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: ACTIVE MANAGEMENT IS REQUIRED TO TURN THE TIDE FOR DEPLETED OSTREA EDULIS STOCKS FROM THE EFFECTS OF OVERFISHING, DISEASE AND INVASIVE SPECIES
Review round: 1
Reviewer: 1

Output:
Basic reporting: There are a few very minor structural and editorial errors - I have included them in my general comments

This is an extensive piece of study - with many researched references. There is some concern that many are used inappropriately - where reference is made to the study of intertidal reef forming oysters when we do not yet know if these studies are relevant to sub tidal European flat oysters.
Experimental design: I think the experimental design is sound and the ideas that are being tackled profoundly important, relevant and timely. I have a major concern on the use of a small grab sample with low replication to determine the current oyster stock densities. I have discussed this extensively in my general feedback - but I do not see any apriori design in the approach to formally test whether there is a competitive interaction between crepidula and the oysters. We need more information on the methods of the 1998 study to know whether the historical and current oyster densities are comparable. If these have similar methods I think it can be concluded that there has been a decline in oysters - but acknowledging that the method is inappropriate to provide an accurate density estimate.

There is an excellent approach taken to the demographics and disease dynamics with very clear policy implications - this is good work that is supported by the data.
Validity of the findings: See above and general feedback.
I have a significant concern about the density estimation methods and the jump to stated conclusion that competitive exclusion is occurring.The conclusion as stated is not well supported by the results.

 For sure competitive exclusion could be occurring but no data has been provided or formal test undertaken to show this. This is easy to remedy by using different language in communicating these ideas - communicating them as hypotheses and not as evidenced outcomes. I have some concerns about the data analysis - these are easy to fix and some suggestions have been provided. My biggest problem is lack of reporting of why transformations were chosen and whether they worked - lets see the data distributions - based on the descriptions in the text it appears GLMs are more appropriate and multiple testing needs to be dealt with or justified.
Additional comments: Line 89 	What is the expected recovery since 2007 – would you have expected recovery in this time period?
Line 94 and 96	italicise species name
Line  109 - insert probable or likely before unsustainable
Line 127 – so the fishery remained open after the crash until 2013?
Line 131 – is this expert opinion or do you know this? Do you know the production to make this statement? Otherwise state  - likely exceeded
Line 134 – Is this referring to all species or only in the context of flat oysters. In the context of flat oysters – can you differentiate between reefs and beds – I see later you do exactly this.
Line 157 – did Blanchard confirm or measure consequences – or discuss what could be consequences? In 2009 Blanchard discusses this again – but also finds that despite significant colonisation by Crepidula – they remain co-associated with extensive flat oyster beds. But there are clear level of effects based on %cover and density. I will ask about this later – can you relate your data to the % cover in the French study?
Line 163 – again – potentially inducing difficulties with recruitment.
Major point – From Line 167 – It is important to not (yet) overegg the potential ecosystem services that could be gained from O edulis restoration.  The Cohen paper is brilliant – but it is not relevant to O.edulis. It should be stated that there are potential O.edulis ecosystem services and that here too knowledge gaps remain. For the following statements made through to 173 – please differentiate which oyster species each of these studies refer to. Many appear to be about intertidal reef forming oysters.
Line 178 –of different species – or only of oysters as per the acronym?
Line 180 – decline of reefs, beds and other habitats?
Line 190 – to link with the previous paragraph – this study is being done for baseline data to then embark on restoration? Are you really measuring ecological resilience?
Line 191 – the increase is the result, no? The “change” in abundance….
Line 194 – can you directly link any change in abundance to causal change?

Line 224 – this sentence should come later after you say what this paragraph is about? This is for the B.ostreae  determination so say that at the beginning of the paragraph.
Line 260-279 – with important consequences for the discussion on using grabs below – you don’t state what the methods were in 1998 – did it use the same sized grad, differ grabs, more grabs or dredge to estimate density? Are the two methods comparable? The link to the Farrell study is not working. This is crucial – and would help justify your use of these methods again – if the 1998 study determined its density estimates with the same method – small grabs with 3 replicates
Major concern- Line 271 – we need to discuss the use of a grab to determine the densities of oysters. The vast majority of your sites had a measured density of zero – other than three sites. You already present information that there are oysters in these harbours. Your grab samples 0.1m/2 which would – on average – need to take 10 replicates of low density area to accurately estimate densities of 1-2 oysters per m2. But you state your replication at each sample area is 10. Blanchard used three grabs but of 0.25m2. These concerns increase if we assume most areas won’t have homogenous densities but very patchy distributions of oysters. For example in a 10x10m patch with a density of oysters of 1m2, if a 2x2m2 sub-patch contains 25 oysters the remaining 1m2 subpatches will have >1 oyster m2 – making the area very difficult to sample by grab.  In the abstract you state clearly that you cannot differentiate between any of the densities and zero – and I do not believe this reflects the density in the harbours.
That on line 373 you state you only found 3 oysters in your entire survey suggest to me you have to consider dropping a calculation of density from this.  This does not apply to the crepidula – where given the abundance you are encountering the grab is appropriate.
Are there no associated data from the 2015 dredges to estimate density?
Line 283 – Is Manova not more appropriate here – if not then correct for multiple testing.
Line 287 (and 292) – Why a square root transformation? Did it normalise the data? You need to confirm that the transformation worked  - or whether there is otherwise good reasons to proceed with this model.  Are GLMs nor more appropriate in this context – you need to better justify model choices. Potentially include species as a dependent variable – then you reduce the number of models you are building. What is different between the benthic survey data and density data? Given the number of oyster you found – the density data is likely very zero inflated and anova is in no way appropriate (but see points of method suitability – it is unlikely your method has the statistical power to detect any real differences).
Line 289 – what do you mean by densities were analysed against total abundance? Again are the 1998 and 2017 surveys comparable?
Line 388 – The use of the term haul suggests the 1998 surveys were done by dredge? 88/m2 – that is huge – please confirm if correct and again how this was measured – does this include spat?

Line 405 –You have undertaken a point sampling study with a grab of a size only suitable to measure high density organisms. That being said – you could determine what the minimum effective density your grab can ascertain with 3 replicates and then find the maximum density that could be in your study area?
Line 409 – you have provided more evidence that credpidula is an ecosystem engineer than O.edulis. I want to back you on this this but I think it is important that you have evidence that O.edulis is an engineer either in this study or from others.
Line 412 – this is important and I think you can state this – as densities are clearly low. Whether there are sub patches you have not sampled that are at higher density could affect this. Clearly if there are 55-90mm oyster throughout the harbours in 2015-2017 – that must mean they have recruited to the population both just before and after 2007. Is the lack of smaller oysters in these samples due to the dredge mesh size – 45mm?
Line 414 – there are some big claims here but do you know or have you evidenced that this is the reason for the crepidula expansion. Dredging will spread it around for sure – dosnt Blanchard discuss the spread of crepidula.
Major point –  Line 416 - you have no formal test of competition between the shellfish. You don’t have enough variation in your data (which is due to the grab not that it may not exist) to test whether the decline in O.edulis is highest where Credpidula gains are greatest. There is no reasonable way to conclude the O.edulis is suffering from competitive exclusion in the Solent. This is a viable hypothesis – but I cannot support this statement in its current form.
Line 419 – is it appropriatre to link the Jackson study to a “likely” decline in water quality. Was there a decline in water quality in 2007-2008 after the crash?  So many other multistressors in the UK coastal environment are likely to affect this – the biomass of crepidula – also able to filter feed – could be taken into account. I am not comfortable  with repeating ideas and hypotheses as likely effects – taking from studies of extensive intertidal oyster reefs and using this to predict effects of O.edulis loss.
Line 421 – Korringa 1946 is not in the reference list. Does this reference find a 3D oyster bed/reef like habitat in the Solent? For sure we know/suspect that many UK estuaries have increased mud and subtidal mud coverage – this includes where crepidula are and are not present in high densities. So habitat change is not all about crepidula – but it is certainly a part of it.
Line 423 – again you are jumping to major conclusions here about the implications of credpidula when you have not measured ecosystem function. You have stated that the results are mixed with more studies suggesting negative effects than potential positive effects – although those positive effects are more likely in a mud dominated low species diversity estuary.
Can you formally test any change in oyster density with change in crepidula density - a regression maybe? I missed this if you did it already.

Line 439 – 440 – this is good on competition – it is here you should suggest that where crepidula at highest density there is a possibility of competitive exclusion – a hypothesis that could be tested.

456-501 – this is brilliant! – a very good policy and impact relevant discussion that is supported by the data presented.

Line 509-511 – we have no idea if O.edulis – at even reasonable densities of 5m2  - has the ability to do this. Again I stress the danger of taking work on intertidal very high density reef forming oysters and placing that in the context of lower density O.edulis.
Figure 4 does not have an explanatory legend or state what the summary statistic being displayed is. It appears to be median, IQR and range but you are analysing this data using an ANOVA that tests for differences between means? Present mean and SD if you want to provide descriptive information or Mean and 2 standard errors if you want to convey significant differences between sites.
Figure 5 – y axis spelling error


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: ACTIVE MANAGEMENT IS REQUIRED TO TURN THE TIDE FOR DEPLETED OSTREA EDULIS STOCKS FROM THE EFFECTS OF OVERFISHING, DISEASE AND INVASIVE SPECIES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is reasonably well written and the standard of English is good.  However, it is over-length, cluttered in places and the structure could be improved.  The authors should revisit some of the material throughout and stream-line to match more clearly defined USPs / hypotheses (see comment below).

The article conforms to professional standards of courtesy and expression.

Literature references are sufficient to provide an introduction to the field and appropriate background/context. The authors should use an additional recent publication that might help in lines 181 and 184:

•	Fariñas-Franco JM, Pearce B, Mair JM, Harries DB, MacPherson RC, Porter JS, Reimer PJ, Sanderson WG. Missing native oyster (Ostrea edulis L.) beds in a European Marine Protected Area: Should there be widespread restorative management?. Biological Conservation. 2018 May 31;221:293-311.

The structure of figs and tables is of a professional standard. Figure 1, has a passing reference to it in the Introduction and the case for it’s value to the m/s is therefore not well made.  Given the title of the manuscript, a graph that illustrates the decline in the Solent oyster fishery may well be more appropriate.

Figure 3 and 5 have dark text on a dark background such that a better contrasting combination should be considered. There are also inconsistencies in labelling such that Southampton Water is in CAPS whilst “The Solent” and ”…Harbours” are not.  Font sizes also differ between “A” and “B” panels in Figure 5.

Raw data is shared.

Lines 90 to 96 do not appear to be well placed at this point in the Introduction:  They go some way to articulating the importance of the work but might be better merged with the last paragraph in the Introduction.  The last paragraph of the Introduction should be clarified.  Baseline data are useful but the justification for the study in lines 188-193 needs to much more clearly articulate hypotheses or study aims.  Clarifying this paragraph will far better define the relevance of the various Results and Figures that follow.
Experimental design: The m/s presents original primary research within the Aims and Scope of the journal.  Research questions need to be better defined (above) but broad content appears to be contemporary, relevant and meaningful. How the research fills an identified knowledge gap needs further clarification in that the research questions need more exact articulation.

The title of the m/s suggests that Ostrea edulis has been outcompeted by Crepidula fornicata.  The study shows that when two studies in 1998 and 2017 are compared, Ostrea edulis has been replaced in its former locations by Crepidula fornicata.  It is possible that the authors are correct but competition is not demonstrated and therefore “competitive exclusion” is a ‘stretch’ for the title (disease, habitat destruction and life history are also cited by the authors as contributing factors to decline of Ostrea edulis).  Similarly, Ostrea edulis is shown to have declined but the case for overfishing needs to be more clearly articulated since there is no evidence presented that establishes a causal link (see above comments).

Rigorous investigations were performed to high technical & ethical standards.  However, the relevance of morphological data is not entirely clear (see comments on hypotheses and study aims) and the authors should therefore remove these data and the ensuing Figure 4, include as supplemental information, or better justify their inclusion.  If the morphometric data are retained the authors should consider the implications identified for Modiolus modiolus in:
•	Brash JM, Cook RL, Mackenzie CL, Sanderson WG. The demographics and morphometries of biogenic reefs: important considerations in conservation management. Journal of the Marine Biological Association of the United Kingdom. 2017 May:1-0.
•	Fariñas‐Franco JM, Sanderson WG, Roberts D. Phenotypic differences may limit the potential for habitat restoration involving species translocation: a case study of shape ecophenotypes in different populations of Modiolus modiolus (Mollusca: Bivalvia). Aquatic Conservation: Marine and Freshwater Ecosystems. 2016 Feb;26(1):76-94.

Methods are described with sufficient detail & information to replicate.
Validity of the findings: With some re-working, this study is of interest to an emerging international audience in marine environmental restoration.  Data is robust and statistically sound.
Conclusions need to be better linked to original research questions (above).
Speculation should be identified as such.
Additional comments: Check italics of species names throughout
Portsmouth, Langstone and Chichester Harbours are inconsistently Capitalised throughout.  As place names they should, presumably, be u/c.
Line 224:  Insert ‘were’ before “randomly”
Line 225-226: sentence in note form
Line 233-234:  This sentence indicates the purpose of the paragraph.  Open paragraph with indication of this purpose.
Lines 249-252:  re-visit
Line 254:  Start sentence with words
Line 255: What were they analysed for?
Line 260:  Here and elsewhere you refer to “1998-2017” rather than ‘1998 and 2017’.  This gives the impression there is a time series rather than two surveys in the respective years.  Care how this is presented throughout.
Lines 270-279:  Was the same methods used in 1998 and 2017?  1998 is not mentioned.
Lines 275 and 286: “Ostrea edulis and Crepidula fornicata” is referred to then “oyster and limpet”.  It would help the reader to know that Ostrea edulis is an oyster and Crepidula fornicata is a limpet at the first mention in this section.
Lines 314-330:  Better in table-form
Lines 334-335:  Common recruitment event/source (?) [both may be connected to elsewhere and not each other…. Unless there is additional evidence to support the assertion].  Either way, the Discussion section is probably a better place for this speculation.
Line 340-342:  Improve clarity here.
Line 345:  consistency with CAPs
Lines 395-396:  The collapse of the fishery could be usefully evidenced in the present work as a foundation for the ‘before-after’ comparison implicit in the 1998 and 2017 part of the study.
Lines 405-412:  Revisit revised study hypotheses / aims here to clarify the outcomes of the present study
Lines 413-427:  Tighten-up this text.  There is a lot of supposition and speculation that goes well beyond what the study shows.
Line 416:  Where is the evidence that C. fornicata is “stable and persistent”?

Discussion in general needs to be made more succinct and condense speculation


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: ACTIVE MANAGEMENT IS REQUIRED TO TURN THE TIDE FOR DEPLETED OSTREA EDULIS STOCKS FROM THE EFFECTS OF OVERFISHING, DISEASE AND INVASIVE SPECIES
Review round: 2
Reviewer: 1

Output:
Basic reporting: The paper is much improved.
I think the authors have engaged with revisions in a positive manner.
Some more speculative claims remain - but have been toned down.

I remain uncomfortable with the title as it is misleading - especially relative to the authors acknowledgement in the rebuttal that they do not have a formal competition test. The narrative that is presented - which is evidenced and supported - is that the decline in oysters is caused by over fishing and environmental change - including pollution; and this left the habitat in a poor soft mud state over time that is low in hard substrate for oysters to re-settle on; slipper limpets then arrived and when at high density could also have negative effects on recovery of oysters but are not indicated in their original decline.

So this is less about competitive exclusion and more about a potential for competition and mixed interactions (predation of larvae is also raised) preventing recovery IF slipper limpets are at higher density. While also acknowledging that they may help when at lower densities by providing some hard substrate.

Therefore could the title not be better phrased - drop the first part and drop competitive exclusion? Change to start with " Is competition with the invasive....."

402-406 - this is unclear due to being broke up with the references. But it is a very important point. The habitat is now generally impoverished - independent of the slipper limpets. The impoverished state is a prime opportunity for expansion of the slipper limpets. And if they reach high densities - "potentially" have competitive interactions with oysters.
Experimental design: From line 282 - The comments on the use of GLM are strange. Its unclear why square root transformations would normalise count data - i.e. the densities. I just plotted the histograms of both the limpet and oyster data and neither are normalized by such transformations? The expected transformations would be log - but please see several papers that discuss why better to use GLM (as below).

All that said - the use of GLM should mean transformations are not required - just use the appropriate family of error distribution to best represent the data. limpet data will conform to neg.bin or poisson. The Oyster data is not in my opinion useable in any standard statistical model format due to the zero inflation.

You also state that your GLM had random effects - which is a different family of models. And you state that replicates were both independent variables and random factors - they should be neither! They are replicates not explanatory variables. And replicates are not different levels within a factor?

I found this all very confusing. Please have this checked and rewrite to make clear.
Validity of the findings: See other points
Additional comments: In the conclusion - given the clear opportunity for competition and other interactions you have identified - perhaps state that the full range of potential +ve and -ve interactions between different stages of different shellfish is as yet unclear and more work needs to be undertaken.

Otherwise thankyou very much for engaging with revisions so positively.


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: ACTIVE MANAGEMENT IS REQUIRED TO TURN THE TIDE FOR DEPLETED OSTREA EDULIS STOCKS FROM THE EFFECTS OF OVERFISHING, DISEASE AND INVASIVE SPECIES
Review round: 3
Reviewer: 1

Output:
Basic reporting: none further
Experimental design: none further
Validity of the findings: none further
Additional comments: A big thank you to the authors for engaging positively in this review process.

Consider dropping “effective” from title – it flows better without it and focuses on the intervention

Analysis description now much improved – what was the chosen or best fit error structure of the GLM you settled on? This should be stated.

Line 285 – Oyster data “were” – plural?
Line 286-290 – t-tests used while acknowledging Oyster data are highly zero inflated requires caution. The t-test results don't give the degrees of freedom to understand sample size and/or what kind of t-test was undertaken to account for any differences in variation between groups. I suggest the analysis is probably sounds and can keep as is but confirm that same result is obtained with non-parametric equivalent. Only if it is not the same should you consider changing.
Line 286-290 – limpet data compared across sites using t-tests while previous text says harbour*site evaluated using GLM? Is this only to compare between limpets and oysters - if so then this is fine. But see points above about whether any of these parametric approaches are suitable with your oyster data.

I am now really excited by the narrative in the beginning paragraphs of the discussion – it reads well and is supported by good quantitative historical and regional information.


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: INCIDENCE OF ACUTE KIDNEY DISEASE AFTER RECEIVING HEMATOPOIETIC STEM CELL TRANSPLANTATION: A SINGLE-CENTER RETROSPECTIVE STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: I would like to commend the authors on an interesting study on the risk factors for acute kidney disease in patients receiving hematopoietic stem cell transplantation. The study is generally  clear, unambiguous, and well written. The background could include more introduction to the different known risk factors for acute kidney disease among patients receiving hematopoietic stem cell transplantation. The structure of the article conforms to an acceptable format. Figure 1 is readable, although the lines could be thicker. Also, there is a small fragment of the Kaplan Meier curve below the number “20” on the x-axis.
The raw data is individual based micro data. I am not aware of the legal basis of sharing data in Japan, but where I come from it would be illegal to share such detailed information.
Experimental design: The background introduces the reader to the concept of acute kidney disease, and the possible advantage of using this, compared to acute kidney injury, to assess the incidence of decreased renal function after receiving hematopoietic stem cell transplantation. One important thing missing, namely a clear aim of the study. The study aim is reported by the authors “…to determine the incidence of AKD after HSCT”. However, the title claims otherwise. Please clarify and amend accordingly. The authors do not clearly states how the research fills an identified knowledge gap.
The methods section is clear, concise, and described in detail. It would be possible to reproduce the study. The authors have chosen to perform univariate statistics, which is applauded given the low number of outcomes. However, some questions regarding the statistical analyses should be answered:
1 – The authors state that continuous variables were presented as medians. How was the variance presented? As interquartile range? In the results section (line 105) no variance in age is presented. And more importantly in table 1 the age is presented as 46 +/- 15 years. The discrepancy is most likely that the authors present age in mean and standard deviation there. Please amend to median with IQR. Also, the authors state (line 92) “…compared using the Pearson’s chi-squared test. Fisher’s exact tests were used.” This is not intuitive. One could guess, that the authors used Fischer’s exact test, when the numbers were below X. Please clarify.
Validity of the findings: The authors use much of the discussion (from line 144-151 and 164-174) to discuss topics not directly relatable to their results. Two potential risk factors were identified (ABO incompatible and acute GVHD), all other listed variables were not associated with acute kidney disease. The authors should discuss their findings and relate them to the literature.
The limitations section needs to be amended. The authors could discuss the low number of outcomes and the appertaining lack of multivariable analysis. Also, the impact of the two listed limitations (retrospective analysis and single-center study) should be discussed more in detail.
I do not agree with the conclusion. The results do not offer the probabilities of finding out which ABO-incompatible HSCT or HSCT related acute GVHD patients are more prone to developing AKD, but rather that there is an association with ABO-incompatible HSCT and AKD as well as an association with HSCT related acute GVHD and AKD.
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: INCIDENCE OF ACUTE KIDNEY DISEASE AFTER RECEIVING HEMATOPOIETIC STEM CELL TRANSPLANTATION: A SINGLE-CENTER RETROSPECTIVE STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a generally well-written single center retrospective study of predictors of acute kidney disease post hematopoetic stem cell transplantation.  The authors propose a new concept, acute kidney disease (AKD), and seem to suggest this may be a better way to characterize kidney injury in HSCT patients.

Some issues to consider-
1. The KDIGO AKI definition is never fully stated.  Instead, they reference that use of KDIGO guidelines based on creatinine only.  On my brief review, KDIGO guidelines  include:
1. increase in SCr >/= 0.3 within 48 hours or
2. increase in SCr >/== 1.5x baseline within 7 days or
3. urine volume <0.5ml for 6 hours.

Which creatinine based criteria did they follow?

2. More rationale for the "new" definition of AKD is required.  There is mention that this will allow better characterization of kidney injury during the first 3 months when GVHD may also occur but the authors should elaborate more.  Also, there are renal manifestations of acute GVHD itself which should be mentioned  (Eg. nephritis or nephrotic syndrome).  Are there any references to support the new AKD definition?

3. Minor grammatical corrections:
- last sentence of methods section capitalized
- first sentence of introduction is vague. Consider instead "HSCT is a fundamental therapy for high risk and refractory hematological diseases.  Several types of HSCT procedures exist based on conditioning therapy (myeloablative or reduced intensity), donor source (autologous and allogeneic, including matched related, matched unrelated, haploidentical and umbilical cord) and stem cell source (peripheral blood stem cells or bone marrow stem cells).  Some of this is highlighted in table 1. which needs a key to abbreviations used below it.

4. Just out of curiosity, did any patients require renal replacement therapy (dialysis or CVVH?)  This should be reported.

5. In the discussion, it should be explained why the rate of AKD (15.7%) is lower than that reported in other studies using AKI as definition (20-92%).
Experimental design: Standard retrospective review with appropriate statistical analysis.
Validity of the findings: No comment
Additional comments: See basic reporting 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: INCIDENCE OF ACUTE KIDNEY DISEASE AFTER RECEIVING HEMATOPOIETIC STEM CELL TRANSPLANTATION: A SINGLE-CENTER RETROSPECTIVE STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed my concerns and only minor grammatical errors persist.  Please run an English spell and grammar check to fix these.
Experimental design: No issues.
Validity of the findings: No issues.
Additional comments: The authors have addressed my concerns and only minor grammatical errors persist.  Please run an English spell and grammar check to fix these.


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: QUANTITATIVE HETERODONTY IN CROCODYLIA: ASSESSING SIZE AND SHAPE ACROSS MODERN AND EXTINCT TAXA
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. The manuscript includes incomplete sentences, particularly early on in the main text. Please make sure that the authors proof-read the manuscript carefully before re-submission. I've listed minor errors in the "General comments" section but it's likely that I did not catch all minor errors.

2. Avoid the use of slash character “/” and instead, write out “and” or “or” (e.g., Ln 21, 39)

3. The Introduction section should be tightened with respect to narrative and logical flow. The section jumps back and forth discussing quantitative vs. qualitative; literature survey; and how previous quantitative work on non-mammalian teeth has been used. I suggest re-organizing the Introduction section so that these individual topics are organized into paragraphs and discrete chunks for efficiency and clarity of understanding.

4. The Introduction section should present justification and rationale for the study. For example, how is this study an improvement over previous studies? And why is geometric morphometric method being used?

5. The goals of the study are too vague and, in my opinion, not effective at providing a clear setup for the study. For example, what is meant by “multifaceted” (Ln 99), “developmental consistency” (Ln 100), and “individuals” (individual specimen or taxon (Ln 102)? These goals should be far more specific and give readers a clear impression of the hypotheses and topics covered in the study.

6. In my opinion, presenting the regression coefficients for skull against tooth shape (e.g., Ln 242; Fig 3) seems unnecessary since the relationship of PC1 values is not useful for further research (i.e., PC1 is not a very interpretable variable beyond this particular study).

7. The authors state that “size varied significantly between positions” (Ln 284). The word “significant” or “significantly” implies statistical significance. Was the variation across positions tested statistically? Similar statements are made in Ln 299 and possibly other places in the manuscript. I suggest revising these statements if statistical tests were not actually conducted.

8. Please provide an explanation as to why the Zahnreihe pattern appears “to be unrelated to the morphological variables investigated here” (Ln 359–360).

9. Much of the Discussion section seems too ‘adaptationist’ to me, although this is largely a personal stylistic issue. What would strengthen this section greatly is to construct a morphospace of tooth shape and see how they cluster according to species or ecological types. I feel this is essential for making the points authors make in the Discussion section. With a morphospace, for example, one can see to which extant taxon is a fossil specimen closest morphologically. This would help with the subsection on modern analogues for extinct crocodylians.

10. Somewhere in the Discussion section, there should be some discussion on variation in tooth count (e.g., Brown et al. 2015 J. Anat.) and its implication for this study.
Experimental design: 11. It’s not clear to me how the tooth numbers were assigned based on the description given (Ln 122–124). From P4, how was P5 or M1 determined? Additional statement(s) clarifying the numbering system would be very helpful to fully understand this step of the study.

12. Is there a justification for the “40% measurable teeth” cutoff point for sampling the specimen (Ln 130–131)? If so, please mention this in the manuscript.

13. The statement “Specimens where the only teeth available biased towards the upper or lower size extremes were excluded” (Ln 131–132) is unclear to me. Please clarify.

14. I appreciate that juveniles were excluded from sampling, but how were “juveniles” specimens determined?

15. I am concerned about the use of two different cameras and (more importantly) camera lenses because parallax could incur significant artifacts to resulting shape data. The potential effect of parallax needs to be evaluated and reported in the paper to confirm the validity of the shape analysis in this study.

16. How was the number of semi-landmarks determined? Also, it was not entirely clear from the Materials and Methods section that the apical point is treated as a fixed (discrete) landmark.

17. Could the bilateral symmetry of the jaw and teeth be truly assumed (Ln 159–160)? Depending on the sample size of corresponding teeth, this should be tested and reported in the manuscript. Also, were shapes of corresponding left and right teeth averaged as well as centroid size?

18. There needs to be a specific description of how the orientation of the teeth and skull, as well as the camera, was standardized. This is a critical information for any morphometric analysis using photographs.

19. I wonder if centroid size is an appropriate metric for tooth size. Centroid size places more weight to (semi)landmarks at ends of structures due to the sum-of-SQUARES calculation. Therefore, a very narrow tooth can have exaggerated centroid size values. I would like to see the degree of correlation between, for example, tooth height and centroid size to confirm that use of centroid size is not introducing any artifacts to the analyses.

20. “All CS values were divided by it [head length] to normalize relative tooth size”. I would think that absolute size would be biologically meaningful. Please provide justification for normalizing the centroid size this way.

21. “Photographs of intact skulls of conspecifics were used instead [of incomplete fossil skulls] to derive head shape and length”. This statement immediately raised a red flag for me because the size and growth stage may be completely different between conspecific specimens. Please provide additional details and justification for this step.

22. Foote’s morphological disparity is a summary statistic of multivariate data. As such, I am not sure what the authors mean by “it [Foote’s MD] is not descriptive of multivariate measures such as shape” (Ln 201–202). Furthermore, the authors mention that to rectify this ‘issue,’ they use PCA to show shape variation in reduced dimensional space (primarily just PC1). This argument does not make sense to me unless they use the full dimensionality of original shape data.

23. Correlations between skull and average tooth shape should be performed with two-block partial least squares analysis that can analyze in full shape spaces.

24. Use of qualitative descriptions with highly subjective cut-off points (Ln 234–236) seems counter to the goals of this study. The need for associating words to numbers should be justified. Minimally, the actual values should be reported whenever these qualitative terms are used throughout the manuscript.

25. Given the undulatory pattern of tooth shape and size variation across tooth row, the use of linear regression seems inappropriate to me on a fundamental level, although it may model the overall shape changes adequately in practice based on what we see in Fig 5. Nevertheless, a critical problem is that non-significance of shape-to-position relationship does not mean lack of heterodonty because undulatory changes across tooth position (i.e. still heterodonty) can yield a non-significant linear model. The authors should provide a rationale for using linear regression analysis for investigating shape changes across tooth position.
Validity of the findings: 26. There are many assumptions being made at all levels of the study, and thus, it is very difficult to assess the validity of the findings. From what I can see, the assumptions and potentially questionable practices in this study include, but not limited to: (1) mixing of captive and non-captive individuals; (2) suitability of semi-landmark sampling used in this study; (3) artifacts related to parallax from using two different camera lenses; (4) lack of detail on how photographing of specimens was standardized; (5) incompleteness of teeth across samples; (6) lack of clear definition of "juvenile" specimens; (7) assumption of perfect bilateral symmetry; (8) use of conspecifics to have size and shape data for incomplete specimens; (9) use of linear models to model shape across dental arcade; and (10) PC1 as adequate representation of variability across all tooth positions.

27. Authors state that shape and size heterodonty are decoupled (e.g., Ln 353), but to my knowledge, this was not explicitly tested in this study. This is easy to do with multivariate regression of shape onto centroid size.

28. Authors state that the study provides “a numerical range of morphology as opposed to cherry-picking an average tooth or single position” (Ln 589). While this is partially true, I would not consider analysis based on only PC1 of shape to be much useful for continuing the study. PC1 values are only particular to specific sample.
Additional comments: D'Amore and colleagues present a modern quantitative approach to investigate tooth size and shape variation in crocodilians.They employ a 2-D geometric morphometric approach and find results that support previous qualitative studies on the topic, as well as discovering statistically significant tooth shape differences among species and similar tooth shape variation in upper and lower jaws. The content of their study would be appropriate to be published in PeerJ and would benefit researchers working on crocodilian biology and dental and feeding adaptations. However, I found many serious issues and methodological details that need be reported and addressed. I have listed general and major comments above and also list more minor, specific comments below:

Ln 18, 98: insert “of” between “members” and “Crocodylia”
Ln 31: Change “gengeticus” to “gangiticus”
Ln 35: insert “are” between “shapes” and “typical”
Ln 35: Is the “former” referring to “Leidyosuchus and Borealosuchus” or “Alligator”?
Ln 36: “Hamadasiuchus rebouli similarities” should be “Dental similarities of Hamadasuchus rebouli”
Ln 39–41: Be more specific about the implications of this study.
Ln 62: Change “been” to included”.
Ln 63, 65: “Euclidean distances” should be changed to “linear distance measurements”. This would be more precise because Euclidean distance could be distances in multivariate space (e.g., shape), which is the basis for Foote’s disparity metric. Please revise other instances of “Euclidean distances” in the manuscript.
Ln 71–72: These descriptive words should be in quotations if they are direct quotes from the literature.
Ln 99: What is meant by “multifaceted”? Be specific.
Ln 121: One does not “atrophy” a structure. The structure becomes atrophied.
Ln 123: Add “tooth count” or “tooth assignment” after “standardize.
Ln 127: Change “resulting” to “resulted”.
Ln 129: “data” is plural, so “was” should be “were”.
Ln 139: Change “in” to “by”
Ln 157: Add “total” before “bending energy”
Ln 158: Generalized LS Procrustes superimposition is the over-arching procedure that would include the sliding semi-landmark step. Therefore, it is awkward (and inaccurate) reporting them separately as it is done here.
Ln 183: Ordination is a statistical approach, so should not be separated into “ordination and statistics”.
Ln 339: Change “morphotypes” to “morphotype”.
Ln 336: This sub-section label should go after the summary of main points (i.e., Ln 353).
Ln 394: Change “method” to “results”.
Ln 416: Would “considerably” be a more suitable word than “noticeably”?
Ln 458: In organismal biology, a structure is not “designed” for a function.
Ln 470: Add “of” after “reminiscent”.
Ln 544: The first letter of “Grand” should be lowercase. Also, I prefer to call it “pooled mean.”
Table 1: The variables should be explained thoroughly in the table caption.
Fig 1D: What does the deviation represent? For example, how many units along PC1. Have the deviations been magnified in any way?
Fig 3: Add confidence intervals for the regression lines.
Fig 4: Specify what the different colors indicate.


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: QUANTITATIVE HETERODONTY IN CROCODYLIA: ASSESSING SIZE AND SHAPE ACROSS MODERN AND EXTINCT TAXA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This interesting piece of work aims to find a quantitative way to define and describe the hotly-debated concept of “heterodonty” in Crocodylia. The data collected mostly cover extant crocodilian species and some fossil taxa.
This novel method has the merit of breaking down the concept of heterodonty in quantifiable metrics describing both size and shape, and has immediate applications in interpreting the feeding style of extant and extinct animals. This topic has been long ignored and only vaguely dealt with in the past years, causing some confusion and the proliferation of different (qualitative) interpretations on the subject. With this regard, this work ought to be read by a broad audience including – and exceeding – zoologists, biologists, palaeontologist and ecologists.

I find this effort well thought and executed. The dataset is robust, the analyses appropriate and the few limitations of the method are openly acknowledged (although some clarifications are needed – see below). The importance of the finding is clearly stated in the background which is concise and requires only minor modifications. However, the results, and discussion are – in places – difficult to follow and should be clarified within the text.

Accordingly, my comments below largely concern the presentation of the finding, which I found difficult to follow in places. I suggested very limited changes and addition in the analyses for the authors, but I think that significant modifications are needed in the presentation of the results. The majority of my suggestions concern the organisation and presentation of the results and discussion, which I strongly recommend the authors consider to making this work clearer and more broadly accessible.

I overall enjoyed reading this manuscript and I’d recommend its publication upon satisfactory clarification of the detected issues.
I would be very happy to be contacted via email if the authors needed any clarification davide.foffa@ed.ac.uk

Davide Foffa
Experimental design: The research question is clear in the paper context. It is original, important and fits within the scope of the journal.This work is relevant and fills a gap of knowledge that has long been matter of debate. Rigorous tests have been performed using appropriate techniques.

However the methods, but also the results (and partially the discussion) are in place chaotically presented and need in my opinion re-organisation and tiding up. Although, the direction of the research is clear, its presentation is currently not as immediate.

The authors are openly transparent presenting their method in a comprehensive way, including a section listing limitations of the study.
Some clarifications are needed in order to ensure full replicability (see below and PDF).
Validity of the findings: Tindings of this work are meaningful, and based on an extensive dataset that could be the basis for future work. Their interpretation is also sound and supported by literature references. Further speculations are clearly identified as such.

The authors should add and appropriate Conclusion section because the paragraphs identified as such in the current version only describe merits, limitations and future directions of the method. This section is welcomed – and I think necessary (with some modifications), but clearer conclusions summarising the results of the study should also be added.
Additional comments: Numerous comments were left in the PDF attached. Besides those I have some concerns regarding some sections of the manuscript.
The phrasing of several paragraphs is awkward and difficult to follow, and there are few repetitions and organization issues within the text.
The use of terminology is often confusing. Terms are sometimes overlapping and are randomly introduced within the text (e.g. “procumbent teeth” vs “pseudocanines”). Each of these important nomenclatural terms should be unambiguously defined in an early section of the text (e.g. a nomenclature section in the Methods?), and consistently used through the manuscript to prevent confusion.
Figure and bibliographic referencing should be improved before publication.
The authors should for example decide whether they want to use abbreviations or complete generic names. Currently the same taxon is called interchangeably in 3 different ways (complete generic name, genus (spelled out) + species or genus (abbreviated) + species). Often in the same paragraph. If the authors will decide to adopt abbreviated generic names they should also make sure that they are unique (e.g. Caiman and Crocodylus should have different abbreviations).
Sentence repetitions and spelling should also be re-checked.

INTRODUCTION
I appreciate the effort that the authors made to summarise the vast background and descriptive terminology. This section provides a much needed summary of the state of the field and clearly identifies the rationale behind this study.
However, some of these terms are only mentioned in the introduction and there is no additional reference of them and how they relate to the current study. Others suddenly (and confusingly) reappear in the last section of the Discussion without being mentioned in the Methods or Results. It is thus unclear how the authors’ quantitative description of crocodilian dentitions reconciles with the past (largely qualitative) observations.
I suggested additions to qualitative descriptive labels to the figures, but I would also encourage the authors to add a table in which they compare their quantitative tooth types (high molariform to high caniniform) with the literature qualitative descriptors (e.g. do high-molariform correspond with globidonts)? Similarly with “pseudocanine”, “procumbent teeth” etc…

MATERIAL AND METHODS
This section has numerous clarity issues, that are fortunately easily solvable. The information here is presented in a fragmented way and early in the sections there are references to analyses that are explained long after.
For example at line 162, the authors explain the importance of rostrum shape, how they derive PC proxies for it and skill length, but they did not explain what these data are used for. That is explained later in the method section, leaving the reader unsure about the pertinence of such information until they have read the whole text.
The authors should re-think the logical presentation and succession of this whole section, systematically describing what data they used, for which analyses and why. I find that in the current version this information are scattered and difficult to follow.
I suggest that the addition of an “Institutional Abbreviation” (and perhaps a “Taxonomic Abbreviation Section”).
The morphometrics analyses done to the skulls are central to the discussion of this method and should absolutely be figured in a similar way as the tooth analyses have been (e.g. Fig. 1 -2 ) (see also PDF and figure section below).
The authors also use statistical jargon that should be avoided or at very least explained to facilitate the read to a non-specialist audience.
A list of PC scores and the % of variance they represent should also be provided for both teeth and rostra.
The taxonomic groups adopted for each specimen should be included at least in the supporting information.

RESULT
My biggest concern in this section is the PC-based description of the tooth shape (lines 233 to 236) and how they relate to the qualitative descriptors used in the literature – if they do. The authors should comment on that – ideally adding a comparative table (or figure) that shows the equivalence (if any) of their proposed terminology with the qualitative ones available in the literature.
Similarly, it should be stated how their PC results compared to “brevirostrine-longirostrine” transition. Ideally the use of these descriptive terms should be added in the relevant figures.
The organisation of some section is also confusing with an inconsistent succession of paragraphs that are sometimes organised by topic and sometimes by “extant vs fossil” (e.g. see comment on paragraph starting at line 272).
Rarely the sections in result and discussion start with a general statement on the finding, and often begin with in-detail description taxon per taxon.
Figure referencing should be improved and more frequent with references to specific sub-figures.

DISCUSSION and CONCLUSIONS
Also in this section the referencing should be improved and more frequent with references to specific sub-figures.
In places indicated in the PDF the authors should be more cautious in their explanations (e.g. “may be”or “likely is” instead of “is”).
The “Conclusion” is essentially a “limitation and future work” section, which should be incorporated in the discussion or left separated. Several points of the this section are not even mentioned (or should be expanded) in the main text (e.g. limitations, application to incomplete fossil specimens).
Nevertheless an appropriate “Conclusion” section summarising method, discussion, limitations and future work is currently missing and should be added
Refer to PDF for specifics.

REFERENCES
Reference formatting is inconsistent and inadequate, often missing key information such as volume, issue, and page numbers. Book references are incomplete. The entire section should be thoroughly checked.

FIGURES
The size of the figures should be clearly indicated. The format of sub-figures is inconsistent in the figure captions.
Figure 1. Add mesial, distal, labial, lingual labels. It would make a cleaner figure if the backgrounds of the skull and tooth figures were removed.
Figure 2. Half page width?
Specific comments on each figures are attached in the PDF

TABLES
The current format of the tables (landscape on a portrait page) should be re-evaluated and tables presented in a single page each

REFERENCES
References are inadequately formatted. Nearly one each two reference has some issues. Several entries are incomplete with inconsistent formatting, missing information (volume/issue and/or page numbers and/or book reference). Please, spend some time fixing these avoidable issues thoroughly. Double check again the alphabetical and chronological orders and the spelling of authors names and surnames.
There are also some in-text references in which the publication years do no match with the full reference in the bibliography.
I have pointed some of these mistakes out but there are likely many more.

Specific comments
Refers to PDF for specific 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: QUANTITATIVE HETERODONTY IN CROCODYLIA: ASSESSING SIZE AND SHAPE ACROSS MODERN AND EXTINCT TAXA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The English used in this manuscript is generally high quality and grammatically correct. Where possible I noted instances where sentences need to be modified for clarity and flow. The work conforms to high standards of courtesy and expression. There is sufficient background and citation of literature. There are a few instances where I suggest further exploration of the literature. For the most part section headings are consistent and professional. I noted one heading that was unlike the rest (line 237). Figures and tables are of a high quality.
Experimental design: The morphometric analysis is based on methods found in the published literature. The methods are sound. Data collection, specimen reporting, landmark schemes, and statistical analyses are well documented in the manuscript and should be clear to replicate if one wants to do so.

I do have a concern regarding that some specimens are sourced from unknown locations. I agree that few anatomical loci are located on crocodylian teeth and the landmark scheme does well in using loci that are homologous to all specimens in this analysis.

Extant specimens whose toothrows are incomplete should be avoided. I know of many specimens housed in other collections that could be used in place of the incomplete specimens used here. This is especially important as the authors admit that the incomplete toothrows may potentially inflate/deflate the morphological disparity of a species. Additionally, I would like to see larger sample sizes for each extant species, especially those species that are represented by a single individual in this analysis (Alligator mississippiensis, Gavialis gangeticus, Mecistops cataphractus).

I am slightly confused as to how snout shape was quantified - some clarification is needed in this section. I am also concerned about head length being used to calculate body length.
Validity of the findings: The findings presented here are well supported and valid. In the introduction the authors put forth four goals they would like to accomplish in their study but their second goal (line 100) is not well supported. They seek to document developmental consistencies found within the clade as a whole but did not include juveniles or a complete ontogenetic sequence for any of the species found in this study. This point should be elaborated upon or omitted.
Additional comments: Significant differences were found between the degree of heterodonty in extant crocodylians. However, captive specimens were not adequately controlled for by the authors. Captive rearing of crocodylians appears to affect the shape of the skull and teeth in these animals. This is problematic and affects the findings of this study. I would suggest that the authors only use animals that have records indicating that they were wild caught. Alternatively, if the animals with no information regarding their sourcing were proven to demonstrate little variance in skull and tooth shape relative to their wild-caught conspecifics I would be satisfied with their inclusion.

I disagree somewhat regarding the application of these methods in determining the shape of missing teeth in fossils. There may be too much variability present among toothrows of various species to accurately predict shapes. A good example of this would be a longirostrine taxon whose distal teeth are missing. It may be impossible to predict that the distals would be caniniform as found in Gavialis gangeticus or relatively more molariform as found in Mecistops cataphractus and Tomistoma schlegelii. Regardless of the complications, a relatively complete toothrow could be assigned with more certainty than a loose tooth, which unless diagnostic for a taxon would be impossible to assign with any measure of certainty.

Additionally, some terms need to be defined. Please add them to the nomenclature section under the Materials and Methods heading.

Comments by Section

Introduction
Line 55 - What is meant by size changes? I presume that you mean changes in the degree of heterodonty through ontogeny.
Line 100 – How were developmental consistencies explored? Juveniles were excluded and ontogeny is stated as beyond the scope of this study (lines 132-133).
Lines 101-102 – Distinguishing morphotypes between individuals is nebulous. Are these individuals of the same species or individuals from different species?
Line 123 – What is meant by procumbent? I would describe a tooth as procumbent if it projects labially however as used here it seems as if procumbent means a tooth that is proportionally larger than neighboring teeth – this term needs to be defined or a new term needs to be used as a replacement.

Specimens
Although correctly stated that captivity may have an affect on the morphology of the snout and teeth why was this not controlled for? It would be prudent to exclude all specimens that were not wild-caught or whose method of collection is unknown. I feel that including those specimens that were raised in captivity adversely affects some of the findings of this study, especially those that seek to aid in ecological predictions, dietary behaviors, and life history characteristics.
Lines 131-132 - Why were individuals whose only remaining teeth representing the largest and smallest size extremes excluded from this study? How were the extremes measured – relative to other individuals within the same species? How does their exclusion influence the findings of this study?
Lines 135-136 - It is understandable that incomplete toothrows were included for fossil taxa but why for extant taxa if incomplete toothrows inflate/deflate morphological disparity? Complete specimens could be found elsewhere.

Data Collection
Why were landmarks representing the occlusal surface excluded? Is it unnecessary in light of the information gained from the labial perspective? Additionally, two teeth that are similarly shaped from a labial perspective may have divergent occlusal surfaces. An example I can think of are two mesiodistally broad teeth, from a labial perspective, which may have flattened or blade-like occlusal surfaces respectively.
Lines 162-180 – There is some confusion about how snout shape was quantified, being explicit would help to avoid this confusion. Did you use pre-determined snout shape categories from Drumheller (2016) and Wilberg (2017) as stated on lines 165-167 or did you use the method described on lines 167-168? Should the latter be used to determine snout shape then it is inappropriate as the snout lies anterior to the orbits but the measurement extends to the posterolateral corner of the skull.
Line 174 – There are a number of considerations when using head length to measure body length. Ratios of cranial length to body length may differ between longirostrine, mesorostrine, and brevirostrine forms (Hutton, 1987; Fukuda et al., 2013). The ratio of head to body length may also change through ontogeny (Fukuda et al., 2013). Some have said that the femur is a better estimator of body length (Farlow et al., 2005).

Ordination and Statistics
What is the permutation test for? What is the null hypothesis? I assume that it is testing the association of Procrustes distance between the cranial and mandibular teeth.
Lines 198-199 – What is being normalized?
Lines 207-209 – By PCs do you mean PC scores? If so, explicitly state that you are comparing PC scores for the regression analysis.

Results

Shape Variability in the Sample
Why is the first PC the only one considered? Is it the only PC that accounts for greater than 5% of the variance as stated much earlier in the paper?
Line 229 – How is the crown elongate? Mesiodistally or basoapically?
Lines 233-236 – How were the corresponding values determined for the descriptors? Were the values assigned randomly, were there gaps present between the values in the data, etc.?
Line 237 – This heading is unlike the rest.

Foote’s Disparity and Morphotype Ranges
Line 258 – Gavialis gangeticus
Line 276 – Here and elsewhere properties are assigned to higher taxa. Species interact with their environments, higher taxa do not. Instead of saying “Leidyosuchus” has a property say that “species of Leidyosuchus have that property.”
Line 278 – Species of Crocodylus, see above.

Heterodonty Along the Toothrow
Line 289 – Replace has with have.
Line 290 – Insert ‘is’ between peak and relatively.
Lines 291-292 – Is this variability present in specimens of different species or within species?

Discussion

Developmental Trends in Crocodylian Heterodonty
Line 387 – Omit ‘the’ between by and captive.
Line 398 – Omit ‘a’ between with and specific.
Line 424-427 – It is possible that the proportion of hard prey items in a species diet has a more profound influence than the occasional predation of a hard-bodied prey item – this is alluded to on lines 433-434. Presumably species with a higher proportion of hard prey items in their diet should have more molariform distal teeth.
Line 439 – Define compliant in this sentence or elsewhere in the paper. This word comes up often and I am unsure what it means. It appears to mean that the prey item is subject to puncture.
Line 442 – What Brochu (1999) is referring to as pseudocanines are the enlarged third and fourth dentary teeth found in species of Diplocynodon. As used by Brochu this term has a limited definition.
Line 448 – The authors are making an assumption that all processing is accomplished by the distalmost teeth.
Line 466 – M. pterygoideus posterior is smaller in the long snouted forms (Endo et al., 2002) but M. adductor mandibulae externus profundus is generally larger in these forms (Iordansky, 1973; Holliday & Witmer, 2007).
Line 474 – Which groups? Gavialoidea and Crocodyloidea?

Fossil Taxa and the Appropriateness of Analogs
Line 499 – Species of Borealosuchus and species of Leidyosuchus. Assigning properties to higher taxa, see above.
Lines 525-526 – Species of Allognathosuchus and species of Brachychampsa.
Line 534 – Add ‘are’ between affinis and on.
Line 538 – Species of Allognathosuchus.
Lines 542-544 – Species of Allognathosuchus. Brochu (2004) found the genus to be a wastebasket taxon where many taxa were assigned based on characters that are plesiomorphic to the base of Alligatoroidea, the result of his study was to restrict the membership of the genus. Some of the dental variation found in this genus may be a product of historically including taxa that are not phylogenetically allied with the genus.

Conclusion
Lines 577-585 – I disagree somewhat regarding the application of these methods in determining the shape of missing teeth in fossils. There may be too much variability present among toothrows to accurately predict shapes. A good example of this would be a longirostrine taxon whose distal teeth are missing. It may be impossible to predict that the distals would be caniniform as found in Gavialis gangeticus or more molariform as found in Mecistops cataphractus and Tomistoma schlegelii. Regardless of the complications, a relatively complete toothrow could be assigned with more certainty than a loose tooth, which unless diagnostic for a taxon would be impossible to assign with any measure of certainty.

Tables and Figures

Table 1.
Crocodylus siamensis – host bone – mandible runs onto the second page, this looks awkward. It                        may be better to have this species on the next page.
There are two numbers (1 and 2) that are found at the bottom of the first table. What are they for?

Table 2.
There are two numbers (1 and 2) at the bottom of the first part of the table and one number (3) at the bottom of the second part of the table. Are they supposed to be there?
Close off the margins for all tables with lines. Some sections of the tables are open ended.

Figure 1.
The numbers representing the landmarks and semi-landmarks are too small to read.

Figure 2.
I am used to “Principal component one” being reported as the first principal component.
These are vector diagrams but not a principal component diagram. I would change the title of the figure.

Figure 3.
Which specimens do the vector diagrams represent? It is not clear.
The vector diagrams may look better as their own figure. As presented here it looks chaotic.

Figure 4.
Why are some of the fossil taxa not represented in the MD (size) or Centroid Size figure? I could not find an explanation in the manuscript.

Figure 5.
Gavialoidea not Gavialoidae in the figure caption.
In this figure CS is straightforward in that it is measuring size. However, the first principal component is presumably measuring the variability in shape. It is not obvious in the figure caption or the body of the manuscript describing the findings that go along with this figure.

Figure 6.
I would like to see all specimens in a lateral perspective. Some are from dorsal or ventral perspectives – consistency would make this figure look more appealing.
The length of the scale bars needs to be indicated in the figure caption. Make sure that the scale bars are of the same weight.


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: QUANTITATIVE HETERODONTY IN CROCODYLIA: ASSESSING SIZE AND SHAPE ACROSS MODERN AND EXTINCT TAXA
Review round: 2
Reviewer: 1

Output:
Basic reporting: If number is less than ten, it is customary to spell out the number (e.g., Ln 135: “eight” instead of 8).

Ln 240: It’s not clear if “Figure 1F” is showing the shape variation along a PLS axis or simply depicting what a vector diagram looks like. If it’s the latter, I don’t think it’s perfectly appropriate to reference this sub-figure.

Ln 246: As with the above comment, I’m not sure that referencing “Figure 1D” here is appropriate if it is just showing what a vector diagram looks like. Instead, the explanation of what the figure is depicting should be explained in the figure that uses these diagrams to show shape variation.

Ln 279–280: Reporting the range of PC scores is not biologically useful or relevant. It’s purely a mathematical construct.

Ln 287–288: Factors do not account for proportions of shape covariance. Is this the R-value of PLS? If so, this value accounts for the proportion of shape variation of dependent shape variables by the independent shape variables.

Ln 304–305: One cannot state disparity increased twice as fast as size because these variables are not comparable metrics. I would remove this statement and only state the overall trend (positive, negative).

Ln 305–306: I don’t see the point of reporting that “[a]lligatoroids occur on both sides of the regression [line]”. These types of observations are typically mentioned when certain groups are either above or below the regression line. Unless there is a good justification for reporting this, then I would remove this sentence.

Ln 315–316: “Because of this poor correlation, we do not consider residuals as very biologically meaningful.” The biological meaning of residuals is not dependent on the degree of correlation. For example, one may choose to analyze residuals from allometric trend if they wish to analyze size-independent data regardless of the strength of the allometric signal.

Ln 473–480: In this section of the Discussion section, I would discuss the possibility of tooth pressure being a more important metric for functional capabilities than bite force (Erickson et al. 2012 PLoS ONE).
Experimental design: Ln 198: How was the coordinates mirrored? Which landmarks were used to define the median plane?

Ln 265–266: The comparison of slope based on regression of PC scores of shape on proportional position along the dental arcade is not sound. What is the biological meaning of slope? Why not use the full shape data to conduct a MANOVA? This is not difficult to do with available programs and computational tools and it is a far more preferred method when analyzing high-dimensional morphometric data. This way, one can also readily and more visualize the shape changes occurring along the tooth row than inelegantly translating PC1 scores back to qualitative descriptions of tooth shape, which also counters the aim of the study. That being said, results from PC1 can be arguably kept since it shows the degree to which tooth shape changes along the dental arcade on a plot. However, results from MANOVA should also be reported.

Ln 262: I don’t see how subtracting 0.5 from the proportional position along the dental arcade is necessary because this would not impact the statistical significance and slope coefficient of the regression analysis. Later, the authors claim that the “y-intercept would represent shape value for the median position, as the intercept is located half-way along the tooth row”. However, I do not see the biological significance of the intercept, especially when PC scores are used where linear combinations of shape data are defined purely mathematically (i.e., by variance).

As I commented on the previous version of the manuscript, I still do not think that performing a **linear** regression on centroid size and tooth position is sound when one knows that the size undulates across the tooth row. Although the authors inserted a caveat with this analysis (Ln 451–452), they misinterpret the results stating that “size varied significantly between positions” (Ln 337–338), but this is not what they test. They are testing whether size has a linear trend with tooth position.

Ln 399: “Regression analysis of shape is appropriate based on significance and high r2 values.” This reasoning is circular. R-square values do not dictate whether the use of regression analysis is valid. A theoretically and practically valid use of regression analysis can still yield low R-squared values.
Validity of the findings: Ln 272–275: R-squared of 0.09 for allometric signal in shape data is within a range of typical values expected in biological systems. Therefore, I would not consider the allometric signal to be “very weak […] overall.” This is because shape data comprise many variables, so the capacity of an explanatory variable to account for proportional variation diminishes.
Additional comments: The revised manuscript is considerably improved from the previous version. I appreciate the authors taking the time and effort to revise and refine their manuscript based on my previous comments. Below is a list of my more minor comments:

Ln 44: What is precisely meant by “moving target”? Please clarify in text.

Ln 74–76: Grammatically, each of these adjectives should be in quotations.

Ln 96–97: I don’t think the hyphen after “size” and “shape” are needed.

Ln 99: “geometric morphometrics” is the name of a field, not method. Change to “geometric morphometric methods/techniques/approach”.

Ln 112–116: Although it is fine to leave as is, these dental terms are firmly established in anatomical literature so I do not think the explanation is necessarily. Similarly, I don’t think Fig. 1B is necessary.

Ln 117: I would remove “independent of shape” because shape is not independent of size. These are strongly coupled aspects of morphology (i.e., allometry).

Ln 135: commas not necessary before and after “and 8 extinct”.

Ln 176: It is somewhat odd to mention “calculated centroid size” after “superimposition on the data” because the former is done before alignment. I would change the order of steps so that centroid size calculation is mentioned before superimposision. Also, the sliding of the semilandmarks is performed during the alignment procedure, so I would combine the two stating GLSP was done with sliding semilandmarks minimizing total bending energy.

Ln 260: Values between 0 and 1 are technically not a “percentage”. I would replace the word with “proportion”.

Ln 280: I would describe “negative-most condition” as “shape changes towards negative PC1 values include…”

Ln 317: Remove “relatively”.


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: QUANTITATIVE HETERODONTY IN CROCODYLIA: ASSESSING SIZE AND SHAPE ACROSS MODERN AND EXTINCT TAXA
Review round: 2
Reviewer: 2

Output:
Basic reporting: As the previous version the exposition is professinall and is appropriate, the literature is sufficiently cited (some comments on the pdf on potential additional references to be included). Overall the authors have done a very fine job and have been clarified the flow and contents of the text in numerous places. Intro, context and background have also benefited from substantial rewriting and simplification of the manuscript.
There are few issues with the figure format and in-text reference (see General Comments) and all data are supplied.
Experimental design: The design and execution of the study has also been simplified and it is considerably more focused now. The methods are clear, and should only be clarified in minor details (see PDF) but none of the required modifications affects the replicability of the experiment.
My major concern (but it is a small one), is that the authors should be more consistent in explaining the limitations of adopting incomplete specimens through the text. This is done very well in the final section of the manuscript but references to it should be present in the method section too.

The results and discussion are the parts that were mostly improved. The results are better linked with the methods and discussion. Furthermore the discussion has been largely expanded to include implication with the right amount of speculation (when needed). These sections are balanced and honest. The authors are very open on the merit and limitations of their method (perhaps understating in places the future possibilities of using it with in clades and associated with direct data on diets/ecology – particularly if the method will be expanded on fossil taxa).
Validity of the findings: No further comment from the previous version.
In the first and second submission this study fills in a gap in our knowledge and it does so in a robust, honest and meaningful way.
Once published this work will be surely applied to numerous other case studies.
Additional comments: General Comments
I am pleased to notice that many changes suggested by the reviewers have been implemented. I think the manuscript is clearer now and has a more specific and better-defined focus. I also agree with the authors that the new design of the study make some of the comments redundant of inapplicable, and I am pleased to notice that the authors spent time to deal with some of them anyway.

In my opinion there are still few problems that still persist, as minor issues, but I think they would be an easy fix. Nevertheless, I would like to see these issues addressed and I think that some of the authors’ choices should be better explained in the text.

I have left a pdf with some specific comments, the main of which are summarised here below.

a) I think that the title is currently misleading: the dataset is almost entirely made of crown crocodylians with only 1 crocodyliform (non crocodylian) specimen.  In other words I don't think that the inclusion of a single non-crown crocodlylian justifies the change of the title from Crocodylia to Crocodylifomes. It probably is the case, but this dataset is, in my opinion insufficient to live up the title claim.
I would either change it back to "Quantitative heterodonty in Crocodylia: ..." or if the authors want to maintain the title as it is, they should increase their sample size by adding several more non-crown crocodylian specimens - with a (possibly) even distribution in the clade (e.g. several lineages represented). This may not be possible - depending on the fossil record.

Accordingly several citations of crocodyloforms should be double-checked.

This change may stem from a previous comment of mine in which I asked to explain the inclusion of Hamadasuchus rebouli in a crocodyilian-base study. A simple explanation of the fact is enough: perhaps Hamadasuchus is interesting because it is thought to have strong heterodonty and the authors wanted to check this in their study?

Related to this there is the sample description issue. The numbers of species, specimens, crown-crocodylian and non-crown crocodilian crocodyliforms is unclear and confusingly stated in different part of the manuscript (see pdf comments), and should be addressed.

b) The text would greatly benefit from many more in-text figure references that are very scarce at the moment. Ideally they would include sub figure references (e.g. Fig. 3A) as it is done in some parts of the manuscript, but not consistently.

c) There are weird grey/white halos and lines and grey blocks around all the figures – most likely left from formatting the images for publication. I imagine they may have passed unnoticed because of screen settings, but they are there and should be deleted. Please address and make the figure backgrounds a uniform solid white.

Further minor comments (mostly related to formatting and rephrasing) are included in the PDF.

Upon the fulfillment of these modification I will be looking forward to seeing this very useful manuscript published and I won’t need to review this manuscript again.


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: QUANTITATIVE HETERODONTY IN CROCODYLIA: ASSESSING SIZE AND SHAPE ACROSS MODERN AND EXTINCT TAXA
Review round: 2
Reviewer: 3

Output:
Basic reporting: The English used in this manuscript is for the most part grammatically correct. Below I noted instances where sentences need to be modified for clarity and flow. Background information is sufficient and literature is thoroughly cited, I noted a few instances where I think additional citations are needed. Section headings are consistent and professional. Figures and tables are of a high quality but there are a few changes that need to be made (see additional comments for each section below).
Experimental design: The morphometric analysis is based on widely used methods, there are a number of instances in which terms are being misused – I made note of them below. Data collection, specimen reporting, landmark schemes, and statistical analyses are well documented in the manuscript and should be replicable.

I am still concerned about some specimens being sourced from unknown locations as captive specimens may have skull and tooth morphologies that differ from wild-caught conspecifics. It was appropriate for the authors to address this issue in the second draft.
The results may be stronger with the exclusion of some of the very incomplete specimens. I understand that the fossil taxa are out of the author’s control but some of the specimens (Caiman crocodius UCMP 42844, Crocodylus palustris AMNH 75707, Crocodylus siamensis AMNH 49231) were missing more than half of the teeth of the upper jaws. What effect on the results does excluding these specimens have? Does keeping them in improve the results? An interesting example of the effect of incomplete specimens is found in Caiman crocodilus. Comparing the more incomplete fossil specimen of this taxon to the more complete modern specimens the author says “Any differences in size and shape ranges appear to simply be a consequence of the former’s incomplete arcades; no distal maxillary or any dentary crowns were available.” It would appear that incomplete specimens may negatively impact the findings of this study. I am glad that this shortcoming was addressed in the “Limitations and Future Work” section of the discussion.

As stated in my first review using head length as a proxy for body length is suspect. There are a number of considerations when using head length to measure body length. Ratios of cranial length to body length may differ between longirostrine, mesorostrine, and brevirostrine forms (Hutton, 1987; Fukuda et al., 2013). The ratio of head to body length may also change through ontogeny (Fukuda et al., 2013). Some have said that the femur is a better estimator of body length (Farlow et al., 2005). Comparing heterodony with head length is sufficient in my opinion and tells and interesting story without having to make leaps of faith regarding the determination of body length from cranial specimens. However, the authors addressed this shortcoming within the body of the manuscript.
Validity of the findings: Other than some concerns with experimental design, the findings presented here are well supported. The limited the scope of the latest draft made for a better product.
Additional comments: Captive rearing of crocodylians has a pronounced effect on the shape of the skull and teeth in these animals and should be obvious to a trained observer. From those specimens in figures 1 and 7 it appears that none of the figured specimens were sourced from captive populations. Should captive reared specimens be included they will negatively affect the findings of this study. If the specimens with no information regarding their sourcing were proven to demonstrate little variance in skull and tooth shape relative to their wild-caught conspecifics (of similar size) their inclusion is justified. I would like to see the datapoints in the various figures labeled (fig. 3 for example). This would make for a more informative figure and would help illustrate any specimens that may have aberrant values relative to their conspecifics.

The addition of a graph showing morphospace occupation would be a welcome addition to figure 2. This figure should show the taxa plotted in morphospace along the first and second principal components. Tooth morphology at the positive and negative extremes along the first PC should be placed at their respective ends of the axis. Doing so would make this easier figure more informative and easier to visualize. Plotting of morphospace, with minimally PC1 compared to PC2, is pretty standard in these types of studies.

Throughout the paper genus names are used in place of a specific species. For example Borealosuchus in place of Borealosuchus sternbergii. Unless one is referring to all taxa within the genus the binomial name should be used.

Below is commentary for each section of the paper with the lines in which the revision needs to be made.

Abstract

21-22    Change Principal Components Analysis to Principal component analysis
29-30 and 35-36    If slender snouted taxa have low shape heterodonty shouldn’t regression be adequate to predict the shape of their teeth?

Introduction

47    …issue has not been fully resolved.
59    Also (Ősi, 2014)

Nomenclature

113-114    Central premaxilla – I know what is meant here…where the premaxillae meet at the midline. However obvious to us, it could be misconstrued. I would reword this term.
116-117    Enlarged teeth are determined relative to other teeth in a given section… how are sections of teeth within the arcade being defined? Whether this was defined or not I missed it.
127-129    I understand that some taxa may lose a premaxillary tooth as they grow but for consistency it may be best to omit those specimens possessing more than 5 premaxillary teeth.
138-139   Postcrania, especially the coossification of the neural arches to the neurocentra may be used to determine maturity (if associated postcrania are not included with the specimens I understand). Diet changes over ontogeny and evidence suggests dental morphology does as well (Gignac and Erickson, 2014).

Statistical Approaches

216-217    The confirmation of the null hypothesis should be reported in the results section.
222    Report this in the results section.
226    Variable i – is this being compared within species or between species?
231-233    Allometry needs to be measured over ontogeny, no ontogenetic sequence used here.
236-238    This averaging technique could potentially produce an average shape that has no biological basis, in that the average shape may not represent any of the teeth found in the specimen. What effect does this have on the study?
242    Axis instead of axes?
244    Principal component analysis
248    Why is CS being normalized against head length? This is not clear to me.
255-256    Why was 7 chosen instead of another value?

Results

304    Possessed instead of possessing
305    Which clade is being referred to?
305-306    “Alligatoroids occur on both sides of the regression (line)” – as do crocodyloids.
308    Which species did this individual belong to? Was this significant or an aberrant specimen belonging to a species with multiple individuals in this analysis? I would like to see the data points numbered (or an alternative way to keep track of which specimen is represented by each data point) so one may reference the specimens in this study.
312    “greater” means larger?
314    “correlated significantly” Did you perform a hypothesis test to determine the significance of the correlation coefficient?
316    Omit ‘very’
320    Which specimen was the most shape heterodont? The one with most of the teeth intact or the one with more than half of the upper teeth missing?
328     Use Borealosuchus sternbergii instead of Borealosuchus (only one species used in this analysis)
333-335    Revise this sentence – “The vast majority of the modern taxa tooth rows had over 60% their tooth positions represented by measurable teeth (Supplemental Information Table S3).”
358    A PC score is reported as cartesian coordinates and must have two numbers. In your case the first would be the value along the first PC axis and the second would be the value along the second PC axis. If you want to report the value along one PC you cannot call it a PC score. Call it a value along a PC axis instead.
361    Revise this sentence for clarity.
365    Report this in cartesian coordinates if you want to use scores - or say that the species had certain values along the first PC.
366-367    Revise this sentence - Both taxa showed a similar progression from caniniformy to molariformy as the alligatoroids and crocodyloids.
377    “had the y-intercepts” -  omit ‘the’

Discussion

390-391    I think referring to head length instead of body size is better practice. Head length to body length ratios are variable for the species.
444    Using the word interlock has a specific meaning to most croc workers, we think of the interfingering dentition found in crocodyloids. I would use another word to describe this morphological pattern.
540    These species instead of caimanine – do not assign properties to higher taxa.
557-558    Tomistoma schlegelii and Gavialis gangeticus, only looking at one species in each genus.
576-579    It seems as if an argument is being made for Gavialis (presumably Gavialis gangeticus) undergoing a reduction in size and shape heterodonty over its phylogenetic history. From my observations of its close and distant relatives this is not the case.
604    Leidyosuchus canadensis
610    Which species of Crocodylus?
636    Any instead of ‘another’

Figures

Figure 1    From my observations of Alligator and Caiman the fourth maxillary tooth is often the largest. In Brachychampsa and Crocodylus the fifth is the largest. You say as much on lines 340-344. Indicating that you are referring to the specimen in the figure and not to the sample as a whole would get rid of the confusion.
Figure 2    I would like to see this figure showing the taxa plotted in morphospace along the first and second principal components. Placing the tooth shapes representing the tooth morphology at the positive and negative extremes along the first PC (at their respective ends of the axis) would make this easier to visualize.
Figure 3B    I would like to see which taxa each of the points belong to. Being able to visualize the taxa that the datapoints belong to would be informative for me. It’s possible that you could number the points and indicate which taxa they belong to – in this case little would have to be done to the figure to alter it.

Supplemental

It is suggested that the second PC describes the amount of “lean” with positive values indicating a tooth that leans mesially and negative values describing a tooth leaning distally. The second PC should be plotted, along with the first PC, in figure 2. Plotting of morphospace, with minimally PC1 compared to PC2, is pretty standard in these types of studies.
I’m assuming that PCs 25-114 represent a proportion of the variance in the data (even though reported as 0.00). Add more digits after the decimal point and report their values, no matter how small, or omit them from the supplemental data altogether.
Table S3    Change ration to ratio


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: QUANTITATIVE HETERODONTY IN CROCODYLIA: ASSESSING SIZE AND SHAPE ACROSS MODERN AND EXTINCT TAXA
Review round: 3
Reviewer: 1

Output:
Basic reporting: Basic reporting generally meets expectations with some minor issues which I list in "general comments".
Experimental design: Experimental design meets expectations.
Validity of the findings: The findings are valid.
Additional comments: The manuscript has been improved compared to the previous version. I appreciate the time the authors have taken to revise the manuscript. I only have minor comments that I would like the authors to address before accepting the manuscript for publication:

Basic Reporting

Ln 22: principal components analysis itself does not “visualize shape variance.” The statement should reflect the fact that principle components analysis is used to extract PC axes and scores that are then used to construct a morphospace that visualizes shape variance.

Ln 231–231: “The null hypothesis of bilateral symmetry was confirmed.” A subtle yet important distinction is to state that the test failed to reject the null hypothesis, as opposed to “confirming” the null hypothesis.

Ln 259: It is not clear what “shape coefficients” are referring to (e.g., full shape data or PC scores).

Ln 321: Insert “partial least squares” between “two-block” and “test”.

Ln 339–340: My comment on a previous version of the manuscript questioned the use of reporting the absolute value of the slope coefficient when regressing morphological disparity against skull length. The slope of “two” does not mean anything biologically because the disparity values for tooth size and shape are not comparable. As before, I recommend reporting whether the trend is positive or negative.

Ln 412: Instead of “strongly linear”, I suggest writing “shape heterodonty was found to strongly correlate with tooth position.”

Ln 439: “Discrete” is not an appropriate term here. “Continuous and quantitative” may be more precise adjectives to use in this case.

Ln 443–444: Measuring Procrustes variance (equivalent to Foote’s disparity) is not a less traditional approach in GM. In fact, it’s a core aspect of geometric morphometric analysis. I suggest removing the statement suggesting that the use of Foote’s morphologicaly disparity is a derived or innovative GM technique.

Ln 454: Replace “resultant” with “resulting”.

Ln 463: “Data” is plural, so the verb should reflect this: “data suggest”.

Ln 480–487: I recommend that the discussion on the potential effects of rearing conditions on the results should be discussed in the main text (i.e., not restricted to supplementary information). I believe there is useful information that is worth including in the main text.

Ln 605–607: The interpretation of the particular trend in tooth size in caimanines as an adaptation for “more mobile and/or compliant prey” is not clear to me. Please elaborate.

Ln 679: More data “are”, not “is”.

Ln 717: Remove “so” after “more”.

Ln 720–722: Not sampling small teeth would also have the potential to decrease size-heterodonty if the smaller teeth in general are not being collected. As such, the statement that not sampling small teeth would lead to less deviation from grand mean is inaccurate. Please revise the sentence.

Ln 746: Insert “partial least squares” between “two-block” and “test”.


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: QUANTITATIVE HETERODONTY IN CROCODYLIA: ASSESSING SIZE AND SHAPE ACROSS MODERN AND EXTINCT TAXA
Review round: 3
Reviewer: 2

Output:
Basic reporting: Nothing new to add.
Experimental design: Nothing new to add.
Validity of the findings: Nothing new to add.
Additional comments: Nothing new to add.


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: EFFECTS OF ROOT PHENOTYPIC CHANGES ON THE DEEP ROOTING OF POPULUS EUPHRATICA SEEDLINGS UNDER DROUGHT STRESSES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The oveall structure, the way of presenting, the reasoning, and the English of this MS is well done.
Experimental design: pot-grown seedlings was the basis of this experimental set-up. While there is nothing wrong in doing-so, it should be noted that the results and conclusions are limited within this set-up, and might be rather different from real field conditions.
Validity of the findings: validated within their own context.
Additional comments: the limitation of the experimental set-up should be note in discussion and conclusion.


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: EFFECTS OF ROOT PHENOTYPIC CHANGES ON THE DEEP ROOTING OF POPULUS EUPHRATICA SEEDLINGS UNDER DROUGHT STRESSES
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comments
Experimental design: No Comment
Validity of the findings: No Comment
Additional comments: One Correction:
1) In Line 297, it is reported as Wang (2015), but there is no reference for this in the reference section. I guess, this should be Wang et al., 2015.

Suggestion:
1) The supplemental figure with the scanned images under different drought conditions is pretty nice one. It could be included in the text as supplemental fig; Not sure if the authors forgot to include about this in their text.