINIUM TYPES TO MENTHOL AND DCMU TREATMENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: The introduction is too sparse.  For example at L60 the authors state the mechanisms of menthol bleaching are “not clear,” but the cited references discuss the potential for menthol to interfere with the action of membrane receptor TRPM8 and lead to calcium-stimulated expulsion.  These ideas are included in the discussion but they should be addressed in the introduction as well.

The authors state in L64 of the introduction: “Whether the PSII breakdown in endosymbiotic Symbiodinium in corals is directly or indirectly caused by menthol irritation of cnidarian hosts was also evaluated.” However, these results aren’t reported or discussed.  To fit the data presented, this line needs to be removed, but if the authors did investigate it, I would rather they include the data.

The introduction could do a better job of establishing that no other studies have compared the responses of different Symbiodinium to both menthol and DCMU, and that this work investigates the important but underexplored topic of functional diversity among Symbiodinium species.

Across all figures and tables, please use the same order for the Symbiodinium types.  Right now each figure has a different order.  For Figure 2, I recommend including a label of the Symbiodinium type and menthol concentration in each panel.
Experimental design: The replication scheme should be reported in the materials and methods, not in the results.

Three of the Symbiodinium types are taxonomically described, and these names should at least be included at the first mention of each type: B1 = S. minutum, D1a = S. trenchii, C1 = S. goreaui
Validity of the findings: It appears that the ROS assay fluorescence data (presented in Table 3) was not analyzed statistically, even though replicates were measured.  Such an analysis should be performed (or the reason it was not performed should be stated explicitly).  Also, Table 3 should include the background control fluorescence values (reported in L167).

In the results (L155), the authors note that DCMU-treated Symbiodinium showed no ROS generation.  I feel like this point should be addressed in the discussion, specifically tying back to the Jones 2004 study where the working model was that DCMU drove ROS production and subsequent bleaching.

The idea presented in L192 that clades B and D are more closely related to each other than either are to clade C is incorrect.  B and C share a more recent common ancestor (take a look again at Pochon et al. 2014).

In L194-200, the authors discuss the mechanisms of menthol bleaching.  As I mention earlier, this should be addressed a bit more in the introduction.  In the discussion, I would like to see more explanation of how the results of this study inform our understanding of the mechanism of menthol bleaching, especially with respect to ROS production.  The results run counter to previous ideas (e.g. Jones 2004) and this should be highlighted.

In L204, the authors suggest Symbiodinium minutum (B1) may lack a TRPM8 homolog.  This would be easy to check, as the S. minutum genome is published and easily BLAST-able at reefgenomics.org, as are the genomes of S. microadriaticum (A1) and S. kawagutii (F1).  Unfortunately, those other species were not tested here, but I think it would be valuabe to check all three anyway.

The discussion ends abruptly and does not adequately address the implications of the results.  What does this mean for researchers considering using menthol or DCMU for future studies?
Additional comments: Wang et al. exposed several types of Symbiodinium to two common chemicals used in studies of coral bleaching (DCMU and menthol) to investigate their effects on photochemical efficiency and reactive oxygen species production.  The authors establish functional variation among species with respect to the point at which 50% photosystem II inhibition occurs and the level of ROS that is produced.

This is useful data, but the manuscript is incomplete in several ways.  The introduction is brief and presents an idea that is not tested, a key result lacks statistical analysis, and the discussion does not do a good job of exploring the implications of the findings.  A major revision would be required to make the manuscript acceptable.

John Parkinson
Oregon State University

Minor Comments

Abstract
L23: change to “have been studied extensively”
L24: “cell depletion” is ambiguous.  Later on it becomes clear you mean coral ‘bleaching’  (in the broadest sense, any loss of symbiont cells or reduction in photosynthetic pigmentation).  I would use this term instead of “cell depletion” throughout the manuscript.
L31: as is, the sentence implies that B1 is most sensitive, while C3 and C1 are the least sensitive, when in fact the result is the opposite.  Just change “PSII sensitivity” to “PSII tolerance” to fix this.
L35: could use a summary/implication statement here

Introduction
L41: change to “nine Symbiodinium clades (A-I) and numerous subcladal types”
L48: include additional examples and references for other types of functional variation (as you do in L183-187).
L48-49: rephrase or delete the clause that starts with “which provides a chance…” As written, the statement is host-centric and an oversimplification.
L54: change to “evidence has been given”
L57: change to “cells have been studied extensively” and provide references

Materials and Methods
L93: start at new paragraph at “When determining…”
L95: need to indicate that Fv/Fm values >0.6 are generally considered healthy/normal
L98: spelling. “photosynthetically”
L110: delete “Practically,”
L111: explain why values of 1.73 mM menthol and 0.13 mM DCMU were used (also, everywhere else DCMU concentration is reported in pM—why not do the same here?)

Results
L126: replication should be described in the methods.  Unless it’s really important, I don’t think indicating triplicate sampling should be done so often in the results.
L160: change “significant” to “measurable” or some other word; I prefer to use ‘significant’ only in the context of statistical results.
L173: move the clause that begins with “indicating a typical ROS burst” to the discussion, talk about it more, and include references.

Discussion
L180: again, I’d avoid “algal-depletion” and use coral bleaching
L183: change to “Diverse physiological performances among different Symbiodinium types have been observed with respect to thermal tolerance…”
L206-209: Rephrase.  This is a bit misleading, because D1a did produce ROS, while B1 did not (but B1 isn’t considered to be as stress-tolerant as D1a).  Moreover, one of the most heat resistant Symbiodinium is S. thermophilum, a C species.  This is why broad generalizations about clades should be avoided.


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: DIVERSE RESPONSES OF SYMBIODINIUM TYPES TO MENTHOL AND DCMU TREATMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: I commend the authors on a clearly written and professionally composed manuscript. If there were any areas where the text could be improved, lines 54-55 “…indicate coral bleaching caused by ROS generated by DCMU-treated Symbiodinium” reads a little unclear, and perhaps the term coral bleaching needs to be defined for the wider reader. Also Line 50 “…Symbiodinium depletion” may need to indicated that this is depletion from cnidarian host cells.

The references are generally sufficient, although I would like to suggest some more recent references in some areas:
Line 41 – there are many more detailed and recent references on the translocation of photosynthetic products and nitrogen cycling, e.g. Hillyer et al 2017, and Pernice et al 2015. A more relevant review of compound exchange than Douglas 2010 is Davy et al 2012.
Line 49 – needs a reference e.g. the review by Blackall et al 2015.
Lines 50-53 – there are many more recent papers investigating the mechanism of Symbiodinium depletion from host cells, e.g. the review by Weis 2008.
Line 80 –  “Exaiptasia” needs the reference Grajales and Rodrigues, 2014.
Line 173-174 – need a reference for this statement.

The raw data are complete and the tables and figures are all necessary to better understand the results. My only comments are that sample numbers would be helpful in the figure and table legends for readers to better interpret the results.
Experimental design: The methods are well explained and utilise well-established methods of investigating Symbiodinium functionality. However, I think some justification as to why all Symbiodinium types were tested under the same 25˚C temperature is required in the text. While I appreciate this is a traditional reductionist approach (to target PSII differences in response to the chemical treatments), this decision needs to be alluded to in the text. As shown recently by Silverstein et al (2017), there are variable effects of temperature on photodamage between Symbiodinium types. The 25˚C may have been suitable to the B1 symbionts (as this is presumably, the temperature the anemone hosts were maintained under?), but this may not have been the case for the other types e.g. we know D1a photosynthetic performance is hindered under low temperatures (e.g. Silverstein et al 2017). For example, line 148-149 – are B1 the most tolerant because this is their optimal temperature? When considering Symbiodinium type responses in terms of photosystem function and ROS production, some consideration of the experimental temperature conditions will make these methods and interpretation more robust.

Other areas where the clarity of the methods could be improved are:
Line 79 –  “corals were acclimated to lab conditions…” could be improved if there was a reference to another section of this manuscript or previous publication where these are detailed. The same point can be made for line 97.
Line 86 – DGGE is not currently thought to be the most effective way of identifying Symbiodinium type composition (e.g. Wham and LaJeunesse 2016), particularly if there may have been some background types, as suggested in line 86 with the description that only the “dominant” type was identified. This is particularly important in regards to the overall functionality of the Symbiodinium population, as background populations are functionally active (e.g. Cunning and Baker 2014, Cunning et al 2015).
Line 110 – A reference for how the Symbiodinium cells were counted would support these methods.
Validity of the findings: This study provides impactful information regarding the functional variability between Symbiodinium types. Specifically, this manuscript provides intriguing findings regarding the variability in sensitivity and ROS production between types. The statistics are well conducted and valid.
Additional comments: This manuscript by Wang et al provides a very important and interesting first step to understanding the mechanisms of menthol-induced Symbiodinium depletion in host cells, with vital comparisons to the traditional DCMU treatment. Furthermore, this paper is of great value to our understanding of the diverse responses between Symbiodinium types, particularly in ROS response.
Additional areas that may improve the flow of the text they are:
Lines 131-125 – The equations were very useful, although the authors may wish to consider whether they would be better placed in the methods section.
Line 194 -200 – This paragraph provides a useful background understanding of the cellular responses to menthol, and provides context for the following paragraph. For this reason, the authors may wish to consider combining the two paragraphs into one.