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: IDENTIFICATION OF AUSTWICKIA CHELONAE AS CAUSE OF CUTANEOUS GRANULOMA IN ENDANGERED CROCODILE LIZARDS USING METATAXONOMICS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript #31617 "Rapid identification of cutaneous granuloma pathogen that causes many deaths in crocodile lizards using metataxonomic next-generation sequencing" describes identification of Austwickia chelonae as pathogen for cutaneous granulomas in crocodile lizards. Experimentally infection was performed in Chinese skinks for confirmation of pathogenicity. The manuscript is well referenced and important for reptile medicine as well as conservation issues at least in crocodile lizards. Abstract and introduction is well written and later one provide a good background for the presented content. Structure of the manuscript is conforming with the journal standard, but needs improvement by reorder of the material and methods part as well as using of subheadings in the result part. Raw data are shared mostly, but Sequence of strain LK16-18 have to be stored in the NCBI database and Acc. Nr. have to be given.

Major concerns:
Material and Methods:
Line 102-105: As the lesions and animals, which suffered on this lesions, comes first before diagnostic methods, it should appear at first. Therefore, a subheading would be useful, like: Animals and sampling.
Please give coordinates of the Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve.
Please give a comment if the lizards were free living ones or not. If they were free living ones, give the capture method. Where do you samples the animals? I assume you sampled them in-house, as you stored the obtained samples immediately in liquid nitrogen.
Give age of the lizards, or at least if all were adult ones.
Please stated clearly under this subheading how many animals were sampled. In total 11 granulomas were sampled but it is not clear, how many animals were sampled, even not in table 1. Reference to Fig. 1 is not helpful, as eight locations of the granulomas are shown. Please add here also, if you have stored samples obtained from one animal different, as you mentioned later bacteriological cultivation, histopathology and scanning electron microscopy.
Line 140-146: This part needs more explanations and should be the last paragraph inside material and methods part.
How many skinks were infected, age of the animals, were they tested before infection? How long was the experimental period? What happens after the experimental part at the end with the skinks? How do you re-isolate the pathogen? Did you perform histopathology to obtain pathomophological correlate? Please insert this paragraph after Bacterial isolation and cultivation.

Results:
Subheading are needed for structure.
Line 191-192: This sentence is a method and should be added and explained more in the material and method part.
Line 194-196 have to be placed and discussed in the discussion part.
Line 201-204: This sentence has to be placed in the method part under subheading “artificial infection”

Figures:
Fig. 1: Delete or change number B, C, D and E, as animals were held without gloves on this photographs. As the zoonotic risk is discussed and at time point of sampling the outcome is unclear, it is not adequate to handle reptiles with skin lesions without gloves – biosecurity! Delete the term “symptoms and”. Please give explanation in the caption for labelling with A, B, C….
Fig. 2: Change or delete this micorphotograph. Use a lesser magnification, so that the whole lesion is shown. I assume a fibrinous granuloma, but it is not shown on the used micriphotograph. Grocott-Gomori's methenamine silver stain of the lesions would be useful to give an adequate histopathological correlate.

Tables
Table 2:
Definition of sensitivity grade is unclear. Please provide measurable data for replication of your results.

References:
References in the text have to be ordered chronologically. DOI numbers have to be included in the reference list.
Experimental design: Content of the manuscript is a veterinary one about a disease and finding of the etiological pathogen, which seems not to be covered by the Aims and Scope of the Journal.
Cause of cutaneous lesions in crocodile lizards has not described before, which has been identified as a knowledge gap. The diagnostic work up is interesting, advanced and an ethical statement is given, but the method part need much more attention for replication as well as for approving the robustness of given data.

Major concerns:
Material and Methods:
Line 147-150: What did you mean with “round papers containing antibiotics”? If you used standardized disk diffusion test, please state so and give the content and provider for the disks correctly. How many isolates were tested? Give the definition you used for sensitivity.
Validity of the findings: Major concerns:
Results:
Line 191-196: As you have not performed histopathology including PAS-reaction or Grocott-Gomori's methenamine silver stain in all 11 nodules to prove your molecular biological results, you can´t give such conclusion.
Line 199: Sequence of strain LK16-18 have to be stored in the NCBI database and Acc. Nr. have to be given here.

Discussion:
Line 246-253: Most of the given references in mamals and humans are for D. congolensis, therefore it is not useful mix both pathogens here. Please indicate clearly, in which species (excl. reptiles) infection with A. chelonae has described so far. To my best knowledge A. chelonae has only be isolated from reptiles so far, so that a zoonotic risk is unlikely according to the scientific knowledge.
Line 285-286: Co-infection with ranavirus seems to be very interesting, beside skin traumata, for formal pathogenesis of the disease. Why didn’t you examine your lizards for ranavirus to exclude this etiology? Please discuss this issue here.
Additional comments: Minor comments:
Title:
Change to: Identification of Austwickia chelonae as cause of cutaneous granulomas in crocodile lizards (Shinisaurus crocodilurus)
Material and Methods:
Line 104 and 106: delete the term “epidemic material”, as you sampled skin lesions or skin nodules
Line 106-108: Could you describe the composition of the soil sample and the origin of the water sample.
Line 130-132: add cultivation time
Line 142: change to Plestiodon chinensis
Line 152: delete “epidemic materials”, see above
Line 153-156: Grocott-Gomori's methenamine silver stain of the lesions would be useful to give a histopathological correlate.

Results:
Line 162-163: Delete this sentence, as already mentioned in the material and method part.
Line 169-170: Describe or name the cells you have seen.
Line 184-185: Delete sentence, as Koch´s postulates are well known to the readers.

Discussion:
Line 223: Please give a reference for the sentence: “Dermatosis…in lizards”, or delete this sentence.
Line 289-293: see above, include this part into the discussion above


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: IDENTIFICATION OF AUSTWICKIA CHELONAE AS CAUSE OF CUTANEOUS GRANULOMA IN ENDANGERED CROCODILE LIZARDS USING METATAXONOMICS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Spelling and grammar as well as structure should largely improve. References are missing in certain sections.
Experimental design: Especially the protocol for antimicrobial susceptibility testing is missing as well as the experimental inoculation protocol. Many other aspects are missing in the M&M and Results section as indicated below.
Validity of the findings: Certain inappropriate or invalid conclusions are made or should be nuanced 'see further remarks).
Additional comments: Few reports document the occurrence of a bacterial disease posing a conservation treat to a wild living, endangered Squamate species. Although this article provides valuable information this article should be thoroughly reworked.
Some general and more specific remarks are made below.

Title
The formulation of the title is awkward. Please use scientific terminology. What was the main goal of the study; revealing the causative agent of the observed disease or developing a rapid identification strategy? Why does it seem as rapid identification is the main emphasis, while the unravelling the role of the bacterium as a primary or facultative pathogen causing high morbidity in a critically endangered species seems to be more important?

Abstract
The abstract should be rewritten. It is unclear if the authors are talking about wild, rescued lizards or lizards that are part of a breeding/conservation program. What part of the wild population is affected (quantitatively, geographically,…)? The authors claim that serious diseases affect the population but eventually focus on a single clinical entity caused associated with a single agent.
Conclusions should be formulated appropriately: did the authors try to fulfill Koch’s Postulates? Is A. chelonae considered as a primary pathogen or a facultative pathogen? The use of antibiotics would only be a part of a control strategy. Is this really considered as a cure, a solution for this problem? Having performed antimicrobial susceptibility testing does not necessarily mean that the use of antimicrobials will be achievable or efficient in the field… What about the origin of the disease and the factors promoting it?

Introduction
L60: this sentence seems to be redundant
L61-64: reformulate. Clearly state the impact, occurrence of the observed disease. What are the other skin diseases besides the granulomas?
Did the lizards die because of the skin disease and why (also see further)? Did the disease appear in captive bred animals, wild caught animals? Was this also seen in wild animals?
L66-67: this seems to be a different clinical presentation. Did the authors sample these lesions?? Was A. chelonae also isolated and if yes, was it related to the other isolates obtained in the other site? If not, this information should be excluded or only mentioned in the discussion. In other words, did the authors investigate these animals?
The authors should explain what was found during necropsy of affected animals and how a dermal disease led to the death of affected lizards. What was the pathogenesis/pahtology? Please provide results of cultures (including mycology) performed on internal organs as well as histology. Was acid fast staining performed?
L71-72: Again, please check the entire text for grammar and spelling. Does this conclusion belong in the introduction? This needs to be discussed in the discussion section. A control strategy taking into account all factors that promote disease and allow the bacterium to have such an impact should be proposed.
L73: this should not necessarily be a general statement. Not all infectious agents can be cultured. The authors already assume that the observed skin disease has a bacterial origin in the introduction section while e.g. viral, mycotic parasitic and even non-infectious causes, environmental should be considered. For this reason the next paragraph should not(necessarily) be part of the Introduction.
L78: fertile? L84: noisy?
L90-95: please formulate the primary objectives of the study

M&M
This section should be ordered more logically. All materials and methods are focused on A. chelonae isolation and identification but at this stage all possible causes should have been considered and all methods used to screen or exclude these should be described here and in the Results section. Mycology, virology?
L105: 96 lizards showed the disease but only 11 were sampled. See previous remark: only lizards from one site were sampled? Why? Please describe full necropsy results. Other testing should have been performed as mentioned above. Please provide the results.
L140: inoculation? Why were Chinese skinks used? Why  was this inoculation dose used? Why was this inoculation route used? The entire follow-up period should be described: what signs were looked for, how many times a day, what were the housing conditions? Were animals/lesions sampled post inoculation? Etc.
L141: please clarify candidate pathogen
L151: Histology and SEM? L154: is this the most appropriate stain for A. chelonae?
What protocol was used for susceptibility testing and why? What are the limitations in comparison to another methods? Can the others draw conclusions based on a limited number of isolateS?

Results
L162: please provide numbers throughout time
L169: was acid fast stain, Gram staining performed?
The authors should discuss the importance of the cultured bacteria in the discussion in the light of known pathogenicity in reptiles/lizards based on the available literature: what agents were considered as contaminants vs pathogens.
It is quite unusual to have such elaborate mixed infection in a single skin lesion. The owners really need to explain this. Why was A. chelonae eventually selected? If they would have inoculated most of the other bacteria at the same dose subcutaneously diseases would also have developed I guess…? Please clarify.
Did the isolates fully correspond to A. chelonae based on sequencing. Were variations observed?
L175-176: What are the authors trying to state?
L186: the context seems to be missing? The criteria towards fulfilling Koch’s postulates should be explained clearer, how these were met and especially the reason why the authors chose A. chelonae as the main causative agent of the observed nodules. What is the role of the other bacteria that occurred in all lesions? Many of this will also have caused granulomas/abscesses if inoculated at the same dose? Why granulomas and not abscesses?
The main argument seems to be the SEM results. The histological and SEM findings should be described better. How were these samples processed to assess the importance of the other 4 bacteria that were found in all nodules?
L195-196: results of histology (was PAS stain performed) and culture should be included, otherwise this is too speculative.
L199-201: context?
L203: another seems to contradict the previous sentence. Why exactly Chinese skink? Again, the experimental inoculation protocol seems to be missing in the M&M and Results section: how many animals, how was follow-up performed, how many animal (!), general disease signs developed etc. How was the inoculum prepared? What isolate was used (type strain submitted)? How was the used strain related to the other isolates from the crocodile lizards and to other type strains of closely related Actinobacteria?
L207-208: please rephrase
L209: is the soil considered as the main source? What about other substrates? Can animals be asympotmatic carriers?

Discussion
This section should be rewritten and reordered. Check for correct referencing.
L219-222: this paragraph is poorly written. Please rewrite and certainly provide references (what literature data are available of outbreaks of infectious diseases with an impact (endangered ) in free ranging lizard populations or reptiles in general)?
L223: what does this sentence mean? References? L227: only agamids? Recent outbreak in wild iguanas has been published?
L233: see previous remarks? Do the authors consider this as a sound scientific approach?
L241-242/244-245: can this really be put forward as a conclusion? Specific for wildlife rather than e.g. sample type?
L246: Why did the crocodile lizards succumb to localized granulomas taking into account the literature described here? L260: supplementation What about the zoonotic potential
L268: Formulating an opinion about the route of infection and the reason why the lizards are susceptible to developing A. chelonae associated disease is highly important. Is the bacterium new in the lizards’ environment? Why have they become susceptible to wound infection? What research is needed to unravel this?
L282: What are the authors tring to say? Is A. chelonae a primary pathogen? What is the true importance?

Conclusion: please reformulate based on the previous remarks

Figure captions: the information provided should be provided more elaborately
Figure 1
Why do the lizards succumb to these relatively small skin lesions? Any proof for systemic infection (see previous remarks)?
Figure 6 and 9: relevance?


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: IDENTIFICATION OF AUSTWICKIA CHELONAE AS CAUSE OF CUTANEOUS GRANULOMA IN ENDANGERED CROCODILE LIZARDS USING METATAXONOMICS
Review round: 2
Reviewer: 1

Output:
Basic reporting: All points raised in the initial review has answered and corrected sufficiently. English is clear, references are sufficient, structure of the article incl. figs and tables presented understandable to follow the results and the hypothesis.
Experimental design: All points raised in the initial review has answered and corrected sufficiently. Identification of Austwickia chelonae as pathogen for cutaneous granulomas in crocodile lizards has been described. Experimentally infection was performed in Chinese skinks for confirmation of pathogenicity. The manuscript is well referenced and important for reptile medicine as well as conservation issues at least in crocodile lizards. Cause of cutaneous lesions in crocodile lizards has not described before, which has been identified as a knowledge gap. The diagnostic work up is interesting, advanced and an ethical statement is given. Method part has been improved, so that replication seems possible and underlines the robustness of given data.
Validity of the findings: Method part has been improved, so that replication seems possible and underlines the robustness of given data. Conclusion are well stated and linked to original research question.
Additional comments: Well done, thank you for corrections and answering all raised questions by the reviewers.


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

Input:
Title: IDENTIFICATION OF AUSTWICKIA CHELONAE AS CAUSE OF CUTANEOUS GRANULOMA IN ENDANGERED CROCODILE LIZARDS USING METATAXONOMICS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The structure of the article has improved by addressing the reviewers' comments. Spelling and grammar as well as structure should still improve. Several parts of the text can be formulated in a more scientific way.
Experimental design: The authors have done a good job by providing lacking information in the M&M and results section.
Validity of the findings: Certain statements and conclusions could be written more appropriately or can be nuanced more. See suggestions below.
Additional comments: Although the authors have made great effort to address the comments of the reviewers and the manuscript  has improved some concerns remain:
-	I think that the formulation/grammar of the title can still be improved.
-	In my modest opinion, grammar and spelling should still largely improve throughout the manuscript, especially in the abstract, introduction and discussion section. The authors do not always explain why they choose not to rephrase parts of the texts.
Several parts of the text can be written more concisely and clearer. E.g. in the abstract confusing information is provided (‘…have been increasingly infected by serious diseases, which cause many deaths in each year, especially the rescued and the breeding individuals…. However, pathogens underlying these diseases are unclear.’ contradicts the introduction ‘…, infectious pathogens in crocodile lizards have not been previously reported (Brady et al. 2016). ‘. The reader may assume that many (infectious) diseases are known in free ranging crocodile lizards, while they are mainly threatened by human influences. This manuscript details the occurrence of granulomatous skin disease in rescued/breeding animals by A. chelonae in ecological simulation pools. Could the disease be considered as a management related facultative/ opportunistic disease…? To give just one example: the authors correctly state that wound infection due to e.g. biting lesions may be an important facilitating factor but I assume that this facilitating factor is mainly important in the ecological simulation pools. Biting behavior is probably also common in wild individuals but relative overcrowding, high infection pressure, concurrent disease, immunosuppression, semi-natural conditions etc. is what might really enable the bacterium to cause largescale and persistent disease (after all the natural biting behavior in this species is there longer. Although the authors attempt to clarify this to a certain degree in the discussion, clarification of the occurrence of the disease and explaining why the bacterium causes the observed problem/disease could still be improved throughout the manuscript.
-	Is surgical excision and antimicrobial treatment considered as a realistic option? How will elimination of (subclinical) infection be confirmed? Following the identification of this pathogen as a cause of granulomatous dermatitis it may be considered that the focus should be on unravelling the facilitating factors that allow the bacterium to cause clinical infection, studying the possible presence of asymptomatic carriers and environmental persistency to be able to control this problem in the reserves. Should the authors focus more on the fact that this problem would not necessarily occur in a healthy, free-ranging population and that the disease may be vectored into the wild/other populations following (re)introduction from the affected population(s)?
-	The authors could try to reformulate several parts of the text. A few examples:
Introduction: ‘However, during the work of rescue and breeding, the crocodile lizards are prone to serious diseases that cause many deaths each year (Jiang et al. 2017). The most frequently disease is skin diseases.’ Please correct for grammar. Why would the lizards be prone to the work of rescue to serious diseases? What (skin) diseases besides the one that is described in this paper?
‘However, disease diagnosis of wildlife animals can be problematic due to lack of information regarding pathogens that cause these diseases.’ Why would identifying the cause of an enigmatic skin disease in wild animals be more challenging then in animals in a breeding program or even in captive animals?
Discussion: ‘While conservation efforts are currently focused on habitat protection, disease research is a problem that needs to be solved for all types of wildlife, especially for endangered animals, such as crocodile lizards, because the disease may significantly increase the risk of extinction for endangered animals’. Is disease research a problem? The authors may consider to write statements like this in a more concise and clear way.
-	The Conclusion section still does not seem to contain the major, most relevant conclusions from this study


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

Input:
Title: GEOCHEMICAL CHARACTERISTICS OF DISSOLVED HEAVY METALS IN ZHUJIANG RIVER, SOUTHWEST CHINA: SPATIAL-TEMPORAL DISTRIBUTION, SOURCE, EXPORT FLUX ESTIMATION, AND A WATER QUALITY ASSESSMENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The introduction ofarticle sufficiently demonstrates the need for research. The research question is clearly defined, relevant and of scientific significance.
The methods are described in detail and with all the necessary information.
The article is written in technically correct language. The structure of the article corresponds to the format recommended by the authors.
The data are reliable, statistically reliable, provided in the right quantity.
The conclusion is well formulated, linked to the original research question, and limited to confirmatory results. Overall, the research is very interesting, important, and it is certainly worthy of publication in the journal. This study has potential to be an important paper in this field. The article corresponds to the standards of the journal, it is a continuation of previously published articles and adds an useful information to the knowledge base.
There are a few issues that I think should be considered prior to publication. Most of these are relatively minor.
Line 87: it seems incredible - average annual precipitation ranges from 1200 to 2200 m.
Line 104: Link to Table S1, but the table is missing.
Line 382: Link to Table S1, but the table is missing.
On the graphs, the name of the axes in Figure 2 and in Figure 3 should be brought to a generally accepted standard. This would correctly correct the notation µg / L to µg L-1.
In Table 5, I recommend changing the format of the data presented. This format (1.47E-02) is very difficult to read.


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: GEOCHEMICAL CHARACTERISTICS OF DISSOLVED HEAVY METALS IN ZHUJIANG RIVER, SOUTHWEST CHINA: SPATIAL-TEMPORAL DISTRIBUTION, SOURCE, EXPORT FLUX ESTIMATION, AND A WATER QUALITY ASSESSMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: See below
Experimental design: See below
Validity of the findings: See below
Additional comments: The manuscript has a nice comprehensive dataset presenting a large spatial-temporal distribution of metals in the Zhujiang River. And the work on calculating WQI and health risk assessment is very helpful for readers. More importantly, the authors did find a significant heterogeneity in season and space. Therefore PCA and export fluxes are also important and meaningful for scientists in the community. These are the major strength of the MS.

Major concerns here is as following:

1)      The authors made a statement that the water in Zhujiang is suitable for drinking with a low risk based on all hazard index <1.  Here obviously factors influencing water quality is more than several metals in MS, and generally high E. coli or some toxic metals like As commonly occur at some sites. As the work done here never cover those more important parameters, I would suggest the authors narrowing down the statement. For example, the metals measured in this study are all below the hazard level (which is ~~~) if this is true.

2)      PCA led to a conclusion “dissolved heavy metals in Zhujiang River are mainly derived from natural sources 35 controlled by rock weathering, while the contribution of anthropogenic source to heavy metals in 36 river water is relatively weak”. I agree with the point, and however, I didn’t see the logic between PCA and the conclusion. Instead I will suggest that the author consider list which metal(s) are good indicators of rock weathering, (like Ba), which are good for anthropogenic source (e.g., Pb, Cu). And carefully discuss their pattern, and make a more solid logic here. Previously several groups of researchers have done mineral composition work in the watershed, for example, Jing Zhang’s group. Also there is a huge amount of published papers which could be easily assessed online.

3)      Export budget shows with higher fluxes for several metals including V, Cr, Ni, Ni, Mo. Considering the Zhujiang is 13th largest river in the world. It is not surprising, that many metals have higher fluxes than the world average. I suggest that the author go further and think add more calculations, for example, compare the differences of two seasons.

4)      Another big issue is that several metals are easily contaminated during sampling and processing. One example is Pb, which could be easily contaminated due to tiny dust in atmosphere. Although the river water usually have high levels of these metals, careful sampling and processing is still important for high quality.  In the dataset, I see a few spots, for example, one point of Pb at XJR with relatively high level. Most of the data are in good quality and make sense, however please double check those discrete points with extremely high values.

5)      Another issue is the high levels of Cu in NPR in two spots. By the way, that level of Cu (~70ug/L) is not safe any more based on drinking standard in China. I would again suggest the authors refrasing sentences within the MS accordingly. These data should clearly suggest of anthropogenic sources, and so further anthropogenic source must be identified or suggested, although only a few spots that I think these measurements are correct.


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: GEOCHEMICAL CHARACTERISTICS OF DISSOLVED HEAVY METALS IN ZHUJIANG RIVER, SOUTHWEST CHINA: SPATIAL-TEMPORAL DISTRIBUTION, SOURCE, EXPORT FLUX ESTIMATION, AND A WATER QUALITY ASSESSMENT
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript by Jie Zeng  et al. addresses environmentally important question and the general topics is pertinent to the profile of the journal. However, the study has little added value as neither the controlling factors nor the fluxes of metals could be determined. The title therefore does not reflect the content of the paper.

First, the choice of metals is arbitrary and incomplete, despite the fact that ICP MS was used. The authors did not measure Fe, Al, Zn, Sr.
The DOC and Fe are widely recognized as main carriers of trace metals in river waters, in the form of organic an organo-mineral colloids. I do not request characterizing those colloids, but neither Fe nor DOC was analyzed in this study.
Finally, the export fluxes could not be quantified. The two sole sampling campaign of the river (two periods) are clearly insufficient to measure the export fluxes. The temporal frequency should be at least ten times higher
Experimental design: Insufficient.
Validity of the findings: Unlike what is claimed by authors, the export fluxes could not be quantified. The two sole sampling campaign of the river (two periods) are clearly insufficient to measure the export fluxes. The temporal frequency should be at least ten times higher
Additional comments: The manuscript by Jie Zeng  et al. addresses environmentally important question and the general topics is pertinent to the profile of the journal. However, the study has little added value as neither the controlling factors nor the fluxes of metals could not be determined. The title therefore does not reflect the content of the paper

First, the choice of metals is arbitrary and incomplete, despite the fact that ICP MS was used. The authors did not measure Fe, Al, Zn, Sr.
The DOC and Fe are widely recognized as main carriers of trace metals in river waters. Yet, neither Fe nor DOC was analyzed in this study.
Finally, the export fluxes could not be quantified. The two sole sampling campaign of the river (two periods) are clearly insufficient to measure the export fluxes. The temporal frequency should be at least ten times higher


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: CORAL-ALGAL INTERACTIONS AT WEIZHOU ISLAND IN THE NORTHERN SOUTH CHINA SEA: VARIATIONS BY TAXA AND THE EXACERBATING IMPACT OF SEDIMENTS TRAPPED IN TURF ALGAE
Review round: 1
Reviewer: 1

Output:
Basic reporting: Throughout most of the manuscript, the English language needs improvement. For example, lines 26-27, 29-31, 39-42 could be improved because the current phrasing is difficult to understand. In the line by line comments I stated “unclear” to indicate some of the hardest to understand

Also, it should be Lobophora variegata not variegate

Several of the studies that were cited were not the best citations for the statements made and were often misleading. For example:

Lines 237-8  Neither of those studies looked at allelopathy in turfs – the Rasher and Hay only tested allelopathic effects of macroalgae and the Jompa and McCook study hypothesized that effects of the turf species were allelopathic.

References to McCook 2001’s review paper- polyp and tentacle and coral sex were not the focus of any of these studies were hypothesized, but not tested, please make it clear in the text when citations are based on ideas from other papers and have not been explicitly tested

Line 291: Carpenter and Williams 1993 is not about sediment, it was about algal turf height due to grazing and flow profiles, and the implications for reef metabolism, a reference in regard to sediment seems out of place.

The structure of the article was clear.

The hypotheses should be explicitly stated in the introduction, they were mostly relayed in the methods and the results.

From the goals, especially for the sediment-algal turf surveys, I expected a manipulative experiment not a survey- this should be clear in the introduction.
Experimental design: The aspects of this research that are addressing research gaps needs to be emphasized to help focus readers in the introduction

More details are needed in the methods section in order to ensure that this project could be replicated.  Below are examples of the parts that were difficult to understand

There should be information about the study site and the corals and algae that are being studied, especially since so much detail was completed on differences among coral functional groups. Massive and encrusting should be defined and which corals belong to those categories should be stated explicitly.  Additionally, ~50% of the benthic composition were corals and algae, but what made up the remaining 50% ?

Different sites were examined, but there is no information about why there are different sites and what the differences among the sites are.

Additionally, how far apart were the transects, were they meant to describe these sites?

Another aspect of the experimental design that was not clear was if the same transects/quadrats were used for all of the sub studies (coral cover, macroalgal cover, coral-algal interaction extent)

More information about the video transects would be helpful for the repeatability of this project. Additionally, the pixels of the camera would be helpful to get an idea of how clear the image was for identification. Here are some of the questions I have”
        What was the distance between the camera and the benthos?
        Were the distances consistent?
         How were the videos completed, with a diver?
	What happens if a coral colony extends across the distances sampled?
	How does that affect the coral extent measurements?

Also – how were distances along the transect determined to make coral cover measurements – were they random?

It was not clear how the authors determined colonies – what defined a colony? Could the same colony extend past a quadrat?

Top-view photos were not explained before they were mentioned or how that was achieved

The descriptions of extent of algal contact and how percentage of contact were determined should be clarified
	i.e., was it the percentage for a particular colony or for all of the colonies in a quadrat?

Only algal winners were described, coral wins and neutral interactions need to be described as well to help understand how these categories are assessed

To determine sediment cover it was not clear from the description or from figure 2 how sediment cover was determined if the turf was not heavily covered in sediment – even the no sediment seemed to have some sediment. Were photos zoomed in to determine this? By how much?

In the statistical designs, careful attention should be taken to the pseudoreplication of this project. From the descriptions of the methods and statistics it appears that all quadrats or all points or colonies are treated independently, please see Hurlbert 1989 for more information about pseudoreplication.
Validity of the findings: Based on the statements made in the results, some of the statistical tests used were not the best to test for the interactions of interest. This is particularly true for the ANOVAs that were run for morphology vs sediment presence/absence. It was treated as a one-way ANOVA, but I think it would be better treated as a 2-way ANOVA with morphology and turf sediment, this way, if there is an interaction between morphology and sediment (which was suggested based on conclusions made about encrusting corals and the presence of sediments), could be made with statistics backing it up. Here is also an instance where pseudoreplication could be taken care of – i.e., if colony was nested within transect (although this is still ignoring site).

Several statements in the discussion were stronger than they should be based on the data collected and other studies.
	For example, line 232 states that turf “always results in the bleaching, overgrowing or killing of corals,” which was not true in the study that was conducted here or in the studies that were cited.

        Additionally, the first paragraph discusses bleaching vs overgrowth of turfs, which was not directly tested in this study.
Additional comments: Additional sources for sedimentation and coral-algal interactions

McCook, L. (2001). Competition between corals and algal turfs along a gradient of terrestrial influence in the nearshore central Great Barrier Reef. Coral Reefs, 19(4), 419-425.

Gowan, J.C., Tootell, J.S. & Carpenter, R.C. Coral Reefs (2014) 33: 651. https://doi.org/10.1007/s00338-014-1154-1

Figures:

Figure 2: It is not clear what the description of 2D means. From the figure legend it sounds as though the sediment was manipulated, however, based on the text, it does not seem as though sediment presence/absence was manipulated.

Raw data:
Please provide metadata for each of the datasets (i.e., sheets).
Benthic cover sheet
	Live coral cover (m) is this referring to the point where the measurement was made? How were these locations chosen?
	Why are there fewer points for W4-2?

In Algal composition around coral sheet
	“No algal contact” would be good to show in the data, because otherwise it seems as though every coral is in contact with algae.
	Misspelling: coral border

On the following sheets: algal composition, competition outcomes and turfs effect on corals there is no information about the sites and transects.

Line by line comments (some repeated from overall comments)

Abstract

Lines 26-27: wording unclear, should be:
Comparing coral-algal interactions in the presence and absence of sediment showed a significantly more negative effect of turf algae on massive and encrusting corals

Lines 29-31: wording unclear

Introduction

Lines 39-42: wording unclear

Line 48 – polyp and tentacle and coral sex were not the focus of any of these studies , and in some cases (i.e., McCook 2001) were hypothesized, but not tested, please make it clear in the text that these are hypothesized, but not tested.
Line 54 – references have two Barott 2012 papers – be clear which one this is
Line 69 – damaged contiguous tissue wording is unclear
Line 77 – “later trap sediments” not clear
Line 92 –Lobophora variegata not variegate?

Methods

Line 117-118 – were these transects in the same location as the macroalgal surveys or were the methods just the same? The wording for these sentences was unclear.

Line 121 – within the quadrats? I think more information is needed about the video transects – what was the distance between the camera and the benthos? Was a quadrat videoed for the extent? What if the same coral colony extended across more than one quadrat?

Line 124 –how did you a define a colony in a quadrat?

Line 128 – first time a ruler is mentioned and top view pictures – not sure what this is referring to, needs a clearer description of how the extent was measured and how percentage determined – the total perimeter for that coral or within the quadrat determined the percentage of contact?

Line 131 – I do not understand this description for how outcomes of interactions were identified

Line 132 – for each colony, how was win/loss determined? For each algal group associated with the coral, or once per colony in a quadrat? Were multiple outcomes assessed for a single colony?

Line 133 – how were coral wins and neutral interactions identified?

Line 140 – this was all identified from the photos? How magnified were the photos to assess sediment cover? Was there variation in the amount of sediment cover? Again, was this 1 interaction per colony or for every measurement with an extent?
From the introduction I expected a manipulation here, not a survey of sediment no sediment.

Line 148 – date = data?
Line 149 – wording unclear

Line 150 – does “on the same colony” mean for each individual coral or across coral genera – I think it means individual coral from your photos and raw data, but that should be clarified.

Results

Line 169 – The major algal functional group was turf algae (24%).

Line 211 – I think t-tests were completed, but what about a 2 way ANOVA comparing coral genus and algal type? That way the statements can be made for  determining which corals experienced more damage and which algae created more damage in a single analysis

Line 218 - How were letters determined? Through a post hoc test? Which one?

Line 186 – varied significantly?

Lines 207-8, unclear wording

Line 232 – “always result in the bleaching or overgrowth…” of corals is too strong of a statement and the data from this study does not support that conclusion.

Line 234 – instead of “confirmed”, “supported” would be a better word

Line 235-6 – unclear wording – remove "the" before bleaching

Lines 237-8  neither of those studies looked at allelopathy in turfs – the Rasher and Hay study only tested allelopathy of macroalgae and the Jompa and McCook study hypothesized that effects were allelopathic

Line 240 – unclear wording

Line 241 – none of the data shows a bleaching effect of algal turf – this should be clear that this is an observation

Line 242- direct overgrowth

Lines 260-264 – unclear wording “at present research”; “Porites has been found…, yet…”  - I think should be an “and” instead of “yet”; “more dependent on the specificity of the corals” not sure what this is supposed to mean

Line 265 – again, I think that polyp size was a discussion point made by McCook and not something that has been tested. If the present authors want to test that hypothesis, they should do so explicitly, which was not completed, although it was discussed as though it was (line 271)

Line 291 Carpenter and Williams not about sediment, it was about algal turf height due to grazing and flow profiles, and the implications for reef metabolism reference in regard to sediment seems out of place.

Lines 304-5, unclear language

Conclusion

Line 307 – too strong of a statement that turf outcompetes corals more than macroalgae and claiming that it “confirms” this, which I do not think is well established. Additionally, because the opportunity for coral-algal contacts between algal turf and coral were generally higher than between coral and macroalgae it is hard to state that algal turf is a better competitor with corals than macroalgae, especially if other interactions with macroalgae maybe led to coral death, thus there would be no evidence of the contact on the reef.

Too much emphasis on large and small polyps without directly testing it – this is a result that has been discussed (i.e., in McCook 2001), but not explicitly tested


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: CORAL-ALGAL INTERACTIONS AT WEIZHOU ISLAND IN THE NORTHERN SOUTH CHINA SEA: VARIATIONS BY TAXA AND THE EXACERBATING IMPACT OF SEDIMENTS TRAPPED IN TURF ALGAE
Review round: 1
Reviewer: 2

Output:
Basic reporting: Basic Reporting:

Clear unambiguous professional English language used throughout: NO.

     The English grammar and writing need some work. There are numerous grammatical mistakes throughout the paper. There are also many sentences which are unclear. To highlight these issues, I refer to the last two sentences in the abstract (Lines 26-31). The use of presence and present is incorrect (Line 27), and there is incorrect spacing between words (Line 28). The last sentence of the abstract begins with a dangling participle phrase, which makes the sentence very unclear. There are other numerous grammatical errors throughout, which make the paper difficult to understand, including changing tense within paragraphs and even within the same sentence (see for example lines 185-186) and numerous run-on sentences. There are also many uses of the noun form of words as adjectives (e.g., line 205). Lastly, the authors switch freely between British and American spelling of words.

Intro and background to show context. Literature well-referenced &relevant: OK

     The introduction, as it stands, is relatively well-referenced. However, it is a bit of a collection of facts rather than a logically organized introduction to the material that clearly discusses current knowledge gaps and problem in the field that the authors’ work serves to address.

Structure conforms to PeerJ standards, discipline norm, or improved for clarity: OK

     Most of the structure and formatting of the paper seems to conform to the standard norms in the field. One small note is that the in-text references do not have a comma between author and the date. Also, in the reference list, the DOI numbers should be directly following the end of the reference rather than being on a separate line with a different indention. Lastly, as per PeerJ standards, there should not be funding sources included in the acknowledgments section.

Figures are relevant, high quality, well-labeled and described: NO

Figure 1: Countries other than China should be labeled on the map. Latitude and longitude, as well as a scale bar,  should be included in the top panel. A table should also be included that details the site level data such as latitude, longitude, coral cover, and the number of samples taken at each site. Much of this aforementioned metadata could also be shown visually on the map.

Figure 2: Apart from the poorly written figure caption, this figure is mostly OK. I would suggest a scale bar in panel E. Also, after looking at the other panels it is concerning that most of their corals look incredibly small in these interactions (i.e., < 5 cm in diameter).
Figure 3: For all of the bar graphs, I suggest that they change them to box and whisker plots and include the number of samples (i.e., n = ?). The Genus and species names should be italicized.

Figure 4: This needs to be a box and whisker plot. There should also be some indication of significant differences between groups. Both panel A and B should have the horizontal axis labeled. Panel B has no indication of the variance. There needs to be an indication of sample numbers for each group (i.e., n = ?). All of the same goes for Figure 5. Also, there should be consistency in the use of the words corals edge. Throughout the paper, it is written as “corals edge” and “coral’s edge”, when I think they actually mean corals’ edge.

Figure 6: What happened to the Lobophora bar for Pavona, and the Bryopsis bar for Platyyra. Once again, these would be much more effective as box and whisker plots.

Figure 7: The +S and -S should be defined in the caption, i.e., they should not say that “+S = Turfs + S” they should say that +S = Turfs with sediment.

Table 1: they should report their actual p-values, not just *s. They should also report their sample sizes.

Table 2: They need a more descriptive caption. Again, report the actual p-value.
Raw data supplied: Yes
Experimental design: Original primary research within the scope of the journal. Yes

Methods described with sufficient detail and information to replicate. NO
In some parts of the methods, it was hard for me to follow due to grammar errors and poor clarity. In the Statistical analyses section, the authors say that “date [I assume they meant data] were transformed”, but they do not explain how.
Validity of the findings: Validity of finding

Data is robust statistically sound and controlled. Not really

     The data in the results section is presented like there is just a single number for percent of the perimeter in contact with algae, types of algae in contact with coral, etc. Are these really single values, e.g., was there actually 44% of all coral perimeters in total that came into contact with algae (line 174) or was there on average 44% of each coral colony that was in contact with algae? It seems that the authors should report the average percent perimeter in contact with algae, not just the overall total. If these numbers are averages then they should report the sample size for each group, the mean, and the standard deviation, i.e., (n = x, mean + std). Also, throughout the results section and in the tables the authors should report the actual p-values and not just p<X such as in line lines 180, 182 and elsewhere. The authors should also report p-values when they state that things were not significant, or that results were similar between groups.

     They should also make sure that proper and consistent use of the words “between” and “among” is used throughout the paper, as these words imply two different things statistically. For example, in line 185-186 the authors state that “turf algae was the largest and vary [grammar error] significantly among coral genera…” However, it seems as though they actually mean that this varied significantly between genera not among them. Another example is line 216-217 “negative effects…differ from coral genera.” This should also be between coral genera.

     In the Statistical analyses section, the authors state that they transformed the data to be homoscedastic and then performed ANOVAs, but if the data still was not homoscedastic then they used non-parametric analyses. Why not just use non-parametric analyses to begin with instead of transforming the data and then using different tests for different portions of the dataset.

Conclusions are well stated, linked to the original research question, and limited to supporting results. NO

     The discussion section makes many conclusions that are not well-supported by the data. Some examples include the following:
1)	Lines 255-257: “The interactions between macroalgae and coral varied with algae species, and these differences may be ascribe to the growth pattern and the ability of allelopathic of algae.” Apart from the numerous grammar errors in this sentence, the authors also provide no data which would establish a role of allelopathy in the effects of algae on coral.
2)	Lines 301-304: “Hence we conclude that the high frequency of coral–algae contacts and the more negative effects of turf algae on corals should be attributed to the increasing of sediment trapped in turf algae and the decreasing abundance of herbivorous fish.” Here the authors conclude that herbivorous fish somehow play a role in the effects of algae on coral. Although it is plausible that fish may play some role, the authors present no data on fish and do not even provide references from the literature that might support this claim.
3)	Lines 231-232: “ Turf algae… can always result in bleaching…” Here the authors discuss the role of turf algae in bleaching although they do not measure bleaching at all in the study. Also, always is a major overstatement.
Other examples include lines 241-242, lines 246-248, and lines 281-284.
Additional comments: This manuscript by Liao et al. provide in situ data from the South China Sea to argue that the frequency, extent, and outcome of corals interacting with benthic macroalgae are a function of the type of species of the coral. They also argue that the settlement of sediment in turf algal assemblages enhances the negative effects of algae on coral.
	The manuscript is within the scope of the journal and would be of general interest to coral reef biologists. Although the manuscript follows the formatting guidelines of PeerJ, it suffers greatly from a lack of correct English grammar and sentence structure. This leads to the manuscript being hard to follow and confusing at some points. Aside from the grammar and English the visualization of the data, and overall conclusions need some improvements as listed below. As the manuscript stands currently, it is not fit for publication in PeerJ. I would suggest to reject the manuscript with a chance for resubmission after major 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: CORAL-ALGAL INTERACTIONS AT WEIZHOU ISLAND IN THE NORTHERN SOUTH CHINA SEA: VARIATIONS BY TAXA AND THE EXACERBATING IMPACT OF SEDIMENTS TRAPPED IN TURF ALGAE
Review round: 2
Reviewer: 1

Output:
Basic reporting: I struggled with English grammar, word choice, phrasing and unclear definitions throughout the manuscript. This continues to make understanding the manuscript difficult. Additionally, there were several instances of misspellings or poor proofreading (e.g., missing the end of the word, or the incorrect word), including spelling errors that I had previously commented on (e.g., Lobophora variegata not variegate). In terms of unclear definitions it was often not clear what was described, for example – line 55-57, it was not clear to me what dynamics were being referred to, nor what was meant by the algal properties. Other instances were the use of negative effects of algae – was this the frequency of algal winners?
Intro & background to show context. Literature well referenced & relevant.
I found the intro and background to be much improved, but the hypotheses/objectives were not clear, in particular the third objective. I did not understand the motivation or what was referred to in terms of “morphological advantage”, I think some of the information in the discussion could be used to motivate this point, in particular line 318.

Structure conforms to PeerJ standards, discipline norm, or improved for clarity.
Yes, this was fine

Figures are relevant, high quality, well labelled & described.
Figure 1 – no error associated with the means, no information about transects
Figure 2 – labeling should be more specific to each photo. 2D – it’s not clear if the sediments were physically removed by the researcher or if the photo shows low sediment
Figures 4 and 5 – I do not understand the difference between the purple and green shading in the bars. Why there are capital and lower case letters for the SNK post hoc tests is not clear
Figure 6 – SNK results not clear based on what is written in the figure caption –SNK seems to shows the differences among the genera, not when there are differences within a genera.
Figure 7 – what is “negative effect” is it the same as an algal win? This was never defined…This result was confusing because the asterisk use makes the results seem like a t-test was used (which was written in the text), but an interaction result was shown, indicating that a two-way ANOVA was run on the data, and a multiple comparisons test (like SNK) should be used, as a t-test will increase your probability of type I error.

Table – Unclear what the p values associated with each genera (the last column), or the last row (Between genera) was referring.

Raw data supplied (see PeerJ policy).
Summarized data provided (Table 1)
Experimental design: EXPERIMENTAL DESIGN
Original primary research within Scope of the journal.
Research question well defined, relevant & meaningful. It is stated how the research fills an identified knowledge gap.
This is improved upon revision, but as above, I found the objectives of the study not stated clearly, and the points highlighted here (e.g., meaningfulness), not stated clearly.
Rigorous investigation performed to a high technical & ethical standard.
Because I had difficulty understanding the methods and analyses, I cannot assess this. Additionally, the results do not clearly show the results of the tests used, nor which test was used – whether it was an ANOVA or a Kruskal-Wallis test.
Methods described with sufficient detail & information to replicate.
I struggled with the methods. In particular the use of length, is this meant to indicate perimeter of corals? Was it measured from the photographs? Was anything measured in the field? How was the line-intercept method employed versus CPCe?
Speculation is welcome, but should be identified as such.
There were several instances in the discussion (see line by line comments) where there were statements made with no clear data to back them up
Conclusions are well stated, linked to original research question & limited to supporting results.
Again, there was the use of dynamic, which was not supported by the results. The last statement is a strong statement, especially in regard to their last result – where it’s the an interaction between sediment and coral growth form that highlights differences in (I think Algal wins?) as the severity of the effects of sediment depend on coral growth form.
The discussion over states the results, as there were points made that were not explicitly compared (e.g., polyp size of corals, “damage” effects of algae).
Validity of the findings: VALIDITY OF THE FINDINGS
Impact and novelty not assessed. Negative/inconclusive results accepted. Meaningful replication encouraged where rationale & benefit to literature is clearly stated.
Data is robust, statistically sound, & controlled.
Although there was discussion of sites and transects, there was no description of how transects or sites were taken into account in data analysis. For example, were results averaged over quadrat or transect? What is the level of replication?
I found parts of the statistics section difficult to understand.  In particular, I did not understand why a t-test was run after conducting a two-way ANOVA. This is inappropriate, especially given the significant interaction between genera and presence of sediment.
Additionally, although p-values were given, there were no degrees of freedom or F-values provided to aid in the replication of the results (and give an idea of replication).
For the results, such as in line 220, information is provided for overgrowth and bleaching, but no data is shown to compare these (unless green and purple are supposed to indicate that?)
In the methods, results and discussion, there were several misleading statements. For example “negative effects of algae on corals” was often made, what is this referring to? It sounds as though an experiment was conducted or a long-term survey. I think it may be referring to algal wins. However, as I read this, this survey happened only once, and so this shows a snapshot in time, not necessarily long-term effects of algae on corals. Thus these results are not “dynamic” which is another point that was made by the authors (e.g., line 352).  There should be a discussion point about how the data taken were from a snapshot in time, and not necessarily indicative of dynamics of coral-algal interactions on reefs.
Line 263 – I found the interpretation of the interaction difficult to understand, and really do not understand why a t-test was conducted after the two way ANOVA and not a post hoc test that would take into account multiple comparisons.
Additional comments: Line by Line comments:
Abstract –
Line 24: “Absent the effects of sediments” – is poor workding\
Line 29: “Morphological superiority” – unclear what this means
Line 42-44: poor English
Line 53: “witch” should be which
Line 55-58: not clear
Line 71: Logic bounces back and forth between turfs having an effect and not having an effect, which is confusing
Line 75: Unclear what “cause in underlying benthic communities” refers to
Line 77: Not clear how water flow influences sediments in this sentence, or why this is relevant
Line 84-88: I think this is meant to help define the knowledge gap, but does not highlight how this work fills in a meaningful gap in knowledge – but the critique that it starts with (“field surveys of coral-algal interactions are still insufficient….) is exactly what the authors do in this study
 Line 97-98: Again, “morphological superiority” is not clearly defined, so this hypothesis is not clear.

Methods
Line 118 – runon sentence
Line 122-23: I do not understand how CPCe vs the line intercept method was used. Why was coral length measured? Is this supposed to be the perimeter of each coral? Was this done in the field?
Line 125: m/min? not m/mine?
Line 132-134: unclear, not sure what this means
Line 146: unclear wording “interfacial algae” and “damaging adjoin algae”
Lines 152-154: unclear what growth form means – is this meant to be analogous to morphology? Does upright mean branching?
Line 158: “large” should be “larger”
Line 162: poor grammar
Line 179 – not clear if negative effects indicates algal wins or a different designation was used.
Line 181- the rationale for the t-test is not clear, and it is an inappropriate test to use, why not an SNK test?

Results
Line 198 – the number of corals and total perimeter: does this mean that site and transect were ignored? Were there corals with multiple measurements for proportions of wins/losses/neutral? If so, then a treating coral, at least, as random effect would be appropriate (because it’s possible that there is variation due to the specific corals used).
Line 235: unclear grammar

Line 250: “damaging effects” is not clear, again, is this algal wins? This statement makes it sound like a longer –term survey or experiment was conducted
Line 256: “to” should be “on”
Line 263: unclear grammar
Discussion:
Line 278: no data to support this statement
Line 282: “allelochemical competitions” not clear grammar
Line 284-5: high density of biomass – does not make sense
Line 302: “may be ascribe…” – not clear grammar
Line 314: first time since the introduction that polyp size was introduced – not data on this
Line 334: use “comparatively” but there are no comparisons
Line 337: units incorrect, I think “a” should be “s”
Line 352: “dynamics” were not studied


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: CORAL-ALGAL INTERACTIONS AT WEIZHOU ISLAND IN THE NORTHERN SOUTH CHINA SEA: VARIATIONS BY TAXA AND THE EXACERBATING IMPACT OF SEDIMENTS TRAPPED IN TURF ALGAE
Review round: 2
Reviewer: 2

Output:
Basic reporting: Clear unambiguous professional English language used throughout: NO
	Although many of the grammatical mistakes in the first version have been corrected, there are still numerous grammar and spelling errors throughout the paper. This makes the paper hard to read and difficult to understand in some areas.

To highlight the grammar errors I refer to the abstract and introduction.

Line 21: The word "with" should be replaced by the word "between".
Line 24-25: The sentence which reads, "Absent the effects of sediments, the negative effects of turf algae on coral genera increased 1.1-1.9 times." does not make sense. The following sentence is also confusing, as it starts out by talking about comparing the presence and absence of sediment, but then concludes by talking about the effects of coral morphology.
Line 29: "competitive" should be "competing"
Line 42 -44: "The outcomes of such interactions are mainly determined by the species involved, since the variability of mechanisms and strength of different coral-algal interactions." is a sentence fragment, not a complete sentence.
Line 47-50: The phrase beginning with "Barott et al." on line 47 is a run-on sentence.
LIne55-58: another run-on sentence
Line 68: "damaged" should be "damage"
Line 70: Subject verb agreement: "seems" should be "seem"
Line 84: "researches" should be "researchers"
Line 85: "interaction" should be plural
Line 97 is missing a preposition. it should probably read, "... enable their competitive overgrowth of coral..."

This list of errors is by no means comprehensive, and is only what I found in a quick pass of the abstract and intro, but the grammar and English errors don't stop there, as there are still numerous errors throughout the entire paper.

Introduction and background show context, literature is well-referenced and relevant: OK

The introduction has definitely improved, however, there are still some places where statements need to be supported by a reference. Some examples include the following:

Line 35-36: "This is particularly pronounced in reefs where human activity is frequent. " should have a supporting reference

Line 36-39: The sentence starting on line 36, which reads, "...owing to overfishing (REF), eutrophication (REF), sediment deposition (REF), and global climate change (REF)." should have a reference for each of the proposed factors.

Line 42: The statement, "The outcome of such interactions are mainly determined by the species involved..." needs a reference

structure conforms to PeerJ standards: Yes
Experimental design: Methods described with sufficient detail and information to replicate: OK

The numerous grammar errors in this section still make it a little hard to follow.

My biggest concern was the authors' statistical analyses. They state that if data were not homoscedastic then they log transformed the data and used parametric statistics. In their rebuttal they state that they did this because they " think that the accuracy of the parametric test is higher than the non-parametric test.", but this is simply not true. It is not about being "more accurate" it is about using the appropriate statistical test for the dataset. By log transforming the data they do meet homoscedasticity but this is only because they are not only logrithmically compressing the data, but also logrithmically compressing the variance. Thus, when they log transform the data and then use paramtric tests they are more likely to get significant p-values. They even state in their rebuttal that they know that the non-parametric tests on the untransformed data may report non-significant p-values, while the parametric tests may report significance. To me this basically seems like a form of p-hacking. If the data do not meet the requirements of a statistical test, don't transform the data until they meet the requirements; instead use the appropriate statistical test for the type of data you have. This would also solve the problem of having different analyses used for figures 4 and 5.
Validity of the findings: Figures are relevant, high quality, well-labeled and describe: NO

Figure 1 is much better!

Figure 2 is fine.

Figure 3: The caption should read, "percent of coral on coral reef of Weizhou Island", not "in". Also, the caption should be a bit more descriptive. Lastly, the Figure 3 panel B reports data for B. Plumosa, but in the text they report on B. pennata, and in Figure 6B they report data for B. plumose. This is a blatant mistake and needs to be corrected.

Figure 4: I have read the author rebuttal, but still think that at least panel A should be shown as a box and whisker plot so that the entire spread of the data can be seen. Also, why are both purple and green used to indicate algae winning, is there a difference between the purple win, and the green win? Lastly, there should be a legend for the colors in the figure not just a description of the colors in the caption.

Figure 5: Same as Figure 4 Also, I don't like that they used different analyses for the two different figures (i.e., parametric tests in Figure 5 and non-parametric tests in Figure 4).

Figure 6: once again I still think that box and whisker plots would be more informative so that readers can see the full variance in the data. Also, I think that both vertical axes should be labeled in panels A and B.

Figure 7: "Asterisk" should be plural (i.e., asterisks). Also, significant differences should also be shown between the two growth forms.

Raw data supplied: Yes

Original primary research within the scope of the journal: Yes

Conclusions are well-stated, linked to the original research question, and limited to supporting results: OK

The discussion and conclusion have significantly improved from the first submission, but I still have a couple of small comments, which follow.

There are still some grammar and spelling mistakes in this section

Line 281: They might want to add the references Microbial bioenergetics of coral-algal interactions (Roach et al, 2017), Visualization of oxygen distribution patterns caused by coral and algae (Haas et al, 2103), and Biological oxygen demand optode analysis of coral reef-associated microbial communities exposed to algal exudates (Gregg et al, 2013) to the references about microbial growth and hypoxia, as these recent publications show a clear link between microbial growth and algal induced hypoxia.

Line 337: "a¬-1" should probably be "s-1", as it is talking about a rate.

Line 344-345: The authors state that the fish density of 0.03 ind m2 at Wheizhou reef is "high compared to Luhuitou fringing reef (0.51 ind m2)", but it is clear that the fish density is actually lower at Wheizhou than at Luhuitou.
Additional comments: Overall, the revised manuscript by Liao et al. has made some major improvements since its first submission. However, the manuscript still suffers from poor grammar and English, which make it hard to read, and will necessitate further revisions. The manuscript in its current form is still not acceptable for publication, but could probably be published with what are mostly minor 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: CORAL-ALGAL INTERACTIONS AT WEIZHOU ISLAND IN THE NORTHERN SOUTH CHINA SEA: VARIATIONS BY TAXA AND THE EXACERBATING IMPACT OF SEDIMENTS TRAPPED IN TURF ALGAE
Review round: 3
Reviewer: 1

Output:
Basic reporting: Fine
Experimental design: See specific comments
Validity of the findings: I found the statistical design and the presentation in the results not completely clear, two tests appear to be used to evaluate the extent of interaction, one a parametric and one a non-parametric test. This needs to be clarified before publication.

Additionally, figure 2d contains a photo where sediments were removed by "blow air", but the methods do not mention a manipulative aspect to this study. This needs to be clarified and explained before publication.

Please see the specific comments
Additional comments: In general, I find this manuscript much improved. However, I am not sure of the comparisons that are conducted across genera for the extents of coral-algal interactions. It is not clear from the methods and results which tests are comparing across all coral genera, the total linear extent of algae; or specific comparisons of the extent of turf, macroalgae, cca, other. The table does not help to clarify this point. Additionally, based on figure 2 – there seems to be a manipulative aspect to this manuscript (removal of sediments) that is not explained in the methods, or the figure does not accurately represent the methods.

Abstract: fine

Introduction:

Line 86-9: I think there is something missing here – Based on this statement, I would not expect this paper to be based on surveys. Maybe the authors mean that field surveys often do not take into account the diversity of traits associated with corals and the environment that could influence the outcome of coral-algal interactions?

Methods:

line 132: how were corals chosen?
line 156: what growth forms?, ah, it’s below, move up here
line 163: Specifiy which corals (by genera) are characterized as small and large polyps

I was a bit lost in the analyses that were completed here for similar comparisons, and table 1 did not help me understand what analyses go with what comparison. Maybe referencing the hypothesis in regard to the way in which the data were analyzed. Additionally, I do not understand why a two way ANOVA was not used cross algal type and coral genus, instead of a Kruskal-Wallis and a one way ANOVA.

It would be helpful to clarify in the figures what test was done to determine significant differences, and if the results of multiple tests are on the same figure (e.g., multiple 1 way ANOVAs or Kruskal-Wallis test if each coral genus was assessed separately).

Differences in the proportions of different algal contacts (with either turf algae and
176 macroalgae) among coral genera were assessed using a Kruskal-Wallis test.

line 177: what does “Algal types” mean here?
A one-way ANOVA was used to compare the proportions of different algal types on the coral edges within a coral genus.

line 178: what does specific coral-algal competitive outcomes means? Is this referring to the wins, neutral and loss, or between specific coral-algal generas?

To assess the differences in
181 proportions of algal wins, a two-way ANOVA (with turf algae type/macroalgae genus and coral
182 genus as fixed factors) was used, followed by a SNK test.

To assess the differences in the
183 proportions of algal wins and the similarity among groupings, a two-way ANOVA (with turf
184 algae type and coral growth form as fixed factors) was used, followed by a SNK test.

Results are
185 presented as mean =standard error (SE).
line 183 – similarity among groupings is not clear

line 185 – most data are shown as boxplots, why does it say mean +/- SE?

line 197- 208– Now I am confused about what data was used for the Kruskal-Wallis and 1-way ANOVA, based on the summary of the results it sounds like they were testing the same thing (Coral Genus and total extent of coral algal interactions).

line 207 – remove “was”
line 238 – turf algae types? Is this with or without sediment?

Discussion
Are there size differences across these corals? Are the differences across genera (e.g, in terms of algal contact extent) also explained by differences in the sizes of corals?

line 267 – growth was not assessed

line 288 “process” is not appropriate here

line 292 – the Friedlander study refers to Caulerpa, not Bryopsis

figure 2 – I find this confusing and a but alarming – were sediments manually removed to create the present/absence treatmetns? Or were sediments visually assessed – the methods and this figure provide two different explanations.

figure 4 – What do the capital versus lower case letters for the SNK represent?

table 1 – what specific algae? I do understand what this plot is referring to
What does “Different algal contacts” mean? Is this referring to macroalgal or turf algal contact?  Why is there a one way anova conducted in reference to the Turf+S and Turf-S? What are the specific algal contacts for the Kruskal Wallis tests?


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: CORAL-ALGAL INTERACTIONS AT WEIZHOU ISLAND IN THE NORTHERN SOUTH CHINA SEA: VARIATIONS BY TAXA AND THE EXACERBATING IMPACT OF SEDIMENTS TRAPPED IN TURF ALGAE
Review round: 3
Reviewer: 2

Output:
Basic reporting: Clear unambiguous professional English language used throughout: OK
The English grammar and spelling has improved considerably from the previous drafts. However, there are still some parts where the wording could be changed a bit to make things more easily understandable.

For instance the wording in the results section of the abstract is a bit hard to understand and could probably be stated better. More specifically, Lines 21-22 are a bit unclear. It might be better to say something like, Our data suggested that macroalgae was the main algal competitor for all corals, however, the extent of algal contact varied between coral genera. Although this sentence is still a little unclear, as it does not define what is meant by the "extent" of algal contact. You should also define what is meant by the proportion of interaction outcomes.

Introduction and background show context, literature is well-referenced and relevant: OK

The introduction is well-referenced and relevant. the only improvement I would suggest, is that when multiple factors or outcomes are discussed, a reference should be given for each factor unless the single reference given actually showed all of these different factors or outcomes. As an example I point to Lines 49-52. You should provide a reference for each factor (i.e., a reference for polyps size, colony size, growth form, and environmental factors).

structure conforms to PeerJ standards: Yes

Figures are relevant, high quality, well-labeled and describe: Yes

Figure 1: The caption references "the sheet". This is not a normal use of this terminology. It might be better to call it a table inset or something like that.

Figure 3: I would suggest not to use the * symbol to represent the data points outside of the 1.5 quartiles, as this symbol is typically used to denote significant differences. I would suggest using a square or triangle or really any symbol except for a *.

Figure 4: I believe "post hoc" should be italicized as it is a Latin phrase.

Figure 5: I once again, suggest not using the * symbol.

Raw data supplied: Yes

Original primary research within the scope of the journal: Yes
Experimental design: Methods described with sufficient detail and information to replicate: OK
Validity of the findings: Conclusions are well-stated, linked to the original research question, and limited to supporting results: OK

The discussion and conclusion sections have improved greatly, and are in general, well-stated, well-referenced, and supported by the research. The only small improvement I could suggest is that the last conclusion paragraph could be a little stronger and might end with more specific suggestions for follow-up questions and experiments rather than just saying that "experiments should be conducted".
Additional comments: Overall, the revised manuscript by Liao et al. continues to make improvements since it's last submission. The English grammar and spelling has improved considerably from the previous drafts. However, there are still some parts where the wording could be changed a bit to make things more easily understandable. The manuscript in its current form seems acceptable for publication pending some minor 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: ASSESSING ALIGNMENT-BASED TAXONOMIC CLASSIFICATION OF ANCIENT MICROBIAL DNA
Review round: 1
Reviewer: 1

Output:
Basic reporting: In their article "Assessing alignment-based taxonomic classification of ancient microbial DNA" the authors provide a comprehensive assessment of taxonomic characterisation of ancient DNA samples. They compare different methods, databases and quantify the effects of different properties of the data, such as DNA damage, variation in divergence etc. All simulated datasets are provided through figshare.
This study provides a valuable resource for the field.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I am wondering if the authors are aware of the study by Velsko et al. (Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research). I think this paper should be cited and the results should be put in relation with theirs.

In line 75 the authors state "Methods for analyzing shotgun sequencing data broadly fall into two categories: assembly-based and alignment-based."
I suggest that alignment-free methods are also mentioned here.

For running MALT the authors describe that they used blast2rma to convert MALT's blast output to rma.
As MALT is also producing rma output directly I am wondering why it was done this way.

About MALTx the authors say that it "is one of the few methods that can be used to assess microbial protein functionality in ancient metagenomic data sets."
However, in combination with functional annotations this is also possible when aligning to DNA databases. MEGAN, for example, has this functionality.

About the effect of divergence the manuscript states "However, this is at the theoretical limit of DNA preservation (Allentoft et al., 2012) and is thus unlikely to hamper most paleomicrobiological studies."
While this is true I believe the problem is not so much the divergence created by the age of the samples, but rather the database bias. I.e. the exact species is maybe not part of the database and the next relatives might have quite some divergence, which can lead to misassignments.

I have few more minor comments:

In line 36 the citation "Consortium, 2012" needs to be corrected.

"de novo" should be spelled without a hyphen (line 475).

There is a period in line 503 that needs to be removed.


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 ALIGNMENT-BASED TAXONOMIC CLASSIFICATION OF ANCIENT MICROBIAL DNA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This study is complementary to another recently published article (Velsko et al. 2018), and it comes to both similar (damage has little impact on taxonomic assignment) and different (the classification accuracy of MALTn) conclusions. However, this article is not cited or discussed. This paper would benefit from engaging with that study more directly and specifically explaining why some of the findings are different.

Velsko IM, Frantz LAF, Herbig A, Larson G, Warinner C. 2018. Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research. mSystems 3:e00080-18. DOI: 10.1128/mSystems.00080-18.

Additionally:
Line 59: It is relevant to cite the recent Velkso et al. 2018 paper here, which also assesses taxonomic classification of simulated and empirical ancient metagenomes.

Line 89: Update Herbig et al. 2016 bioRxiv citation with Vagene et al. 2018. The latter is the published citation for MALT: Vågene AJ, Campana MG, Robles García N, Warinner C, Spyrou MA, Andrades Valtueña A, Huson D, Tuross N, Herbig A, Bos KI, Krause J. 2018. Salmonella enterica genomes recovered from victims of a major 16th century epidemic in Mexico. Nature Ecology and Evolution 1-9. DOI: 10.1038/s41559-017-0446-6.

Lines 104-107: The two findings listed here (deamination minimally impacts taxonomic classification and reference database choice is important) were also the conclusions of another recent paper (Velsko et al. 2018), which should be cited here. Another recent paper (Warinner et al. 2017) also reviews issues regarding alignment-based classification and database choice, and would be relevant to cite here: Warinner C, Herbig A, Mann AE, Fellows Yates JA, Weiss CL, Burbano HA, Orlando L, Krause J. 2017. A robust framework for microbial archaeology. Annual Reviews in Genomics and Human Genetics 18:321-356. http://www.annualreviews.org/doi/abs/10.1146/annurev-genom-091416-035526

Lines 253-255: Note that your results here are in agreement with previous findings (Velsko et al. 2018).
Experimental design: Using simulated metagenomes, this paper evaluates the performance of the DNA sequence aligner MALT, when run as MALTx and MALTn (genome and CDS), for microbial taxonomic classification. The influence of DNA damage and genomic evolution on taxonomic classification is also assessed. Finally, taxonomic assignment rates are characterized for a set of empirical ancient dental calculus metagenomes using four different databases (2014nr, 2017nt, HOMD, RefSeqGCS). This study concludes that using MALTn with the RefSeqGCS database yields the best results, and that applying this approach to previously published datasets alters the findings of some previous studies.

Overall, this study is a valuable and useful contribution to the field. The direct comparison of MALTx and MALTn is particularly useful. The comparison of databases is important, but the study would be greatly strengthened by performing this analysis on the simulated datasets as well, not just on experimental data.

Additional comments:

Line180-181: Why did you set the minimum support percent filter to 0.1% for ancient datasets and 0.01% for simulated metagenomes? Why not set both to 0.1%?

Line 186: Removing all species found in blanks seems ill-advised to me. First, if cross-contamination occurs at the bench, then oral bacteria are most likely to be contaminated into the blanks. Removal of these taxa from the whole dataset will then remove true oral bacteria from your samples. Additionally, if blanks were pooled with samples on the same Illumina lane (especially an Illumina 4000), barcode hopping during clustering could result in low level misclassification of sample reads as blank reads. If all taxa found in blanks are removed, this would then remove true sample IDs. For example, a given taxon may be present in the blanks with 35 reads (very few) but present in a sample with 35,000 reads (many). Given your current filtering scheme, would you really remove the 35,000 reads from your sample just because a few dozen reads were found in a blank? If that taxon were an important marker species, such as Fusobacterium nucleatum or Methanobrevibacter oralis, how would that affect your downstream analyses? Would it lead you to call a species absent when it is indeed present (but also present in blanks)? Please address whether the taxa you identify in your blanks include well-characterized oral bacteria and in which proportions.

At multiple places in the text (e.g., line 267, Figure 4, Table 1), you refer to the % of sequences being taxonomically assigned or not assigned. Clarify if you mean assigned in general or correctly assigned. Also, when “not assigned” do you mean not assigned to a species node or not assigned at all?

Line 277: In the section on how reference database affects taxonomic classification, only ancient datasets are tested. However, this should really be tested on your simulated dataset(s) in order to properly evaluate the results. Please test one or more of your simulated datasets against these four datasets. Otherwise, it is difficult to interpret the results of this section.
Validity of the findings: The misclassification rates you show for MALTn are much lower than recently observed in another similar paper comparing taxonomic classifiers using both simulated and empirical data (Velkso et al. 2018). Can you explain why your misclassification rate is so much lower? Is it related to the composition of your simulated metagenome? Or perhaps the database you are using? Or perhaps specific search parameters?

Lines 314-317 and 441-444: Note a caveat about uncultured organisms. The disadvantage of RefSeqGCS is that uncultured organisms, such as Saccharibacteria (TM7), are dramatically underrepresented, and these organisms include important oral taxa.

Lines 333-336: I like the inclusion of the tree and the reanalysis using MALTn with the RefSeqGCS database. However, I don’t think this statement about subsistence clustering is at all well supported by the tree. The tree shows little differentiation between hunter-gatherers and forager-gatherers (what is the difference between these names?), and additionally there is an LBK individual among several x-gatherers and a Neanderthal on the branch with agriculturalists. And why is LBK2 colored purple for hunter-gatherers? Additionally, modern humans cluster more closely to chimpanzees and a Neanderthal than to any ancient agriculturalist. Overall, there appears to be little structure in the tree.

Lines 343-346: As a caveat, I don’t think you test both deamination and evolution together. Perhaps rephrase?
Additional comments: Line 52: Age-associated deamination alters cytosine to thymine. Observed guanine to adenine substitutions are artifacts of PCR, created when a complementary strand is produced off of a deaminated template. Rephrase to clarify.

Line 104: For clarity, change “…taxonomic identification and…” to “…taxonomic identification compared to MALTx and…”

Lines 366-367: The meaning of this statement is unclear to me. Functional prediction can be made based on either DNA or amino acid sequences.

Line 395: It is true that UDG and partial UDG result in sequence shortening, but partial UDG does retain a damage signal. Perhaps rephrase?


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 ALIGNMENT-BASED TAXONOMIC CLASSIFICATION OF ANCIENT MICROBIAL DNA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have submitted a new version of their paper "Assessing alignment-based taxonomic classification of ancient microbial DNA". The manuscript has improved substantially. All comments have been sufficiently addressed.
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: ASSESSING ALIGNMENT-BASED TAXONOMIC CLASSIFICATION OF ANCIENT MICROBIAL DNA
Review round: 2
Reviewer: 2

Output:
Basic reporting: I am satisfied with the changes the authors have made in response to the reviews.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I have noticed only two minor things that require correction (but do not require re-review):

Line 95: Sentence needs rephrasing to provide a subject that is not in parentheses
Line 347 and 521: Italics should be removed for "sp. MM1"


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: MICROGEOGRAPHIC VARIATION IN BODY CONDITION OF THREE MEXICAN GARTER SNAKES IN CENTRAL MEXICO
Review round: 1
Reviewer: 1

Output:
Basic reporting: There is some literature that I believe should be strongly considered for citation. Otherwise some key papers are left out that are either conceptually relevant (though with a different species) or directly so because garter snakes are used. For example:

The authors should consult and cite the edited volume Geographic variation in behavior. Perspectives on evolutionary mechanisms (Foster and Endler, eds). Specifically, the chapter by Burghardt and Schwartz, Geographic variations on methodological themes in comparative ethology: A natricine snake perspective. The authors report important results on geographic variation in body size in different populations of garter snakes.

King, R.B. (1989). Body size variation among island and mainland snake populations. Herpetologica, 45, 84-88.

King R.B. (1997). Variation in brown snakes morphology….microgeographic differences. Journal of Herpetology, 31, 335-346.

Krause, M. A., & Burghardt, G. M., & Gillingham, J. C. (2003) Body size plasticity and local variation of relative head and body size sexual dimorphism of garter snakes (Thamnophis sirtalis). Journal of Zoology, 261, 399-407.

NOTE: I can provide pdfs of the Burghardt and Schwartz chapter and Krause et al if the authors would like to contact me directly at krausema@sou.edu)

Lines 78-79. “Garter Snakes” doesn’t need to be capitalized

Lines 84-87. Confusing as worded. Are the authors stating that previous publications have only focused on males or females, and rarely have both been combined in a single study? Might help to reword this. Also, change “sexual” to “sex” (and on line 251 and wherever else in this context).
Line 237. Is there a missing word on this sentence?
Line 257 typo: reflect result
Experimental design: The study is not experimental in nature. In terms of research design in general, the authors are dealing with natural populations of animals so there is nothing that is controlled. This limits the manuscript in terms of hypothesis testing. However, the field sites provide opportunity for “naturalistic experiments” because the variables of geographic location, sex, and ontogenetic status can be compared and related to existing literature.

One item: Is it statistically appropriate to use the MA linear regression to compare body condition to snakes that differ in overall body size/age (e.g., juveniles and adults)? I do not know, but this might be something to clarify. Do Faulk et al (2017) address this?
Validity of the findings: The measures used are standard for assessing snake body size and condition, and the authors cite and use good resources for statistical selection. Discriminant function analyses are an interesting and insightful way of relating geographic, sex, and ontogeny on body condition. I do not have reservations concerning the validity of the findings.
Additional comments: Abstract: “sympatric species are predicted to exhibit similar body condition when they experience similar environmental conditions”. Is this true? This would seem to assume that these sympatric species are independent of each other, but if there are differential effects of resource use/competition or disease, phylogenetic effects, etc then this would not seem to be a valid prediction. The second sentence of the introduction addresses this, and seems to contradict this statement in the abstract. This comes up again in the discussion lines 261-265. This is confusing because on the one hand the authors are stating that closely related sympatric species should exhibit similar body condition. They then state that this can’t be assumed and that competition over resources, etc might create differences among sympatric species. Which is it? I think this needs to be more fully explored, and with relevant literature cited in more detail. This would help strengthen the discussion section too, which I find is overly focused on the garter snakes studied, and less focused on broader ecological and evolutionary questions.

Lines 304-305. The authors operationally define good or poor condition based on the position of residuals above or below the regression line. Here the terms good and poor are used in reference to populations of animals, not individuals (e.g., “the body condition of T. eques is good”). It might help to remind readers how the statistical operational definition of good/poor translates into the real world (e.g., make it biologically meaningful). Is it this based on mean residuals of condition index was below the regression line? Something else? I think it would help to clarify this.

Lines 303-315 of the discussion are very nice. In fact I think this could be expanded and broadened to include parallel findings with other species (snakes or other animals). The discussion as written is highly focused on rehashing the results, and I would appreciate seeing it broadened.