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

Input:
Title: THE IMPACT ON LIFE CYCLE CARBON FOOTPRINT OF CONVERTING FROM DISPOSABLE TO REUSABLE SHARPS CONTAINERS IN A LARGE US HOSPITAL GEOGRAPHICALLY DISTANT FROM MANUFACTURING AND PROCESSING FACILITIES
Review round: 3
Reviewer: 1

Output:
Basic reporting: See below
Experimental design: NA
Validity of the findings: NA
Additional comments: The authors have addressed a lot of my earlier comments mainly by more explicitly positioning the article not as an LCA but as carbon footprint. This would allow them to focus the study on greenhouse gases (GHG) and at the same time to disregard the ISO-standards and comply only with the BSI-standard PAS 2050. True as this may sound, there are two important remarks to be made.
1) With an exclusive emphasis on GHG and climate change, other important types of environmental impact are out. The section "Other impacts of RSC" very briefly addresses other impacts, but these are only cost and sharps injury. Through this, a quick reader can think that RSC are from an environmental point of view superior to DSC. The authors should add a longer text in the "Other impacts" section to inform the reader that there is more in the environment than GHG only, such as ozone layer, toxic emissions, acidifying emissions, water withdrawal, fossil resources, etc etc, but that this study only looked at GHG, so that a full LCA might lead to different conclusions, or might strengthen the preference for RSC, we simply don't know.
2) ISO-LCA allows for a smaller subset of impacts to be considered, when motivated. In that sense, a carbon footprint might still be ISO-LCA-compliant. BSI-PAS 2050 is very much based on ISO-LCA, see e.g. PAS 2050 clause 4.1 "Assessment of the GHG emissions of products shall be carried out using LCA techniques". This includes explicitly the issue of "Transparency: where the results of life cycle GHG emissions assessment carried out in accordance with this PAS are to be disclosed to a third party, GHG emissions-related information is made available that is sufficient to support disclosure and allow such a third party to make associated decisions with confidence". While I agree that it is not easy to create a fully transparent report within the constraints of an article, the present text still leaves out many details or gives a confused presentation. One example: I can hardly believe that "no significant allocation issues were considered", because there is electricity, refineries and carton in your system, and for these items allocation can be a decisive factor. Another example: the online supplementary information contains a "CO2eq Characterization Factor (CF)" for "polypropylene manufactured for DSC Study year", which is plainly wrong. Characterization factors exist for CH4, N2O, but not for polypropylene; check IPCC. Third example: the DSC is incinerated after disposal, but probably with energy recovery, and it is not clear if any recovered enrgy bonus was given for this.
In conclusion, the move from LCA to carbon footprint is a bit too cheap now.


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

Input:
Title: THE IMPACT ON LIFE CYCLE CARBON FOOTPRINT OF CONVERTING FROM DISPOSABLE TO REUSABLE SHARPS CONTAINERS IN A LARGE US HOSPITAL GEOGRAPHICALLY DISTANT FROM MANUFACTURING AND PROCESSING FACILITIES
Review round: 4
Reviewer: 1

Output:
Basic reporting: My previous points have been processed.
Experimental design: NA
Validity of the findings: OK
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: GRAZING EXCLOSURES SOLELY ARE NOT THE BEST METHODS FOR SUSTAINING ALPINE GRASSLANDS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript reports results from a grazing exclusion study conducted in alpine grasslands in China. The authors aimed at to study grazing effect on overall diversity and predefined groups of plant species using line transects and plot-based sampling. The ms in general well written, however, some parts are too voluminous and wordy (i.e. introduction and discussion). The main finding of the ms is that neither continuous grazing, nor exclosures can provide the desired biodiversity of grasslands thus, they suggested an alternative method for some kind of mosaic management, where exclosures and grazed sites alternate both in space and time. The figures and illustrations are appropriate for the study. The manuscript is generally well written and clear.
Experimental design: The study setting is appropriate, however the distance between the different treatments/sites are rather low and falls between the general spontaneous dispersal distance of grassland plants (especially if the dispersal is facilitated by grazing). It cannot be treated in revision but maybe its effects can be discussed briefly in methods (i.e. which drivers motivated the close sampling sites). The statistical analyses are appropriate, however, I don’t know why the authors used two types of multiple comparasions for the analyses (i.e. the default setting of GLMM is LSD but the authors also stressed that they have calculated Tukey). I also think that ‘noxius species’ is not a functional group – it can contain in general many plants species with different plant strategies but unwanted in the sites (e.g. weeds, invasive species mostly grasses and forbs)
Validity of the findings: The results are solid, clear and are in line with other studies. Relatively detailed analyses support the findings.
Additional comments: I have identified a set of minor issues which should be treated in a revision

Title – is rather overloaded (it is not the abstract!) should be more focused on the most important findings – i.e. grazing exclosures solely are not the best methods for sustaining alpine grasslands -  a case study from China – or smthing similar.

l35 noxius species is not a functional group in ecological terms surely
l39 Richness index – it is just species richness – why you don’t write it?
l54-57 Some very recent overviews should be considered here – mostly focusing on grasslands and steppes

Török P., Dengler J. (2018):  Palaearctic grasslands in transition: overarching patterns and future prospects. In: Squires, V.R., Dengler, J., Feng, H., Hua, L. (eds.) Grasslands of the world: diversity, management and conservation. CRC Press, Boca Raton, US. Ch. 2. pp. 15-26.

Wesche K., Ambarli D., Kamp J., Török P., Treiber J., Dengler J. (2016): The Palaearctic steppe biome: a new synthesis. Biodiversity & Conservation 25: 2197-2231.

Török P., Wesche K., Ambarli D., Kamp J., Dengler, J. (2016): Step(pe) up! Raising the profile of the Palaearctic natural grasslands. Biodiversity & Conservation 25: 2187-2195.

l102 Thus, specific research should be…
l132 In order to better understand…
l168 Should be recalculated to Livestock units/ ha LU/ha
l179 Do not understand the sentence – have you sampled the grasslands at the peak of biomass production?
l180 Not “quadrants” – quadrats or plots should be written here and should be corrected in the whole ms
l181 Not sure that it is called “marginal effects” – effect of margin would be better
l184 five groups that included
l194 Simply Shannon diversity – Wiener has nothing to do with it. See original publication of Shannon (1948) there is only one author.
l240-264 Almost impossible to read, so many p values – it should be put in a table.
 for the line 266-291 is almost the same.
l317 Quite recent restoration literature should be cited here – Török & Helm 2017 and/or Török et al. (2018)

Török P., Helm A. (2017): Ecological theory provides strong support for habitat restoration. Biological Conservation 206: 85-91.

Török P., Helm A., Kiehl K., Buisson E., Valkó O. (2018): Beyond the species pool: modification of species dispersal, establishment, and assembly by habitat restoration. Restoration Ecology 26: S65-S72.

l366 typo – The species density and diversity
l390 there is no “vegetation community” – There is either “vegetation” or “plant community”. This case I would prefer the first version – please correct consecutively in the ms.


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: GRAZING EXCLOSURES SOLELY ARE NOT THE BEST METHODS FOR SUSTAINING ALPINE GRASSLANDS
Review round: 1
Reviewer: 2

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: In my opinion authors provide a useful contribution to knowledge about the functioning of pastures, so their work can expect a broad interest from scientist working with this topic. However there are a lot of problems with the structure and the style of the manuscript. There are a lot of abbreviations in the abstract; therefore it is impossible to follow the story line. The denomination of the two studied pasture types (e.g. fenced and grazed) is misleading, because the grazed sites were also fenced allowing the prescribed grazing. I suggest the non-grazed and grazed phrasing. Authors studied the effect of grazing on the edible and on the noxious species, which is an important part of the manuscript; however there are no any information about the classification methods. The result section is quite long mostly because of the lot of repetitive information; it is typical that one result was presented in three forms (text, table and figure); I recommend you shorten the length of this part. The labelling and the legend of Fig. 1 are not consistent. The names of the subspecies in Table 1 do not meet the standards of the scientific nomenclature. Moreover, there are several linguistic problems which require the linguistic correction of the whole manuscript. Overall, the topic of the manuscript is interesting and the conservation relevance of these kinds of studies is undisputed. Besides of the ecological viewpoints, Authors concluded their results also from the practical viewpoint. In my opinion, the manuscript is acceptable, however, because of the several technical problems; the thorough re-write of the whole manuscript is highly required.


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

Input:
Title: THE TETRAPOD FAUNA OF THE UPPER PERMIAN NAOBAOGOU FORMATION OF CHINA: 3. JIUFENGIA JIAI GEN. ET SP. NOV., A LARGE AKIDNOGNATHID THEROCEPHALIAN
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is an important new specimen from both a paleodiversity and biogeography standpoint. It is well-figured and I agree with the descriptive text for the most part. I do however have some worries about the extent of the sutures depicted, particularly in the occiput—the preservation of bone surface on the specimen does not look like it preserves sutures well, and the extents of various bones depicted in the drawing does not closely match that of closely-related therocephalians. I would ask the authors to check these points carefully and note where suture boundaries are estimates.

The text of the paper requires extensive tightening to be ready for publication, and should be edited carefully for grammar. I have noted a number of corrections to make below but this is not an exhaustive list. The Discussion is relatively short and repeats some of what was said previously in the Introduction. I recommend expanding it to talk more broadly about Permian theriodont biogeography, considering that the therocephalian records from China are some of the first of their kind and seem similar to those in Russia. It appears that some provincialism was present even back in the Permian--very similar patterns have now been found for Gorgonopsia (see Kammerer & Masyutin 2018b, on Kotelnich gorgonopsians) and this pattern may be Laurasia-wide. (No gorgonopsians have been published from China yet, but I believe it is only a matter of time before they are discovered). The presence of the otherwise-Scottish Elginia in these deposits also is indicative of a broad trans-Laurasian tetrapod faunal province, which deserves further discussion here.

Sincerely,
Christian Kammerer

Title: It is unnecessarily repetitive to say that this is about the “tetrapod fauna of the upper Permian Naobaogou Formation of China” and also “a large akidnognathid therocephalian from China”. Please change to: “The tetrapod fauna of the upper Permian Naobaogou Formation of China: 3. Jiufengia jiai gen. et sp. nov, a large akidnognathid therocephalian”

Line 21: change “new fossils discoveries that increased” to “new fossil discoveries increasing”

Line 25: change “clear difference respect to” to “clear differences from”

Line 26: change the semicolon to a comma

Lines 28–30: change this sentence to: “Updating a previous phylogeny of therocephalians, we recover the new species as a basal member of Akidnognathidae, above a basal polytomy including the other two Laurasian akidnognathids, Annatherapsidus and Shiguaignathus, adding support to the hypothesis that this group originated in Laurasia.”

Lines 38–39: change “and also has been successful in the record for the first time of member of therocephalians” to “and also has produced the first records of therocephalians”

Line 41: change “a medium-sized and well-preserved snout” to “represented by a medium-sized and well-preserved snout”

Line 42: decapitalize “Akidnognathid”

Lines 49: change “Akidognathidae” to “Akidnognathidae” (Nopcsa originally misspelled it as Akidognathinae, but subsequent usage should be “Akidnognathidae”)

Line 56: change “included into” to “included in”

Line 63: change “Gondwanean” to “Gondwanan”

Line 90: capitalize start of sentence

Line 96: change “intermedium” to “intermediate”

Line 97: decapitalize “Akidnognathids”

Line 102: change “be collected” to “being collected”

Line 116: change “ a short trapezoid” to “a short, trapezoidal, ”

Line 122: add a comma after the closing parenthesis

Line 133: change “foramen” to “foramina”

Line 137: change “maxilla exposure” to maxillary exposure”

Line 140: change “crown having more than 3 cm” to “crown being greater than 3 cm”

Line 142: change “stripes” to “striations” (also, are these latitudinal or longitudinal?)

Lines 143–144: change “wide massive base, posteriorly curved crown” to “massive base and posteriorly curved crown”

Line 171: change “the parietal forms the median of the lambdoidal crest” to “the parietal forms the central portion of the lambdoidal crest”. Also, how confident are you of the extent of the parietal in the occiput? I find it very hard to see sutures in the photograph, and it appears unusually large.

Line 177: change “which form” to “forming”

Line 186: change “of last incisor” to “of the last incisor”

Line 189: change “unpaire” to “unpaired”

Line 189: add a comma after “anteriorly”

Line 192: change “several” to “most”

Line 193: change “with exception” to “with the exception”

Line 205: change “same plane to” to “same plane as”

Line 205: change “crista choanal” to “crista choanalis”

Line 223: change “ventral” to “ventrally”

Line 241: delete extra space after “while”, change “form” to “forms”

Line 296: change “in CT image” to “in the CT image”

Line 297: change “inclined posteriorly” to “posteriorly inclined”

Line 302: change “where it dorsal” to “where its dorsal”

Line 311: change “most posteriorly” to “more posteriorly”

Line 329: change “subcracoideus” to “subcoracoideus”

Line 374: change “have less” to “have fewer”

Line 421: change “Chtonosauridae” and “Akidnognathia” to “Chthonosauridae” and “Akidnognathidae”
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: No comment.


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

Input:
Title: THE TETRAPOD FAUNA OF THE UPPER PERMIAN NAOBAOGOU FORMATION OF CHINA: 3. JIUFENGIA JIAI GEN. ET SP. NOV., A LARGE AKIDNOGNATHID THEROCEPHALIAN
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this manuscript, the authors describe a new therocephalian, Jiufengia jiai, from the Naobaogou Formation, Nei Mongol, China in a comparative framework considering cranial and postcranial material. Moreover, the authors include the new specimen in a phylogenetic analysis in order to test its affinities.
In my opinion, this manuscript is very interesting and worth of publication as it presents a new taxon that represents only the second therocephalian recovered from Naobaogou Formation and the second akidnognathid from China.
The manuscript is well written and it only needs minor re-wording and re-phrasing. The most important issue to be addressed relates to the figures: some captions are not labelled and some labels are not in the captions. The authors should check this thoroughly. Hence, my recommendation is that this manuscript is accepted with minor changes. I have made some suggestions in the two word files attached (main text and table 1).
Please, do not hesitate in contacting me should any question arise.
Leandro Gaetano
Experimental design: This is an original primary research within Aims and Scope of the journal.
Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.
Validity of the findings: Conclusions are well stated and linked to the research performed.
Additional comments: No additional comments


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

Input:
Title: THE TETRAPOD FAUNA OF THE UPPER PERMIAN NAOBAOGOU FORMATION OF CHINA: 3. JIUFENGIA JIAI GEN. ET SP. NOV., A LARGE AKIDNOGNATHID THEROCEPHALIAN
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript has been substantially improved. I still have a number of minor, mostly grammatical, revisions, for which see below:

Line 19: change “to the Member III” to “to Member III”
Line 19: change “resulted in” to “yielded”
Line 20: change “new fossils discoveries” to “new fossil discoveries”
Line 27: change “vomer” to “the vomer”
Line 27: change “lacking ventromedian crest” to “lacking a ventromedian crest”
Line 28: change “after” to “above”
Lines 34–35: change “a meticulous collective effort” to “meticulous collection efforts”
Line 35: change “resulted in” to “have resulted in”
Line 35: change “of the knowledge” to “of our knowledge”
Line 37: change “has also been” to “have also been”
Lines 37–38: change “in the record for the first time of therocephalians” to “in recording for the first time therocephalians”
Line 43: change “parareptile” to “parareptile genus”
Line 48: change “Later, Akidnognathidae was proposed to include” to “Later authors considered Akidnognathidae to include”
Line 61: change “second akidnognathid” to “second akidnognathid genus” (because Ivakhnenko described a second species of Annatherapsidus, A. postum, this is actually the fourth akidnognathid taxon overall from Laurasia).
Line 88: change “Nei Mongolia” to either “Nei Mongol” or “Inner Mongolia”
Line 113: change “upturns” to “is upturned”
Line 115: change “with a short, trapezoid” to “in a short, trapezoidal”
Line 119: change “sharp conical” to “sharply conical”
Line 125: change “with the” to “the”
Line 142: “a wide diastema”—please include a measurement
Line 196: change “contacts with the” to “contacts the”
Line 221: delete comma before “and Olivierosuchus”
Line 275: change “almost form” to “form almost”
Line 291: change “posteriorly to” to “posterior to”
Line 297: change “located laterally” to “located lateral”
LIne 356: change “phalange” to “phalanx”
Line 363: delete comma after “wangi”
Line 370: change “is different” to “differs”
Line 370: change “by the” to “in the”
Line 375: change “Remaining” to “Other”
Line 388: delete extraneous space between “and” and “included”
Line 398: change “politomy” to “polytomy”
Lines 400–401: Totally rewrite this sentence. I think you mean, “Current evidence shows that most Laurasian akidnognathids were of medium-to-large size.”
Line 405: change “represented by Olivierosuchus is the smaller representative” to “represented by Olivierosuchus, is one of the smaller representatives” (n.b. Olivierosuchus is not the smallest akidnognathid; it is larger than Akidnognathus and Euchambersia)
Line 412: change “produce” to “support”
Line 416: add space in “unknownin”
Line 421: change “Whaitsoidea” to “Whaitsioidea”
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Publishable following 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: THE TETRAPOD FAUNA OF THE UPPER PERMIAN NAOBAOGOU FORMATION OF CHINA: 3. JIUFENGIA JIAI GEN. ET SP. NOV., A LARGE AKIDNOGNATHID THEROCEPHALIAN
Review round: 2
Reviewer: 2

Output:
Basic reporting: In this manuscript, the authors describe a new therocephalian, Jiufengia jiai, from the Naobaogou Formation, Nei Mongol, China in a comparative framework considering cranial and postcranial material. Moreover, the authors include the new specimen in a phylogenetic analysis in order to test its affinities.
This is the second time I review this manuscript. The authors have performed the changes suggested and, in my view, it is ready for publication.
This manuscript is very interesting as it presents a new taxon that represents only the second therocephalian recovered from Naobaogou Formation and the second akidnognathid from China. I hope to see it published soon.
Leandro Gaetano
Experimental design: No comments
Validity of the findings: No comments
Additional comments: No 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: FROM DATA COMPILATION TO MODEL VALIDATION: A COMPREHENSIVE ANALYSIS OF A FULL DEEP-SEA ECOSYSTEM MODEL OF THE CHATHAM RISE
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: I do not believe that the methods are described with quite enough detail - see comments for the author.
Validity of the findings: I think the base model used would be better if driven by a repeating annual cycle of oceanographic data - see comments for the author. But the validity of the findings seem sound as is.
Additional comments: General remarks
My overall impression is that this is a thorough, well constructed analyses, with good presentation. I recommend it for publication with minor revisions.

I do not believe that modifications to the methods are necessary for publication, but I think that more explanation of some methods is needed to aid reader’s understanding and for reproducibility.
More discussion would be beneficial in places.
Also, ensure that all modelling choices (parametrisations/functional responses) are available to the readers – I think some things are lacking at present, eg predator-prey functional responses.

The authors use the Atlantis modelling framework to simulate an ecosystem east of New Zealand. I have some familiarity with ecosystem models, but have not used Atlantis. This made following the methods a little troublesome as much of the detail is left to references.

Fisheries management considerations is a focus of the introduction that is not really returned to during the discussion. More discussion of the potential of the model to inform management strategies would be good.

Atlantis is a spatial model, but spatial results were not reported. Asking for a breakdown of spatial results would involve a lot of extra work that is not necessary for this paper. But I think that the spatial aspect should be highlighted in the discussion of potential future work, particularly with regard to fisheries management.

I have only one potentially important methodological concern: the repeating cycle of ROMS years used for the base model. It seems to me that removing inter-annual oceanographic variability by using the average over all years would be preferable to repeating a cycle of 9 years.

See detailed comments below. Most of these comments are simply asking for clarification or more detailed discussion – some are simply questions not necessarily requiring changes to the paper.
Apologies for the review being rather long-winded, but I was surprised by the requested 10 day return time which I found too short to produce a concise review summarising the below comments.

Abstract
Well structured and informative.
As you mention ecosystem based approach to fisheries management I was surprised that model applications in the final sentence did not include using the model for forecasting biomasses under various fishing regimes. If this is a potential application(?) then mentioning it (or something similar) would nicely link back to fisheries management.

Introduction
Well structured interesting intro, gives sufficient context and background information on the study system, very brief synopsis of Atlantis modelling framework, clearly states objectives.

First paragraph says more ecosystem-based approaches are desired by fisheries management, and states the importance of Chatham Rise fisheries. The focus at the very start of the paper is fisheries management. I think that the potential of the model to guide fisheries management could feature more in the discussion section, as the focus seems to drift away from fisheries management.

Second Paragraph summarises the range of habitats and depth, and influence of subtropical front. The results are not presented in these terms, nor does the discussion section return to these factors. In the discussion more mention of potential for interesting spatial results should be included.

Line 79. You mention how ecological changes may influence the distribution of species, and that knowledge of this can be useful for management. The Atlantis model is spatially resolved into 23 compartments. Were there interesting spatial results? Eg were species distributions linked to warm/cold years, or fishing? I don’t know how much extra work would be involved in such analyses… if it’s substantial maybe just mention as potential future application, but if spatial results are readily available and easily analysed then more findings could be reported here…

Line 103. The word response seems dubious here, can you rephrase this line? Section 5 compares trends in model predicted catch to trends in observed catch and CPUE indices. Catch is the result of a certain fishing regime, but wouldn’t response to fishing be tested by examining modelled catch and abundance under various fishing regimes?

Model area
Lines 122-149. Lots of detail from existing studies about species richness-at-depth is presented here. There is more detail than necessary given that modelled spatial (depth) distributions were not reported/analysed in this study. The paragraph could be reduced to lines 122-126 and 139-141, then the focus would be very much on the polygon arrangement instead of extra detail (which could be retained in discussion section) .

Line 142. serve as a discontinuity is a bit cryptic – could be rephrased. Or, given the previous comment, this detail could be removed from the model area section.

Line 155. Model polygons are based on survey strata boundaries. This makes sense as it will make it relatively easy to assess model performance in terms of spatial distributions and species richness in different areas. Perhaps this should be mentioned…

Oceanography
Line 182. ‘The base model presented here repeated the available ROMS variables’. This is too little detail. Were the full ROMS time series repeated in a 9 year cycle? Were the ROMS data averaged over years then used in an annually repeating cycle? What exactly was done?

Figure 3 (right-hand plot). Seems an odd choice of partition for years given that the ROMS years (blue line) are 1996-2004. The yellow line is pre-ROMS years; whereas the black dashed line is some pre-ROMS years, the ROMS years, and post-ROMS years – which is not useful. Please change this so that the black dashed line shows temperature only in post-ROMS years. That way we can see how ROMS years compare with the past and the future temperatures.

Nutrients
Figure 4. This is not an important request, but it would be good if you could change the colour of the arrows because thin blue arrows on a blue/green background look fine on a computer screen but are not very clear on print-outs.

Line 192-193. What were the choices of initial values, and are these available?

Line 204. NIWA acronym should be written in full in first instance. I realise that three of the authors are based at this institution and that the acronym is spelled out on the title page, but as that is not the main text readers are unlikely to recall NIWA by line 204 (I didn’t).

Line 205. A small quibble here: can ‘ammonium is fairly small in terms of the nitrogen budget’ be rephrased to something like ‘ammonium is a small component of the nitrogen budget’?

Species groups – initial condition & parameters
Room for lots of uncertainty in specifying the initial conditions. The model is run on from these initials to approach a steady state before any analysed output is generated, so hopefully uncertainty in the initials is not too problematic… Did you test whether using different initial states influenced model behaviour? It would involve perturbing the initial conditions (possibly strong perturbations if uncertainties in initials are large) then running the model through the spin-up years to see if it approaches a steady state similar to the original. I suspect that the results may be sensitive to the initial states, particularly as there are so many, 53, functional groups. So some discussion on sensitivity to initial state values would be useful. I suppose this ties in with the discussion on knowledge gaps…

Lines 220-223. Fair enough, some sort of method needs deployed to get at initial biomass values. But were these initial values for the entire Chatham Rise, or were they calculated separately for each model polygon? Please explain how initial biomasses were specified for each polygon and depth layer. Also, are these initial values (which are also modelling results) available?

Lines 223-226. A bit more explanation would be useful as I’m unclear about how an absolute abundance estimate for a single year, 2003, was calculated from mean relative abundance over 23 years, 1992-2014. Also, if the authors decided what catchability quotient to use then please write ‘… derived by our expert opinion… ’, otherwise credit the expert with a reference.

Line 229. If it is the author’s expert opinion then please write ‘… our expert opinion’, otherwise credit the expert with a reference.

Table 6 & Appendix B. Here I’m confused by the von Bertalanffy growth parameters. It seems as though the values in the table are only used to initialise weights-at-age, because Appendix B shows that the model outputs different size-at-age from this table. I think this must mean that Atlantis is free to vary the von Bertalanffy parameters, but I also thought that parameter tuning was infeasible due to the complexity of Atlantis… so what’s happening here? How does Atlantis return size-at-age estimates?

Predation
Plaganyi et al. (2007) indicates that 6 predator-prey functional responses are available to use in Atlantis. Why is there is no mention of these functions in this study? The choice of functional response should be made clear.

Figure 5 is a good summary, but as you mention, it lacks detail. The supplementary material should contain a table of numeric values displaying each consumer’s diet as proportions (summing to 1) of individual prey species. Obviously this table would still lack spatio-temporal variation, but at least we could see each prey species.

It is confusing that the description of figure 5 contains the first mention of the ‘fished model’. If you run the model with and without fishing then this needs to be mentioned in the main text before reference to it appears in figure descriptions.

Calibration
Line 265 (and throughout). The syntax used for species group suffixes changes between dashes and brackets, eg invertebrate scavengers – commercial on line 265, and invertebrate herbivores (commercial) on line 277. Can you use the same style throughout? I think the brackets are better  for readability.

Line 266. Although I don’t think it necessary for publication, this could be tested by removing the inter-annual variability from the oceanography data by averaging the data over years to create a repeating annual cycle to drive the model (see comment on line 182).

Line 268 (and throughout). There is repeated mention of Appendix 10 throughout the paper. But I don’t see an Appendix 10. Biomass trajectories (line 268) are displayed in Appendix A.

Lines 271-282. I agree that most of growth trajectory plots coincide quite well. But I don’t understand why the model grows species according to von Bertalanffy parameters that differ from Table 6 (see previous comment). Line 506 states that Atlantis is too complex to fit to data. I understand this to mean that Atlantis does not tune the input parameters to take different values, instead it simply runs the model using a fixed set of parameters. This needs more explanation.

Lines 271-282. The sizes of young animals are often overestimated. I think that this anomaly merits further investigation as it may be due to overconsumption of small individuals by some predator group(s). A more detailed analysis of the predator-prey relationships (age-based and spatial) could be useful here. This is probably best left for future work, but please elaborate on possible causes of the biased sizes at young ages in the discussion section.

Lines 294-301. Why was 2016 chosen? The biomass trophic level relationship should be fairly similar across years. Can you perform this calculation for each year and report the minimum, maximum and mean slopes.

Sensitivity analyses – oceanography
Lines 311-323. I like this section, it’s a nice way to test model sensitivity to variable oceanography. I’m not asking for changes to this section but it has made me wonder, again, about the driving data used in the base model (see previous comments). Surely it would be best for the base model to use an annually repeating driving data cycle calculated as the mean over all ROMS years (this could also be used instead of 2003 data for the burn-in period in these sensitivity simulations).

Line 324. Please mention the metric that these confidence intervals apply to. I assume it’s biomasses…

Lines 324-328. This is an interesting paragraph that could benefit from an extra sentence of explanation. Here the species groups with the highest CVs are those deemed most sensitive to oceanographic variability(?) - and I was not surprised by the species groups listed, the sensibleness of these results could be mentioned.

Lines 329-332. As with comment on line 324, can you rephrase ‘… that went above/below the established confidence intervals…’ to mention the actual metric used.

Lines 329-337. This is a nice way to illustrate effects of warm/cold years. A little more detail could easily be provided. Can you also mention whether it was the same species that fared better or worse during the warm & cold years. For example, during the 3 warmest years was there variation in the species that fared worse or was it the same species each year?

Connectivity and influence
Lines 348-366. The difference between Libralato et al. (2006) and your method is the extra term involving m in equation 4, and possibly a different definition of m (equation 2). I don’t understand the purpose of the m term in equation 4. If you have modified the method then please explain how and why.

Fishing
Lines 380-391. Please make it clearer how the catch data are used by the model. It seems that the catch is driving data used similarly to the oceanography metrics, but this is only alluded to in the description in Appendix D which mentions ‘forced catch history’.

Line 387. No request for a change here, just wondering if the marked decline in orange roughy was due to long life span/long generation times or fishing out the large/most fecund individuals?

Comparison with CPUE and stock assessment
Figure 13 shows that biomass trends returned by Atlantis are similar to some biomass trends estimated from stock assessments and CPUE. Can you also report comparisons of the magnitude of biomasses estimated from these 3 methods, along with the trends?  The description of figure 13 states that the stock assessment and CPUE metrics are scaled, so we do not know how magnitudes compare…

Skill assessment
Lines 422-425. This little section may be confusing. Make it totally clear that n is year in equations 6-8, and that ‘point estimates’ are annual biomass estimates. Also change Appendix 10 to Appendix D in line 421.

Line 429. Mention that the MEF of ling is so low because of the stationary nature of the biomass estimates (displayed in Appendix D). MEF tests whether the model performs better than the mean of the data – well in the case of ling, only the data point with the relatively small CI could differ significantly from the mean.

Line 435. Equation 7 is not simple. Can values of RI>1 be interpreted in a meaningful way for each species group, or is this metric useful only for cross species comparisons? A little more discussion on RI metric may help understanding (is RI=1.5 acceptable, or is that a poor result?).

Lines 440-442. I agree with this sentence, and am not requesting changes to the analyses. But it made me wonder why the highly uncertain survey biomass estimates were used instead of stock assessment estimates. I realise that the survey contains more species, but here stronger results may be available through use of the stock assessments. Can you explain why the surveys were chosen over the stock assessments?

Bringing it together
Lines 448-450. Why is poor knowledge not concerning if paired with high responsiveness? Please provide a reference or explanation. Also, surely the ‘double’ of high keystoneness and low information (eg seabirds) are important considerations for future scenarios.

Lines 461-463. Why could this be? Please include brief discussion of potential causes. Mortality is size based so maybe something is eating most of the small individuals. The last part of this sentence, ‘… so this is probably not influential on the model over all’, is dubious and should be removed unless it can be backed up.

Lines 469-472. It seems that spiny dogfish are well modelled, but abundance is uncertain. There’s lots of them and they have high keystoneness, so it’s worth checking if they are linked to other anomalies like the small pelagic fish mentioned above. It would be good so see this kind of investigation into the causes of the mentioned anomalies. Perhaps that is best left for future work, but here a brief mention of that kind of analyses would be good.

Lines 477-483. Agreed. Data on these groups is often scant… which is frustrating as you have nicely demonstrated their importance in the model dynamics.

Discussion
Line 506. See previous comment. If model is too complex to fit to data, why does the model return growth trajectories that differ from the von Bertalanffy curves (Table 6 & Appendix B). Are the discrepancies entirely due to mortality at size/age? If so, then this should be mentioned (and it would seem that for some species the smallest animals from young age groups are being over-consumed within the model).

Lines 513-517. Agreed. But as ‘the influence of species groups on the rest’ (line 509) are key to developing understanding, digging deeper to see exactly what each modelled species is eating may expose where the model is not behaving realistically. Maybe mention this as potential future work.

Lines 525-527. Solution (a): does data currently exist that would enable this? If so, then mention why has it not been used here? If not, then only solution (b) is currently viable…

Conclusions
Line 547. Remove the word ‘very’. It doesn’t add anything here, and I’m unsure about close the biomass estimates were to each other – it was only the trends that were compared, not the actual values.


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: FROM DATA COMPILATION TO MODEL VALIDATION: A COMPREHENSIVE ANALYSIS OF A FULL DEEP-SEA ECOSYSTEM MODEL OF THE CHATHAM RISE
Review round: 1
Reviewer: 2

Output:
Basic reporting: General comment:
In the manuscript "From data compilation to model validation: A comprehensive analysis of a full deep-sea ecosystem model of the Chatham Rise" the authors present and discuss the application of an end-to-end ecosystem model, the Atlantis model, in the Chatham Rise ecosystem.

Overall the manuscript and the research presented are relevant and well contextualized. The English language is overall good and clear for an international audience. However, the manuscript would benefit of some revisions before acceptance, in particular regarding its structure, in order to improve its clarity.

Specific comments:
1. The authors begin Introduction by describing the specific situation in New Zealand and the Chatham Rise study case. This could be improved if the authors provided a broader background/context of the problem addressed first (e.g. background on ecosystem management) and then described the specific case of the Chatham Rise ecosystem.

2. The authors do not follow a strict Introduction, Materials and Methods, Results, Discussion, Conclusions structure. Instead, they describe their methods and present simultaneously their results through sections 3 to 7. Section 2 refers to Model design.
This structure is acceptable but the paper would greatly benefit of a prior section (e.g. section 2 - Methodological Approach) where the authors provided an general overview of the methodological approach used, which would help the reader to follow throughout the manuscript. Although this is partly done in the the end of the Introduction (lines 95-107) it could be improved for clarity.

3. Section 2 - Model design could be improved by including a brief description and general scheme of the Atlantis model.

4. Figures and tables are overall clear and of good quality, but some improvements can be made. In particular, the legibility in black and white of some figures can be improved (e.g. Figure 9, Figure 15). Figure 1 could also be improved by including a scale, coordinates and North arrow. The acronyms used in Table 1 should also be in the table legend.

5. The authors provided their raw data and the model code, which I acknowledge. However, some additional description of the content of these files could be useful for future readers.

6. The Appendixes are referenced throughout the manuscript as Appendix 10. Please revise.

7. Abstract, line 36. I would suggest to add "which is also to be best of our knowledge the first end-to-end ecosystem model of any deep-sea ecosystem"
Experimental design: General comment:
The research presented in the manuscript is within the scope of the journal.

Overall the research question is well defined and the experimental design is adequate to the aims of the manuscript.

Specific comments:
1. Lines 172-173. The authors refer that used a 12 hours time step. Did the authors performed any sensitivity analysis of the time step? How does the time affect the model results?

2. Section 2.3. Further information or references are required regarding the ROMS application used in the present study.

3. Please clarify if the scheme presented in Figure 4 is a general overview of the Nitrogen cycle of if it also refers to the processes considered within Atlantis model.
Validity of the findings: General comment:
In this manuscript the authors did a great effort in establishing a complex ecosystem model and the findings are supported by the methodological approach followed. This model is intended to be used and improved in future applications regarding the fisheries management.
The main weakness of the model is probably its complexity, which difficult its validation. This limitation is acknowledge by the authors by referring that the model require further exploration

 Specific comments
1. Please clarify the text in lines 334-337, 521-522, 528.

2. Please clarify which were the oceanographic conditions used in the model skill assessment simulations, since the the ROMS data do not cover the entire period.

3. The discussion of the results in section 6 - Skill assessment could be improved, in particular by detailing and improving the justification between the differences found.

4. Conclusions could be improved by including part of the discussion presented in lines 537-545.
Additional comments: I acknowledge the authors for their great effort in establishing such a complex model.
My recommendation regarding Major revisions of the manuscript in mainly related with its structure, since in my opinion the manuscript would benefit if the Methodological Approach was clearly described to help the reader to follow through the remaining sections.


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: FROM DATA COMPILATION TO MODEL VALIDATION: A COMPREHENSIVE ANALYSIS OF A FULL DEEP-SEA ECOSYSTEM MODEL OF THE CHATHAM RISE
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I am happy to recommend this manuscript for publication as the authors have met my concerns with the original submission in their revisions. The methods/results appear unchanged, but the additional text provides more detailed discussion and sufficiently explains modelling choices and aspects of the Atlantis model framework that I previously found confusing. I agree with the other reviewer that the addition of the Methodological Approach section improves the clarity of the paper – it certainly helped me as a reader.


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: FROM DATA COMPILATION TO MODEL VALIDATION: A COMPREHENSIVE ANALYSIS OF A FULL DEEP-SEA ECOSYSTEM MODEL OF THE CHATHAM RISE
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors did a good effort in improving the manuscript taking into account the reviewers' comments and suggestions.
The addition of section 2 helps the reader to follow the manuscript.
Clarifications to the methods and approach used were provided.
Clarifications to the text were made when requested.
The discussion was improved.
Some figures and tables were also improved.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: I acknowledge the authors for the review of the manuscript which, in my opinion, is suitable for publication.


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

Input:
Title: TRACKING DOWN THE LIZARDS FROM GRAVENHORST'S COLLECTION AT THE UNIVERSITY OF WROCŁAW: TYPE SPECIMENS OF CALLOPISTES MACULATUS GRAVENHORST, 1838 AND THREE LIOLAEMUS SPECIES REDISCOVERED
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This is a very interesting manuscript, I congratulate you and thank you for making this information available to all Liolaemus researchers. I recommend the following changes, especially in regard to Liolaemus lineatus.

Line 2: “of Callopistes maculatus”

Authors need to include the authority (name, year), change for: of Callopistes maculatus Gravenhorst, 1838,

Line 32-33: “Johann Ludwig Christian Gravenhorst (1777–1857) was the founder and the first director of the Zoological Museum at the University of Wrocław (currently Museum of Natural History).”

Please clarify that Gravenhorst was German, and also the original location of the Museum (Germany, later Poland?).

Line 57: “Pincheira-Donoso, Scolaro & Sura (2008)”

Change for Pincheira-Donoso et al. (2008)

Line 65: Check the citations in the entire document, “&” is used in lines 57-58 but “and” is used in the line 65. In some journals it is accepted use “&” for species authority, while “and” is used in the citations. Anyway, all citations need to use the same format through the manuscript.

Line 73: In the abstract it is stated that syntypes of Chalcides viridanus were not found but in line 73 is stated that DNA extraction was intended. Clarify in the line 73 that this last specimen of Chalcides viridanus is from other older collection.

Line 92: “Cauquenes Province in Chile”

I suggest change for: “Cauquenes in Chile (in the current Maule Region), collected by Herrn Scholtz”, because the word Province was not used by Gravenhorst.

Lines 92-93: “(currently Liolaemus fitzingeri)”

Change for (incorrect spell and use of the species authorities is needed): “(currently Liolaemus fitzingerii [Duméril & Bibron, 1837])”

Line 121: “Dorsal scales larger than dorsal neck scales but otherwise very similar (Fig. 3A)”

Check, Fig.3A, it actually shows the cloacal zone.

Lines 133-135: I seem to me that there are some dark scales between the shoulders, forming, maybe, what is left (discolored) of one inconspicuous occipital band, as is found in some Andean species from Maule Region. It is what I would expect after 150 years.

Line 141: Pincheira-Donoso, Scolaro & Sura, 2008).

Check “et al.” use in the entire document (only the species authorities should be mentioned one by one).

Line 146-148: This is a good argument. Whereas this character is very variable in some Liolaemus group, the nasal and the rostral scales are always separated in the L. nigromaculatus group, but also could be added that species of the L. nigromaculatus group are known to inhabit in the Antofagasta, Atacama, Coquimbo and Valparaíso regions (north to south), which is approximately 340 km (straight line) north from Cauquenes, you can cite TPet al.2015 (silvai).
Add that the fourth supralabial scale of L. conspersus is curved upward, and then, must be discarded that this species could be conspecific with Liolaemus fitzingerii, because this last belong to the Eulaemus subgenus, which has short uncurved supralabial scales (Lobo et al. 2010: A critical review).

Line 167: At this point of reading your very interesting manuscript, it is clear to me that conpersus synonymy with fitzingerii and nigromaculatus were two great misidentifications. I suggest you point out that L. conspersus, due to its SVL, 77 midbody scales, shape of the dorsal scales, and what maybe can be the “remains” of an inconspicuous occipital band, resembles some species of the Andean Maule Region, which is approximately 80 km to the east from Cauquenes. I refer to L. buergeri and L. flavipiceus, in which some specimen exhibit an inconspicuous occipital band. You can read about these in Garin et al. 2013 (Cuadernos de Herpetología 27 (1): 65-69), Pincheira-Donoso and Núñez 2005, Troncoso-Palacios et al. (2015, Liolaemus scorialis description). You can also state that L. conspersus does not match with the morphological features found among the species that occurs in Cauquenes or surroundings (chiliensis, cyanogaster, lemniscatus, schroederi, septentrionalis, tenuis) and cite PD&N2005 to argue about it.
However, I strongly recommend that you also point out that the holotype probably is not so well preserved to reach a clearly identification (buergeri or flavipiceus). At least to me, the best option is considered it a nomen dubium (uncertain application).
Maybe you should also add in the Line 97: “Undetermined sex”. Usually males have anal pores but these are absent in flavipiceus and are very small in buergeri, so 150 years later I think these could be discolored. Liolaemus can be easily sexed through gonads examination, but these specimens have survived WWII and too much else, it is not good idea open them for this...

Line 170-171: “from Cauquenes Province in Chile.”

Change for: “Cauquenes in Chile (in the current Maule Region), collected by Herrn Scholtz”

Line 172“(currently regarded as synonym of L. chiliensis; Pincheira- Donoso & Núñez, 2005)”

This need to be change for an older one: “(currently regarded as synonym of L. chiliensis; Donoso-Barros, 1966)”

Line 179: Expand and clarify, why it is different in unicolor?

Line 189: If possible, please add a close-up of the dorsal scales.

Line 206: Count the ventral scales.

Line 221: There are anal pores?

Line 235: I agree in that hieroglyphicus is not conspecific with L. lemniscatus. After this, add that the number of midbody scales allows to discard a synonymy with L. chiliensis, which has 31-33 (PD&N2005) and the fourth supralabial curved upward discard to signifer (Eulaemus subgenus, see previous comments).
L. hieroglyphicus is probably conspecific with schroederi or cyanogaster, also it resembles septentrionalis juvenile. This need to be added, see features in PD&N2005 and record of cyanogaster very near Cauquenes in Rubio et al. 2004 Herpetological Review 35(3). However, L. septentrionalis has rounded dorsal scales with no mucron. The Fig. 4 resolution does not allow me check it. These three species should be mentioned as hypothesis but more accurate studies are needed.

Line 251: Clarify that Fitzinger (1843) does not refer to L. lineatus main variety (Hauptart), while he synonymize the three Abarten.

Line 254: “Boulenger (1885) synonymised this species with L. nitidus”

Clarify: Later, Boulenger (1885) synonymized these four varieties of L. lineatus with L. nitidus.
Note that he explicit indicates Fig. 1-7 by Grav. as L. nitidus.

Line 280: If possibly, count the scales around midbody. Only two Liolaemus with this type of dorsal scales occurs in Chile, L. chiliensis and L. nitidus. Both species can be easily differentiated because the throat of nitidus has dark stripes whereas chiliensis always has whitish, without stripes, throat. For me, this is by sure a L. nitidus specimen.

Line 289: I agree, this is a problematic specimen. Stripes in the throat and the dorsal scale shape-size, indicate L. nitidus juvenile. But frontal fragmentation, dorsal scale shape-size indicate L. chiliensis. Both species has nasal and rostral scales in contact with apparent no intraspecific variation (my own data, you can cite me as personal comment).

Line 314-315: “However, its phylogenetic position in molecular analyses is highly variable (Troncoso-Palacios et al., 2015; Panzera et al., 2017; Portelli & Quinteros, 2018),”

This is incorrect. While Troncoso-Palacios et al. 2015 and Panzera et al. 2017 are based in molecular data, Portelli & Quinteros 2018 performed a combined phylogeny with DNA + morphology data. This need to be clearly stated.
Some researchers will conclude that Portelli & Quinteros (2018) result should be taken with caution because data combination can amplify the errors (https://academic.oup.com/sysbio/article/63/4/582/1623176).

Line 321-323: “The matters are further complicated by the fact that L. nitidus is probably a paraphyletic species, with some of its lineages being more closely related to some lineages of L. monticola (which probably is also paraphyletic; Torres-Pérez et al., 2017).”

I disagree. This sentence suggests that L. nitidus is composed by more than one species. I think that this is not what is really concluded in Torres-Pérez et al. (2017). Indeed they point out that nigroviridis and monticola appear to be composed by several hidden species, but in the case of nitidus, although they found that one haplotype of nitidus is nested in monticola northern race and two in monticola southern race, they found eight haplotypes forming the main nitidus clade (only one species), and this main clade even includes samples from the same localities where outsider haplotypes were detected (Cantillana mountain). They suggest incomplete lineage sorting and introgression as explanation for the paraphyletic result but they did not suggest that nitidus is composed by more than one species.
I recommend delete this sentence.

Line 330: “such as presence of two frontal scales rather than one”

It is very interesting, however, although I have no reviewed nitidus specimen with two frontal, I will attach some photograph with variation on this.

Line 331: “and contact between nasal and rostral scales.”

This is interesting. This character is informative for species of the L. nigromaculatus, but it is variable among other groups and even in the same species. However, all my samples of nitidus (n=16), all have these in contact, which suggest that this feature is fixed also in nitidus.

Line 331-333: “It is possible that this specimen represents different lineage of L. nitidus but without molecular data it is currently impossible to evaluate.”

It is too much speculative. As mention before, only some sequences from Cantillana Mountain are nested in monticola (northern and southern races), while other samples from Cantillana and all other nitidus samples are nested in nitidus main clade. This suggests introgression or incomplete lineage sorting but not several “nitidus” species. At least it requires more sampling, but I don’t agree with speculate this based in such problematic specimen. I recommend delete this sentence.

Line 341: After this, explain that L. lineatus Gravenhorst 1838 must not be confused with L. lineatus Gray, 1845, an invalid name (previously occupied) of the species currently knows as L. nigroviridis (see Núñez 2004, Cambios taxonómicos para la herpetofauna de argentina, bolivia y chile).

Line 380: “represents L. nitidus or a very similar species.”
Again this suggests several species in nitidus, which has not been found in phylogenetic studies (paraphyletic samples came from only one locality). I suggest delete or rewrite as “L. nitidus or L. chiliensis”

Line 392: Add the type locality: “at foot of Cordillera, Chile”. By the way, this is a very problematic type locality. There is a label with more information?

Line 397: After this, should be included that previously (ignoring the survival of Gravenhorst specimen), Veloso et al. (2000, Fixation neotype lacerta palluma) intend the designation of the MNHNCL 2909 as the neotype of Lacerta palluma (currently C. maculatus), but this proposal was rejected by Etheridge and Savage (2003) and by the International Commission of Zoological Nomenclature (ICZN 2005, case 3225, International Commission on Zoological Nomenclature. 2005. Opinion 2118 (Case 3225). Phymaturus Gravenhorst, 1837 and Lacerta palluma Molina, 1782 (currently Phymaturus palluma, Reptilia, Sauria): usage of the names conserved by the designation of a neotype for Lacerta palluma Molina 1782. Bulletin of Zoological Nomenclature 62:116–117.).


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: TRACKING DOWN THE LIZARDS FROM GRAVENHORST'S COLLECTION AT THE UNIVERSITY OF WROCŁAW: TYPE SPECIMENS OF CALLOPISTES MACULATUS GRAVENHORST, 1838 AND THREE LIOLAEMUS SPECIES REDISCOVERED
Review round: 1
Reviewer: 2

Output:
Basic reporting: Both authors are not native speakers (neither I am), and this denotes through the text. There are lot of problems with the English, namelly in phrase structure and grammar. I suggest that the authors ask a native speaker to review the English before the next subimission.

The organization of the paper is problematic. The authors need to follow an example from other existing type catalogs. None of the nomina have their taxonomic authorities or date associated, the type localities are not in verbatim, etc.

The other main problem of the manuscript is that, without much explanation, the authors present some brief taxonomic accounts for other taxa, namelly Liolaemus lemniscatus, Liolaemus marmoratus, Liolaemus unicolor, Leiocephalus schreibersii, and Chalcides viridianus. All of these taxa were named by Gravenhorst, but besides that, there is nothing about them that deserves to be noted in the paper, besides the fact that the types are thought to be lost and the authors couldn't find them.

The authors have to decide what they want to present in this manuscript - it is either a paper about the specimens they rediscovered, and then stick to those only, or if they want to present a paper about taxa named by Gravenhorst, and then expand it to include taxonomic accounts of all of them, with or without types.

There is also a lot of inconsistencies that complicate the manuscript - for example, in the case of Liolaemus lineatus, the authors refer that Gravenhorst described one main variety and three subvarieties. In the following sentences the authors call the subvarieties varieties, and start to refer to the specimens by "first specimen" and "second specimen".

This is highly confusing. I understand that both specimens have the same catalog number, but in cases like these each one should be identified separately in a non-confusing way - maybe call one 1323a and the other 1323b, adding a tag to the respective specimen.

I suggest the authors reformat the paper, for example, following my 2014 type catalog of Porto Museum
(Ceríaco, L.M.P. et al. (2014) Catalogue of the amphibian and reptile type specimens of the Museu de História Natural da Universidade do Porto in Portugal, with some comments on problematic taxa. Alytes 31(1/2): 13 - 36)

This is what it would look like:

Extant types

Reptilia

Family

Genus species Author (Date: page of description)

Type specimens: XX holotype/syntypes/paratypes designated by Gravenhorst (date of publication) still exist in the Museum name, being represented by one juvenile/adult male/adult female/unsexed adult specimen from “Verbatim locality” [=current name of the place], other geographic data (province, region, etc), Country, collected in DATE of Collection (if known) (Catalog number), [in the case of more specimens from different places] and add same data as above and then (Catalog number).

Present name: Genus species Author (Date) [according to the most updated or followed taxonomy]

Remarks: in here add everything you have about the species and specimen (now divided by a smaller unnamed introduction, "Redescription of the holotype" and "Discussion"). Maybe start with the taxonomic and nomenclatural story, and then follow with the type material redescription. Do not separate it into different subsections.
Experimental design: There is nothing to add regarding the experimental design itself. It is a straightforward paper dealing with lost types. The conclusions and identification of the specimens are well supported.
Validity of the findings: The discovery and redescription of the types that everyone thought to be lost is an important and valid finding. The data and proofs that the author's show support the unambiguous identification of the types.
However, as noted in my comments in the pdf, there are some problems with the lectotype designations, namelly the designation of a lectotype for Callopistes maculatus, or the designation of a lectotype for L. lineatus main variety using the putative type of one of the subvarieties.
Additional comments: This is a very interesting and important paper, but it has a lot of formatting and language problems. I encourage you to revise the format, and especially make it more consistent. I also suggest that you stick with the specimens you have discovered, and avoid talking much about the ones you didn't. The Chalcides part should be deleted, is highly irrelevant.
As my identity is revealed to the authors, I'm open to any querie and more direct help if they wish to contact me.


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: TRACKING DOWN THE LIZARDS FROM GRAVENHORST'S COLLECTION AT THE UNIVERSITY OF WROCŁAW: TYPE SPECIMENS OF CALLOPISTES MACULATUS GRAVENHORST, 1838 AND THREE LIOLAEMUS SPECIES REDISCOVERED
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is well written in general but I found some typo and format mistakes that must be corrected (see below). The background included in the text allows understanding how this work fits in the broader field of knowledge. Objectives aren’t included; someone can guess what the aim of the study is.  The relevant prior literature is appropriate referenced. Nevertheless, some relevant literature is missing. The general structure of the article is odd. Authors joined results and discussion into a single section. This is not a good choice, since some nomenclatorial acts are proposed. So results and discussion should be located as separate sections. The study is interesting, but in the way that the study was framed, I can’t see the relevance. Authors only take character states of specimens; comparisons are based on literature (since no specimens list are detailed), and no formal re-descriptions are made.
Experimental design: My main concern is about the lack of specimens studied. I understand the difficulty of study some material, but in cases where nomenclatorial and taxonomic results arise, it’s necessary to study the characters from specimens (not based on literature). Especially when in figures I count a different number of scales that the authors made (see below). Perhaps some character states were taken in different way. Authors mentioned that they “focused on describing morphological characters used by previous authors...” There are a lot of character states that authors don’t include. Those can be very useful for comparisons. Author miss scales counts: Number of temporal scales, number of gular scales, number of neck’s scales, Hellmich’s index, among others.
Validity of the findings: Re-descriptions are good. Nevertheless, there are many character states which were taken for one specimen and not for the others. Also, for each specimen redescribed, SVL and sex are lacking. SVL is on Table, but must be in redescription. Authors mention large and robust lizard without mention of SVL. About sex, authors mentioned at the end of the MS that the specimens’ could be females (because de lack of precloacal and femoral pores). Data about sex must be included at begin of the descriptions.
Comparisons were made against single species (except for L. conspersus), and based on so few characters. If the aim of the study is to re-describe the species, a complete diagnosis is necessary; especially for lectotype of L. lineatus.
Why authors report number of infradigital lamellae of third finger? The character state traditionally used is fourth finger.
I count different numbers of supralabials, lorilabials and infralabials (see below).
As I mentioned above, comparisons were mostly made with single species, mainly following Boulenger synonymies. Lines 92-93 authors mentioned that L. conspersus was synonymized with the current L. fitzingerii. Despite this, authors only compare and discuss the taxonomy position of L. conspersus against L. nigromaculatus and the species related. Why not compare it with L. fitzingerii? Just, should look by the presence (or absence) of femoral patch. Similar occurs with L. hieroglyphicus. Authors compare it with L. lemniscatus. But previously they mentioned that this taxon was synonymized with L. signifer (line 171) and L. chiliensis (line 172). Picture of L. hieroglyphicus is far from being a L. signifer, but is morphologically very close to L. chiliensis. So, comparisons with this latter taxon are needed. Since authors compare L. hieroglyphicus with L. lemniscatus based on literature, must include data taken from Quinteros (2012).
Designation of lectotype and paralectotype must follow The Code. There is not citation of the ICZN on the MS. Moreover, if authors propose a lectotype (and paralectotype) a formal description must be included. Many section of a formal description lack.
The “mysterious specimen” is anecdotic. If the specimen is uncatalogued, how authors know that was a Gravenhorst’s specimen? Only Gravenhorst collect Liolaemus specimens for the Museum?.
As for Liolaemus lineatus, I expect a formal description for Callopistes maculatus.
About General comments and implications in Liolaemus taxonomy. Even though there are many species of Liolaemus (and many other genera) based only on specimens from the type locality or the type series, the main concern about Gravenhorst’s species is the number of individuals and the early synonym proposed.
Te comments about asymmetry and mosaic characters’ distribution as evidence of hybrids has no relation with the MS.
If authors want to publish this study, should include data for many more species of Liolaemus, in order to stablish the taxonomic status of the specimens of Gravenhorst. Should perform a formal redescription of Callopistes maculatus, including additional specimens.
Additional comments: I have some minor comments (mainly about format):
Line 55.- Spell out Liolaemus. If the genus name begin a sentence or if is named for first time in a new paragraph, must be spelled completely. There many of this mistakes along the MS.
Line 97.- Include SVL and sex. Please make this changes for all specimens redescribed.
Lines 107-108.- I follow the figures and count different number of supralabials: I count five supralabials (from the right side). And the fourth is upturned but not contacting the subocular scale.
Lines 108-109.- I count six loriabials, three in contact with the subocular.
Lines 114-116.- Include number of temporal scales
Lines 119-120. Sentence about neck scales. Please re-write
Lines 121 and 130.- Figure 3B indicate dorsal scales, and Figure 3A show the lack of pores.
Line 125.- Why third finger? Ussually the infradigital llamellaes are counted from the fourth finger/toe.
Line 130.- No Liolaemid lizard exhibit femoral pores
Most of the previous comments are repeated for all taxa. Especially the scales count (lorilabials, supra and infralabials).
Line 201.- Probably is the figure, but upper temporal show a slight keel?
Line 204.- Provide number of gular scales (for all taxon), when possible.
Line 206.- What about number of dorsals and ventrals?
Lines 246-247.- Sentence is hard to follow. Please re write
Lines 273-274.- I count the same number of lorilabials. I don’t know how authors made the previous count.
Line 306.- “anteriormost nuchal scales” are you talking about occiput region??
Line 317.- “computational method”. For systematic these are Optimality Criterion.
Line 405.- Authors must mention sex of the specimen, at the begin of the description.


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: TRACKING DOWN THE LIZARDS FROM GRAVENHORST'S COLLECTION AT THE UNIVERSITY OF WROCŁAW: TYPE SPECIMENS OF CALLOPISTES MACULATUS GRAVENHORST, 1838 AND THREE LIOLAEMUS SPECIES REDISCOVERED
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This time it suggests few corrections, mainly drafting issues. It is a very interesting manuscript, I hope it will be published son.

Line 54-57: “Here we redescribe other type specimens of lizards that were rediscovered in the collections of the Museum of Natural History, University of Wrocław. We also discuss taxonomic implications of these findings and provide a catalogue of type specimens of all lizard species named by Gravenhorst.”
Move after line 65, as final paragraph of the Introduction. Otherwise, the lines 58-65 seems disconnected.

Line 109: add: collected by Scholtz.

Line 118: “the name”
Change for: these names (Callopistes maculatus and Phymaturus palluma) became universal.

Lines 119-120: “attempted to synonymise C. maculatus with P. palluma and proposed a neotype (MNHNCL 2909)”
Correct, I suggest: Veloso, Núñez & Cei (2000) proposed the combinations C. palluma and P. flagellifer (formerly Centrura flagellifer), and attempted to synonymise C. maculatus with C. palluma, designating a neotype (MNHNCL 2909) for the last.

253-254: “Interstitial granules are present between the dorsal scales, as in some L.
nigromaculatus and L. atacamensis, but not in L. silvai and L. zapallarensis.”
Clarify, in regards to L. conspersus.

255-256: “Liolaemus conspersus has significantly more scales around the midbody than any of the above-named lizards (77), while in the others the range is 48–62 scales (Troncoso-Palacios & Garin, 2013”
I suggest: Liolaemus conspersus has significantly more scales around the midbody (77) than any of the above-named lizards (48–62 scales, Troncoso-Palacios & Garin, 2013)

264-269: “It is also worth noting that the phylogeny and taxonomic content of the nigromaculatus group are not well established. Mitochondrial DNA analysis by Troncoso-Palacios et al. (2015a) indicates that all these species are closely related, but Panzera et al. (2017), on the basis of analyses using 541 ultra-conserved elements and 44 protein-coding genes, suggested that L. atacamensis is only distantly related to the other named species, even though it is morphologically most similar to L. nigromaculatus (Troncoso-Palacios & Garin, 2013).”
I suggest to delete this paragraph, because it is not a contribution to clarify the taxonomy of L. conspersus.

278: “the Maule region”
Change for: Maule Lagoon

412: You can also add that L. gravenhorstii is restricted to the Metropolitan region of Chile, more than 200 km north from Cauquenes.

423:  I suggest you restrict this proposal to L. schroederi and L. cyanogaster, because L. gravenhorstii midbody scale count and distribution strongly suggest that it is not a synonym of L. hieroglyphicus.

425: Check this for L. conspersus and L. hieroglyphicus. If you think that —due to the state of the holotype—it is unlikely that a further study can be succeed in establishing the taxonomic identity, then I suggest nomen dubium, but if the status of preservation of the holotype is appropriate, then I suggest nomen inquirenda.

447: “Unfortunately, for unknown reasons, the first variety was not illustrated”
I suggest: Unfortunately, the first variety was not illustrated

448-450: “However, the survey of two museum catalogues that survived the war supports that, at least originally, four specimens of L. lineatus were present (later updated to two
specimens), In the second catalogue (from 1907), three specimens are listed (Fig. 9).”
This was hard to read for me. Later updated to two specimens? (after 1907?, move at the end of this sentence if that is the case). Check the “, In”, should be “. In”.
Maybe something like this:  However, the museum catalogue before 1907 supports that, at least originally, four specimens of L. lineatus were present, while a second catalogue (from 1907) list three specimens (Fig. 9).

462: “Liolaemus lineatus Gravenhorst, 1838 should not be confused with its younger homonym Liolaemus lineatus Gray, 1845, a species currently regarded as synonymous with Liolaemus nigroviridis Müller & Hellmich, 1932 (Núñez, 2004).”
Move to the line 457, after “…with L. nitidus.” I suggest: Boulenger (1885) synonymised this species (all four varieties) with L. nitidus. We remark that Liolaemus lineatus Gravenhorst, 1838 should not be confused with its younger homonym Liolaemus lineatus Gray, 1845, a species currently regarded as synonymous with Liolaemus nigroviridis Müller & Hellmich, 1932 (Núñez, 2004).

687: “Liolaemus (also called the chiliensis section – a group to which all rediscovered lizards belong)”
Correct, I suggest: Liolaemus – a group to which all rediscovered lizards belong–
This because each Liolaemus subgenus is composed of two sections. Liolaemus sensu stricto is composed of chiliensis and nigromaculatus sections, while Eulaemus is composed of linieomaculatus and montanus sections. By sure all the types rediscovered belongs to the Liolaemus sensu stricto, but it is not necessary to point out the section.


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: TRACKING DOWN THE LIZARDS FROM GRAVENHORST'S COLLECTION AT THE UNIVERSITY OF WROCŁAW: TYPE SPECIMENS OF CALLOPISTES MACULATUS GRAVENHORST, 1838 AND THREE LIOLAEMUS SPECIES REDISCOVERED
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript is much more improved and almost ready for publication. I would still reconsider the "Unidentified Specimen" section - at least do not make it a separate subsection but simply continue the text under the remarks subsection, immediately after the last paragraph.
Not sure if in the case of Liolaemus conspersus and L. hieroglyphicus the authors should say that the present name is respectively Liolaemus conspersus (Line 179) and  L. hieroglyphicus  (Line 308). The authors present a very nice overview of the taxonomic and nomenclatural problems, and realize that maybe none of the current synonymies is correct. However, I would be conservative and follow the most recent revision of the group and maybe just call it "cf." nigromaculatus and cf. lemniscatus. The remarks then explain the problems.
Experimental design: All ok for such kind of study.
Validity of the findings: While I'm not an expert on these taxa, the authors present good comparisons, and the comments of the other reviewers, Jaime Troncoso-Palacios seems to confirm that.
Additional comments: The manuscript is much more improved and almost ready for publication. I would still reconsider the "Unidentified Specimen" section - at least do not make it a separate subsection but simply continue the text under the remarks subsection, immediately after the last paragraph.
Not sure if in the case of Liolaemus conspersus and L. hieroglyphicus the authors should say that the present name is respectively Liolaemus conspersus (Line 179) and  L. hieroglyphicus  (Line 308). The authors present a very nice overview of the taxonomic and nomenclatural problems, and realize that maybe none of the current synonymies is correct. However, I would be conservative and follow the most recent revision of the group and maybe just call it "cf." nigromaculatus and cf. lemniscatus. The remarks then explain the problems.


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

Input:
Title: THE RESPONSE OF SULFUR DIOXYGENASE TO SULFIDE IN THE BODY WALL OF URECHIS UNINCINCTUS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript entitled, The response of sulfur dioxygenase to sulfide in the body wall of Urechis unicinctus  by Zhang and Zhang explores the mechanisms use by Urechis to overcome the noxious properties of sulide. My comments are noted below.

Try and make some improvements to the text. The help of a native English speaking colleague could improve the use of the Scientific English used in the current manuscript. Similarly, some sections appear rather vague and would be strengthened by the inclusion of specific information. Indeed, in the background section the authors could add specific details like, ‘Sulfide is common toxin to organism. However, some organisms can tolerate certain concentrations of sulfide, such as the echiuran worm Urechis unicinctus, which inhabits in a U-shaped burrow in costal intertidal and subtidal mudflats, where sulfide can temporally accumulates’. In this instance this sentence could read, ‘In some sedimentary environments like costal intertidal and subtidal mudflats, sulphide levels can reach millimolar concentrations (2-5mM) and can be toxic to marine species. Interestingly, some organisms have evolved biochemical strategies to overcome and tolerate high sulphide conditions such as the echiuran worm, Urechis unicinctus. Other such changes are needed throughout the text.

A good use of references.
Experimental design: The experimental design is fine and is supported by previously published methods used by this group. See, Gene. 2016 Nov 30;593(2):334-41; PLoS One. 2013 Dec 2;8(12):e81885. doi: 10.1371/journal.pone.0081885. While the findings are interesting and go some way to explain a key mechanisms to overcome sulphide toxicity in this species, the results seem to replicate past work published in the aforementioned papers, Gene. 2016 Nov 30;593(2):334-41 and PLoS One. 2013 Dec 2;8(12):e81885. doi: 10.1371/journal.pone.0081885. Indeed, Figure 2 and 3 of this manuscript are similar to Figure 6-7 in the paper recently published in Gene. 2016 Nov 30;593(2):334-41. doi: 10.1016/j.gene.2016.07.045. Moreover, on close inspection the only differences are the units of expression for the activity data that is expressed as ng/µg protein as compared to µg/mg protein; essentially these are the same figures and this is would not represent new data or results. As such, can the authors describe how the current figures differs from past work and what additional novelty the current manuscript bring to this field base on their past work? Lastly, the graphs in Figure 2 A-C, Figure 3 A-C and Figure 4 A-C, clearly show differences between treatment groups but it may have been better to have combined each of these graphs into ONE graph for each Figure to aid comparison.
Validity of the findings: No comment
Additional comments: Please see text 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: THE RESPONSE OF SULFUR DIOXYGENASE TO SULFIDE IN THE BODY WALL OF URECHIS UNINCINCTUS
Review round: 1
Reviewer: 2

Output:
Basic reporting: I find that the paper, although readable, could benefit from additional translation efforts. There are numerous grammatical errors and typos, and some sentences could benefit from rewording/restructuring to improve clarity.

Additionally, I find that the introduction could improve with a reworked framework. The authors begin by stating the current relevance of hydrogen sulfide as a biological signaling molecule that is endogenously produced in organisms, but do not refer back to this concept at any point. Instead, I think it would best suit the paper to begin discussing the role of hydrogen sulfide as a physiochemical barrier to organisms via disruption of mitochondrial function, discuss the processes involved in sulfide detoxification, and then move into specifics of SDO and their study organism. Sulfide is an important challenge for many different environments which the authors have failed to mention here and this work could be relevant for those organisms as well, so I think these environments/systems should be introduced as well.

The hypotheses explicitly tested in this experiment are not outwardly clear, and the paper could benefit from explicit expectations. The question appears to be "how does SDO concentration, activity, and gene expression respond to sulfide concentrations in the body wall?". What do you expect? Why might that be? Zhang et al. 2016 found differences in expression of SDO upon the same sulfide exposures in the midgut and hindgut, does this influence your expectations? Additionally, lines 71-73 state that Menon and Arp indicate the importance of the body wall. In what ways? It might be best to include this background and state what your experiment will do to investigate this claim.

Lines 175-177 discuss the benefits of increased surface area of the body wall for oxygen uptake. Increased respiratory surface area can be beneficial for gas exchange but also increases permeable surface area for sulfide to enter the body. This may also be important for the localization of SDO activity.

Lines 180-183 are repetitive.
Experimental design: As stated above, I think the question and hypothesis could be more clearly defined. The research question is interesting, but I personally would like to see it related to the broader field of hydrogen sulfide biology and not just this system.

I think that the experimental design is reasonable and the methods are easily followed, but should be rewritten to improve clarity.

There is no mention of protein extraction, which should be included for both the ELISA and SDO activity steps.
Validity of the findings: Lines 142-143 state "Moreover, the negative control had no positive signals (Fig. 1C), which can prove the accuracy of the experiment." I would rewrite this. It definitely provides assurance that the results are accurate, but I am uncertain saying that it proves the accuracy is appropriate. That might just be semantics.

Each treatment was tested individually, but it might also be interesting to test for differences among treatments at each time point as well.

In the conclusion, it may be beneficial to reiterate what the question was and what your findings did to answer that question. Instead of listing out all the components of the body wall, state where the epidermis is located and why that's significant. Same goes for the SDO specifics, it would be good to see a brief explanation as to what these results mean.
Additional comments: I think this experiment and the results obtained are very interesting and provide great insights into the function of sulfide detoxification. It would be great to see the contents of this paper expanded to explain the benefits of this research to the greater hydrogen sulfide biology community.


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

Input:
Title: THE RESPONSE OF SULFUR DIOXYGENASE TO SULFIDE IN THE BODY WALL OF URECHIS UNINCINCTUS
Review round: 2
Reviewer: 1

Output:
Basic reporting: This version of the manuscript is much improved and has addressed the comments of each reviewer.
Experimental design: These are clearly described.
Validity of the findings: No specific comments
Additional comments: This version of the manuscript is much improved and has addressed the comments of each reviewer.


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

Input:
Title: THE RESPONSE OF SULFUR DIOXYGENASE TO SULFIDE IN THE BODY WALL OF URECHIS UNINCINCTUS
Review round: 2
Reviewer: 2

Output:
Basic reporting: I think that the edits made to this paper successfully improved upon the comments made by the previous editors. The text readability has increased and there are few errors when it comes to the grammar of the paper. My comments are outlined as follows.

Lines 115-117: What is your isolation solution composed of? The solutions used in the RNA isolation and immunohistochemistry components of your methods are much more explicit, and for replication purposes it is necessary to include.

Lines 153-155: Revise wording. The emphasis here is that SDO is primarily expressed in the epithelial tissue, so the primary clause isn’t that necessary. If you decide to keep it, just reword it.

Line 190-192: The edited section here is composed of a complete and incomplete sentence. Just modify to ensure correct grammar.

227-233: The conclusion needs to be edited for clarity. The sentences are choppy. Tie in your findings to a broader audience, and I think this will be good.

Figure 1: there is no ER in the figure to represent epithelial tissue as indicated in the caption. Edit this to reflect, either by placing ER in the figure or editing the figure text to E to reflect epithelial tissue.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Overall, I think this is an excellent revision, and the intellectual merit of your findings are much more clear.


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: DIVERSITY, SPATIAL DISTRIBUTION AND ACTIVITY OF FUNGI IN FRESHWATER ECOSYSTEMS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Basic reporting is fine.
Experimental design: The authors need to critically evaluate and discuss the biases associated with different DNA extraction techniques used between the different studies that they analyze.  The should be a new section (e.g. at least one paragraph) added to the discussion dedicated to this important topic.
Validity of the findings: The findings are valid.
Additional comments: This manuscript deals with an interesting meta-analysis of existing fungal sequence data in public databases, and attempts to summarize the biogeography and diversity between many different studies.  I thought it was highly interesting, to compare the overlap in OTUs between different freshwater and marine environments.  That analysis alone will surely have a big impact. My main comments deal with a lack of information regarding why they chose to analyze the sites reported in table 1 and Figure 3, since there are alot of studies on marine systems with public sequence data available  out there that were not considered (for example summarized in Richards et al. ,2012).  Also, the quality of the figures as they are currently presented is rather low, and this should be improved prior to publication.  Furthermore, the authors need to at least acknowledge and discuss the biases associated with the different DNA extraction techniques used between studies as this will influence which Fungi are detected or missed.   Generally I think this manuscript has alot to add to the field and would recommend publication after they can address the following comments.

Comments:

lines 82-95: Since you are analyzing public data - why do you have a section on RNA extraction and amplification techniques?  Or did you contribute new data here ?  Please explain this very important point.

lines 145-157: what was the sequencing depth per sample?  How many sequences were required to reach the plateau?

line 148: Why did you use 95% instead of 97%?

lines 172-175: It is very hard to know whether such low abundances in high throughput sequencing data are due to minute amounts of cross sample contamination during the PCR and library preparation steps.

lines 189-190:  This analysis is highly interesting, and the Table S1 should be moved to the main manuscript (not hidden in the supplemental materials).

line 247: I do not believe that you can make a reliable taxonomic assignment with <80% sequence identity in the 18S V4 region.  These taxa should be flagged as “unidentified”.

lines 277-278: You cannot claim species level identifications with 18S data for fungi.  There is a general agreement that ITS can be used for this (see Schoch et al 2012 PNAS).  Please revise this statement accordingly.

line 324: This should be presented as a main figure and not hidden in the supplemental.

lines 342-351: Please also cite Burgaud et al (2013), since this is highly relevant to the discussion on links between the terrestrial and marine fungi discussed here.

lines 353-354: Is this a study on already published data only?  Reading the methods it seems there is new data being presented ?  Please clarify this important point.

Figure 1: Please add error bars showing the standard deviation across the high number of sampled locations.

Figure 3 and Table 1: There are other studies that looked at the diversity of marine Fungi that are not considered.  For example, Burgaud et al 2013 and Orsi et al 2013 both reported 18S sequence data for marine fungi.  Do the authors have a reason why more studies were not considered?  It is not clear from the text why they only chose the selected samples.  I think the manuscript would benefit from a higher number of marine samples being included in this interesting analysis.

Figure 4: Please change the labeling on the x-axis to the taxonomic information associated with each OTU.  Currently there is nothing to be learned from the label that is there now.

Figure 5: Please explain in the legend more exactly what the y axis is showing.  Is this the percent of total DNA OTUs that were also detected in the RNA dataset?

Figure 6: Same comment as for Figure 5.