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: CLINICAL APPLICABILITY OF THE FELINE GRIMACE SCALE: REAL-TIME VERSUS IMAGE SCORING AND THE INFLUENCE OF SEDATION AND SURGERY
Review round: 2
Reviewer: 2

Output:
Basic reporting: Clear language and narrative to the paper. Some minor errors in grammar and syntax. Check throughout that there is only one space between words and not two. Additionally, there should be either a full line space between paragraphs or they need have an indentation on the first line to make it clear that a new paragraph has been started. When using ‘however’ to link two parts of a sentence their needs to be a semi-colon before and a comma after the however.

Relevant materials included and structure appears to follow the PeerJ standards. Intro and background missing some key references – see section below for more details.
Experimental design: Within scope of journal. Research question and hypothesis could be clearer and better justified. Some basic details missing from methods making replication difficult. The basis of the paper (FGS) is from a paper that seems to be referred to as submitted and not yet published. This should be clarified as to the validity of the scale used.
Validity of the findings: If based on non-published FGS, then validity can be questions – see point above. Some areas of bias and lack of sufficient methods can call into question the validity of the findings. Some statements/conclusions over stated/lack sufficient evidence.
Additional comments: Comments for Author
It is good to see this type of study having been carried out as they are much needed to encourage the use and development of these scales. You have made good use of the resources of another study which helps to reduce the number of animals used. You find it useful to look at Descovich et al., and McLennan et al.’s review papers on the facial expression development and use. In particular the later discusses the use of facial expression scales in clinical practice as well as highlights some additional consideration that this paper has not yet addressed.

Abstract
Clear abstract. Line 23 should have a comma after ‘assessment’.

Introduction
It is mentioned in the discussion (lines 368-370) that responsiveness is being measured again, in addition to it already being carried out in Evangelista et al., submitted. Should this not be made clear in the introduction and so the changing of the aims and hypothesis to replicate what they have done?

The end of your introduction highlights the fact that the effect of sedation and OVH itself has not been studied yet with regards it affects in FGS scores and if there are potential limitations to the use of FGS in clinical practice. Your aims I do not believe really address this point, nor do the results or experimental design really address the aims of the study. A rephrasing and better leading justification is needed here to make it clearer what this study is about and why.

Line 50 – should read ‘under recognized’.
Line 52 – remove additional spacing between reference and ‘Facial expression…’.
Paragraphs need clear spacing or indentation.
Line 53 – mention ‘mammals’ but limited references to cats. Given how many other scales are now present, this is too limited and I suggest you put a few more other papers in the references list to demonstrate this.

Methods
Why only females included – I know OVH, but does this bias the results to just females? There are differences between strains of mice, let alone how males and females react to situations and potential express their affective state.

The cats were from a local shelter, yet you state permission for inclusion was gained from, but it is not clear who was responsible for these cats and whether they were really in the right to give permission. In addition, the ethics was given to the other study, and there is not mention of this particular study (although using another experiment) was assessed. This study has its own ethical concerns that are separate from the other study and so should have been assessed. The main study that the present stemmed from also had a different aim and therefore this should have been addressed within this study as well to show how these two treatments would have also affected the results. I would like to know how this was controlled for and what effect this may have had on the results.

Lines 112-115 is unclear and needs rephrasing.
Line 129 – cats receiving a score of >2 on the SF-UBCPS not included – why? No justification given for this.
Lines 134-138 describe a different method for calculating the FGS score compared to that used previously in these types of studies – what is the justification for this method? Was this the method used for RT or IMG or both?

How are the effects of sedation and pain being separated?

More detail required on how RT scores at baseline were obtained. Line 143 states being ‘undisturbed’, but if an observer is there to carry out the RT assessment, they are not really undisturbed.

Line 143 also states ‘during each minute’, but exactly how in each of these minutes’ assessment was carried out is unclear. It would not be possible to replicate this study with the current lack of details on exactly how the study was conducted.

In addition, more details on when baseline occurred and why animals were included in the study – what was there reason for being there and what previous ailments did these have. More clarity on this is required.

Why were there different times in which FGS was assessed between RT and IMG – why not keep them the same?

When were animals assessed for the need for additional rescue analgesia? What conditions needed to be met to reach this decision? Why was meloxicam given at 12h for each cat? How was the effect of this considered in the results?

Line 166 states videos were not taken if previously had been spayed – is this not what the study was looking at - OVH? Was there not a possibility of sham and surgical, or was it not known before if these animals had or had not been spayed previously? Yet, the videos for baseline and 15 mins were included – how did you get then an equal study design to assess the intra-animal changes in facial expressions?

Line 169 – screen shots taken’ – no detail of exactly how they were chosen within each of the minute e.g. frame by frame, after the first 15secs, or just the very first clear image.

No mention of controls used or match pairs.

Good to have six months in between RT and IMG assessment – any possibility of observer fatigue of training effect? Any intra-observer testing carried out between RT and IMG timings?

Was the RT observer blind to the post and pre-op state of animals?

Why was SAS and GraphPad prism chosen? Why not R, which can handle this type of complex data much better?

A brief explanation of Bland and Altman would be useful here to justify its use.

Results
It is not clear why there is a possibility of 0-20 possible videos. This was previously pointed out by another reviewer and do not feel it has been sufficiently addressed in the paper so that it is clear for any reader to understand.

135 images assessed each day – what about observer fatigue? Were any intra-observer reliability tests carried out from the first to last image etc?

You state OVH did not influence any action unit but figure 4 shows a difference in scores pre and postoperatively? So, I’m unsure how you can have these two things? How are you separating this out? How can total pain be different, but the FGS not affected? Was this an effect of the analgesia? What were the two different treatments like and were they different?

I’m struggling to understand the data in tables 1 and 2, especially table 1 that is titled scores pre and post, yet there is only one score?

Figure 3 shows quite a range in agreement scores given that the actual scores range from 0-1. How would this change if you took the total FGS score and not a fraction of it?

Discussion
Line 288 – avoid ‘proven’. Science proves nothing – it can only demonstrate/show.

Line 384 – How did you eliminate the effect if the observer on the RT score? If you couldn’t, you need to take this into account when concluding what your results truly show.

Line 388 – needs expansion and explaining why you consider the differences are likely to be stress-induced analgesia and not the effects of different regimes of treatment, etc.

Line 397-398 – It is good that you recognise you cannot separate out the pain and analgesic effect, but you also need to consider this in the rest of your discussion.

Conclusion
You state that the IMG assessment over-estimates the RT score, but what if it were that the RT underestimates. You need to be careful with your phrasing if you do not have the evidence to back up the statement.


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: CLINICAL APPLICABILITY OF THE FELINE GRIMACE SCALE: REAL-TIME VERSUS IMAGE SCORING AND THE INFLUENCE OF SEDATION AND SURGERY
Review round: 3
Reviewer: 1

Output:
Basic reporting: Minor changes suggested for change. See detailed comments below.
Experimental design: Minor changes suggested for change. See detailed comments below.
Validity of the findings: Minor changes suggested for change. See detailed comments below.
Additional comments: Thank you to authors for their detailed responses to my previous comments. The changes and responses to my questions have made the much clearer. It is now a much more concise and clear paper and I commend the authors for engaging so well in the process. There are a few minor changes I would recommend:

-	Make clear that the effects of sedation and pain being separated has been fully covered in the discussion as an intrinsic limitation to the study.
-	Again in the discussion, make clear that the lack difference between the RT and IMG scores implies/ suggests no bias from the observer
-	Check that objective 3 and hypothesis 3 match clearly
Line 51: under treated rather than undertreated
Line 78: should read “..OVH (Finka et al., 2019). It is not known…”
Line 120: It wasn’t clear what the two treatments are.
Lines 131-133: Adding in a justification for this would be good, e.g. why assess sedation.
Line 158: Did you carry out one-zero sampling or instantaneous sampling? Adding this in would make this clearer.
Line 175: State why you needed to give meloxicam at 12 hour, as you made clear in your replies from my previous review.
Line 243-244: Delete this last sentence.
Line 248: add in “..to avoid observer fatigue.”
Line 310-311: I’m still not comfortable with this wording here. I think your phrasing in the conclusion that RT scoring over-estimates image assessment is clearer. Consider rephrasing this.
Line 376: Remove the ‘However’ at the beginning of the sentence so that it starts “This influence should be …”.


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: ACCUMULATION OF SEQUENCE VARIANTS IN GENES OF WNT SIGNALING AND FOCAL ADHESION PATHWAYS IN HUMAN CORNEAS FURTHER EXPLAINS THEIR INVOLVEMENT IN KERATOCONUS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This study provides an exome sequencing approach to study a small series of keratoconus-affected corneas. This is a pilot study and should be noted as such. Can the authors comment on the incidence of keratoconus in the Polish population and how this compares with other ethnic groups (for example, Maori, Indian).

The manuscript is quite well written but does require editing for grammar and expression in places.

The Abstract does not have a conclusion but assume this is encompassed by lines 36 to 39.

The Introduction provides some overview of the study background but does miss some key references related to RNASeq in keratoconus (for exmaple, Sharif et al., 2019; Khaled et al., 2028; You et al., 2018). The expression of Frizzled proteins in keratoconus has also been reported in earlier studies (for example, You et al., 2013; Sutton et al. 2010).

There have been several GWAS studies in keratoconus (briefly referred to in lines 64 to 67); a few candidate genes are mentioned but there is limited detail - please provide further references and context.

The study aim (lines 68 to 70) indicates it was “to assess involvement of new genetic variants in KTCN etiology ……of Polish patients with KTCN, previously tested by RNA-Seq, using exome sequencing (ES) approach.” The authors also suggest this is the first exome sequencing study for keratoconus (Abstract lines 36 to 37, Conclusion line 218), however whole exome sequencing for keratoconus has been published previously (for example Magalhães et al., 2019; Karolak et al., 2016, Lucas et al., 2018).
Experimental design: The methods for DNA preparation and gene analysis seem appropriate with patient consent and institutional ethics approval. A major issue that requires further comment is the limited sample size (n=5 keratoconus corneas), and whether the data are thus sufficient to support the manuscript title and the conclusions.

Furthermore, the authors note that DNA from an additional 5 control and 5 high myope corneas was also analysed, however no details are provided for these samples (line 122 to 125). Can the authors clarify that the corneas analysed for DNA were all late stage (just before penetrating keratoplasty surgery)?

The DNA extraction from the keratoconus (and other?) corneas was presumably from whole corneal tissue (i.e. all layers); please state this in the Methods. It may also be worthwhile for the authors to assess gene variants using exome sequencing of the individual corneal layers.

The authors note line 157, that “.. data were deposited in the freely accessible ClinVar database (submission ID:158 SUB3758236)”. Please indicate if the control and myopia gene data is also available (this was not obvious from the ClinVar Submission).
Validity of the findings: As noted in the Discussion limitations, this is a pilot study (line 214) and the authors should clearly state this in the title and abstract, as well as in the Discussion (line 214).

The findings show that there are rare gene variants involved in late stage keratoconus and support the complex and heterogenous nature of keratoconus; bothese concepts have been reproted previously. The involvement of the Wnt/frizzled pathways has also been reported previously (see earlier comments).

Validation of the genes highlighted from the exome sequencing approach, using either protein or qPCR approaches, would enhance the current findings.
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: ACCUMULATION OF SEQUENCE VARIANTS IN GENES OF WNT SIGNALING AND FOCAL ADHESION PATHWAYS IN HUMAN CORNEAS FURTHER EXPLAINS THEIR INVOLVEMENT IN KERATOCONUS
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comments
Experimental design: No comments
Validity of the findings: No comments
Additional comments: The manuscript is well written in professional language, and experiments are well-designed. There are some suggestions to improve the manuscript.

1. In Table 1, pathways listed are redundant, e.g., several Wnt pathways are listed. Please simplify.
2. Table 2, please include variants information, whether it is synonymous or non-synonymous.
3. Table 3 is comparing gene variants expression between patients’ samples.  Please also include information from controls.
4. In Supplementary Table 1: it would be great to include the information of an average corneal thickness (Pachymetry).
5. Some sentence are too long. It is easier for understanding if split into two sentences. For example, in the abstract,  “in each of five patients, the assessment of functional interactions revealed rare …….
6. Please cite supplementary Table 2 in your manuscript, probably in line 134 after ‘ES screening of KTCN corneas revealed 117 potentially relevant variants with MAF ≤ 0.01 in….’.


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: ACCUMULATION OF SEQUENCE VARIANTS IN GENES OF WNT SIGNALING AND FOCAL ADHESION PATHWAYS IN HUMAN CORNEAS FURTHER EXPLAINS THEIR INVOLVEMENT IN KERATOCONUS
Review round: 2
Reviewer: 1

Output:
Basic reporting: This revised manuscript is much improved and is suitable for publication .
Experimental design: No comments
Validity of the findings: No comments
Additional comments: 1. Line 174, unify the use of numbers, ‘nine’ should be ‘9’
2. Line 189, change ‘has’ to ‘have’
3. Line 190, should be ‘genetic variants’


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: PROTEOMIC PROFILING ANALYSIS OF POSTMENOPAUSAL OSTEOPOROSIS AND OSTEOPENIA IDENTIFIES POTENTIAL PROTEINS ASSOCIATED WITH LOW BONE MINERAL DENSITY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The methodology part is missing
Experimental design: No Comment
Validity of the findings: No Comment
Additional comments: This manuscript by Huang et al. describes proteomic profiling of the plasma from postmenopausal women with or without low BMD (osteoporosis and osteopenia) using a tandem mass tag (TMT) labeling followed by the validation of the candidates using parallel reaction monitoring. This study highlight important aspect of the Postmenopausal osteoporosis and will be accepted after following major concern have been addressed

1.	The mass spectrometry data needs to be deposited in the public repository
2.	The method section were not written properly and it was not possible to reproduce the results using the method. For e.g. The authors used Agilent System Column for the depletion. The catalog number column details are missing
3.	The parallel reaction monitoring assay used for validation. The method section was incomplete. It is written that TMT labelled peptide were used for PRM analysis. This means author has used TOMHAQ for validation. If not mentioned same in the method section
4.	The author has mention normalized collision energy in ev. NCE does not have unit.
5.	 Figure 1 does not mentioned about depletion
6.	 The author should elaborate on the  rational for the shortlisting candidates for the validation
7.	 The mass spectrometry data analysis information is completely missing. How this differentially regulated molecules identified
8.	The reported number of proteins were supported with more than 1 peptides. Add this information in the results
9.	Why the samples were pooled for the TMT experiment. It can be done individually either with 11 plex or 16 plex TMT to get sample specific 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: PROTEOMIC PROFILING ANALYSIS OF POSTMENOPAUSAL OSTEOPOROSIS AND OSTEOPENIA IDENTIFIES POTENTIAL PROTEINS ASSOCIATED WITH LOW BONE MINERAL DENSITY
Review round: 1
Reviewer: 2

Output:
Basic reporting: Your introduction needs more detail. I suggest that you improve the description at lines 64-71. The authors should contextualize the study better and acknowledge other studies about proteome serum and bone mineral density. I suggest to add references related to these issues as:
1. Bhattacharyya, S.; Siegel, E.R.; Achenbach, S.J.; Khosla, S.; Suva, L.J. Serum biomarker profile associated with high bone turnover and BMD in postmenopausal women. Journal of Bone and Mineral Research , 2008, 23, 1106–1117.

2: Martínez-Aguilar MM, Aparicio-Bautista DI, Ramírez-Salazar EG, et al. Serum Proteomic Analysis Reveals Vitamin D-Binding Protein (VDBP) as a Potential Biomarker for Low Bone Mineral Density in Mexican Postmenopausal Women. Nutrients. 2019 Nov 21;11(12).
Experimental design: The Authors should better describe the eligibility criteria they used to enroll the subjects participating the study. In particular they should clarify if they excluded or not (and why) subjects with metabolic diseases or taking drugs influencing the bone metabolism. If not, how this could influence the results of the study.

I suggest paying special interest to the BMI. The authors, as they ensure that the proteins observed, were not due to differences in the BMI between the groups studied, this point should be discussed in detail.

The data of biochemical measurements should be reflected in Table 1 Participant characteristics or Supplementary Basic_information.

A major cause for concern is the statistical approach, and validity of a t-test when only n=2 replicates are analyzed for the three conditions after sample pooling. Furthermore, given that multiple variables are tested, what adjustment is made for multiple comparisons?
Validity of the findings: In the discussion, I would spend some word comparing the performance of these proteins in respect to other candidate biomarkers, on how to combine, in the future, with other markers to improve specificity and sensitivity.

The authors should discuss in detail the limitations and strengths of their study to enrich the manuscript.

Perhaps, the most important limitation of the present paper is the lack of follow-up. This issue should be further clarified.

Another point that should be clarified, is because they did not individually validate the total of the samples, n = 54.
Additional comments: Firstly, I would like to thank the journal for letting me review such an interesting paper. The look for new biomarkers is a field of great interest. The present paper has several strengths, such as the proteomic approach. However, in my opinion, several drawbacks should be clarified.

Data quality is acceptable overall. However these results could be regarded as preliminary and limited, mainly due to the methodology used, and do not significantly advance the cause of biomarker development for OS/OP.


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: PROTEOMIC PROFILING ANALYSIS OF POSTMENOPAUSAL OSTEOPOROSIS AND OSTEOPENIA IDENTIFIES POTENTIAL PROTEINS ASSOCIATED WITH LOW BONE MINERAL DENSITY
Review round: 1
Reviewer: 3

Output:
Basic reporting: 1.	The authors don’t mention if they have submitted their proteomic data to a public proteomic repository. The authors should submit their proteomic data to some public repository or database where the data files can be accessed by other researchers.
Experimental design: 1.	The authors also need to mention the product code or catalog information for the Multiple Affinity Removal Column Human 14 or some other Agilent serum depletion columns they have used in the study. So that other researchers can in future can replicate their findings using the same columns

2.	The authors also don’t mention anything about the database they have used to search their TMT-labeled MS data against. It looks like they have used UniProt database. The authors should provide information regarding the version of the database they have used in the study and the number of the protein entries in the database

3.	The authors need to describe in detail the in-solution peptide digestion protocol they used to generate the peptides which were further labeled with TMT-tags.
Validity of the findings: Major points:

1.	In the introduction section line 43-44: the author talk of global prevalence of OP cases in future (2035- 48.03 million cases; 2050- 5.99 million cases) according to Shi et al. 2015. However, the numbers provided by authors need to be corrected as the real numbers quoted by Shi et al is as follows
“Projection of annual fractures and related cost to 2050: Projection of fractures by sex for each fracture site is given in Fig. 3 and Appendix Table 3. Fracture number and related costs at the included fracture sites were estimated to increase through to 2050 in both sexes. Relative to the base year, annual total fracture number and costs were predicted to double by year 2035 (4.83 million fractures at a cost of 19.92 billion US dollars) and were projected to rise to 5.99 (95 % CI 5.44, 6.56) million fractures, accounted for approximately 9.84 per 1000 people aged 50+ years, costing $25.43 billion (95 % CI 23.92, 26.95 billion US dollars) by year 2050.”
2.	The authors have strangely not provided the peptide list of all the identified proteins in the study for OP, ON and CN. Especially, the differentially abundant proteins (DAPs). This call into question the authenticity of the data
3.	One major criticism of the study is the authors provide no MS/MS spectra for the DAPs at least MS/MS spectra for one peptide for each of the eight DAPs mentioned in Table 2

Minor points:
1.	The authors should abbreviated the term SDT buffer on line 113 in the methods section of the manuscript
2.	The authors need to name the proteins mentioned on line number 234 in the result section of the manuscript. It is highly inconvenient for the readers to check table 2 each time.
3.	In the abstract of the manuscript line 28-29 the authors need to rephrase the sentence to “Collectively, our results suggests that postmenopausal women with low BMD have a different proteomic profile or signature”
Additional comments: The manuscript by Huang et al. utilized Tandem Mass Tag (TMT) labeling-based quantitative proteomic approach along with parallel reaction monitoring (PRM) approach to study the comparative serum proteome from postmenopausal osteoporosis (OP), osteopenia (ON) and age matched healthy controls (CN). The authors identified differentially expressed proteins in serum of OP and ON samples when compared to controls (CN). Additionally, a selected subgroup of differentially expressed proteins was further validated using the PRM approach. I strongly feel that the work undertaken by the authors is quite important in the field of postmenopausal osteoporosis considering the lack of osteoporosis associated biomarkers and early detection disease markers. However, the manuscript has major issues and the authors have not provided all the experimental and result information in the current version of the manuscript. The authors have to address the issues before the manuscript could be accepted for publication.


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

Input:
Title: PROTEOMIC PROFILING ANALYSIS OF POSTMENOPAUSAL OSTEOPOROSIS AND OSTEOPENIA IDENTIFIES POTENTIAL PROTEINS ASSOCIATED WITH LOW BONE MINERAL DENSITY
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comments


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

Input:
Title: PROTEOMIC PROFILING ANALYSIS OF POSTMENOPAUSAL OSTEOPOROSIS AND OSTEOPENIA IDENTIFIES POTENTIAL PROTEINS ASSOCIATED WITH LOW BONE MINERAL DENSITY
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have successfully addressed most of the queries in the revised version of the manuscript.
Experimental design: The authors have successfully addressed most of the queries in the revised version of the manuscript.
Validity of the findings: The authors have successfully addressed most of the queries in the revised version of the manuscript.
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: ASSESSMENT OF LOCOMOTIVE SYNDROME AMONG OLDER INDIVIDUALS: A CONFIRMATORY FACTOR ANALYSIS OF THE 25-QUESTION GERIATRIC LOCOMOTIVE FUNCTION SCALE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is written in a clear and concise English that allows the correct interpretation of the data.
In relation to the bibliographical references these are according to the studied topic, updated and support the basic idea of the investigation.
I suggest to the authors that Table 1 be developed in the section on material and methods and not in the introduction.
the theoretical framework proposed is in accordance with the objectives and subsequent results expressed in the research
Experimental design: The article is original and is related to the editorial line of the journal. On the other hand, the research design is clear and can be replicated in other types of populations.
Validity of the findings: The sample size used in this study is a representative sample of the population that allows to interpret the results in a clear way, has a great clinical and replicable applicability.
Additional comments: Dear Authors:

I consider that the work done presents a great clinical applicability, I suggest to remove table 1 of the introduction and incorporate it in the section of material and methods.
The results are in accordance with the stated objectives.


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: ASSESSMENT OF LOCOMOTIVE SYNDROME AMONG OLDER INDIVIDUALS: A CONFIRMATORY FACTOR ANALYSIS OF THE 25-QUESTION GERIATRIC LOCOMOTIVE FUNCTION SCALE
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1)	The last paragraph of the introduction is a bit hard to follow from a flow perspective. The potential problem of scoring and scale applicability for some individuals (i.e., lines 58-64) is a valid and important point, but it feels out of place in the introduction. Unless this contributes to establishing the problem and/or gap in the literature, it feels like this may fit better in the discussion. For example, does it help set up the problem/gap that this paper will address? The problems that are mentioned are valid, but this paper doesn’t specifically address those problems, so it may be better-suited for the discussion leading into future research.

2)	There is a brief mention of factor structure in the introduction (e.g., Tanabe et al., 2018), but this is not elaborated on until the discussion. I think elaborating on the findings of previous literature in this area will help set up the problem and purpose statements more effectively.

3)	Models were a bit difficult to follow due to arrows crossing different directions and lack of uniform size (e.g., latent variables different sizes, etc.). It also appears that models present standardized values. If so, some terminology may need to be updated (e.g., error covariances should be error correlation).

4)	There are some typos and poor sentence structure in the abstract (e.g., line 52; 32-34), making it difficult to follow what is being conveyed. There were also a couple typos throughout the paper that should be addressed (e.g., line 95). The scale name is also changed in the discussion to GLSF-25 rather than GLFS-25. Sentences on lines 84-86 are unclear with how they are currently written. Some times verb tense seems to switch back and forth (e.g., Methods, lines 124-128).
Experimental design: 1)	The research question seems to be asking one thing, while the model structure is assessing something slightly different. Specifically, it is a bit confusing as to why sex and age are included in the models depicted in Figures 3 and 4. It seems like the research question is only asking about factor structure of the scale. This is a great first step, especially because this has not been done before. However, because the factor structure has not been confirmed, the relationship with other variables should not be tested yet. If this was a secondary purpose, it needs to be clarified in the paper, but it does not seem to fit as a next step within the scope of this paper and the current findings. I think the goal of identifying the factor structure is adequate given the current results. If sex and age were included for different reasons, then this also needs to be clarified in the paper.

2)     Is the six-factor model that is tested in the paper the same as was found in previous literature? This seemed to be the case but was not completely clear with the way that the methods are written currently. Was a single-factor model supported by the literature or was this chosen some other way? A 3-factor structure as identified by Tanabe et al. (2018) through exploratory factor analysis, was also mentioned. Is there a reason this model was not tested in this study using this set of data? This seems like a potentially missed opportunity. These results also need to be compared more extensively in the discussion. Both the present study and Tanabe et al. (2018) found three-factor structures, but were these the same? What are the implications of this?

3)     The alternate model generation process seemed to involve mostly the assessment of modification indices. What were the cut-off values used for these decisions? You also mentioned the need to potentially identify a more parsimonious GLFS-25 (line 220). When considering alternate model generation, did you consider the removal of items in an attempt to identify a more parsimonious model?

4)     It sounds like the error correlations in the alternate model were statistically supported, but were they also theoretically supported? The theory aspect behind decision-making did not feel like it was addressed or discussed.

5)     I think there needs to be a bit more detail in the methods in general.
               - For example, how was data cleaned? Were there any missing cases, and if so, how were these addressed?
               - The discussion of a 100% response rate, while good information, may be a bit misleading. Instead, how specifically were participants recruited? This detail seemed to be lacking a bit and could provide context about the data collection process.
               - What specific cut-off values for CFI and TLI were used?
Validity of the findings: 1)     Part of the discussion highlights the cross-loadings and the potential issues here. However, the conclusion states that the scale could be useful. I think this needs to be stated with extreme caution, and the limitations and potential issues with the scale need to be addressed further instead, as well as the clinical implications. As a clinician, the most important question is, should we use this scale? If so, how? If not, why not? While the factor structure tells us these things indirectly from a statistical standpoint, it feels like the practical application piece can and should be addressed in more detail.
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: ASSESSMENT OF LOCOMOTIVE SYNDROME AMONG OLDER INDIVIDUALS: A CONFIRMATORY FACTOR ANALYSIS OF THE 25-QUESTION GERIATRIC LOCOMOTIVE FUNCTION SCALE
Review round: 1
Reviewer: 3

Output:
Basic reporting: General Comments: Minor grammatical errors throughout.

Specific Feedback
INTRODUCTION
Well written and provides ample support for why the factor structure of the GLSF-25 should be investigated.

FIGURES
Figure 2 is not necessary; it can be deleted.
Experimental design: General Comments: Research question is defined however, there are significant issues with the methods described.

Specific Feedback
METHODS
Participants
Line 79: error – comma after the semicolon – should be deleted

Model Specification
Line 95: error – comma after the ‘m’ in movement-related
Lines 97-101: consider rephrasing as it is difficult to follow (i.e., difficulty using the stairs, walking briskly, walking without rest, leaving the vicinity, carrying a 2-kg item, doing light level housework, and performing somewhat heavier housework).
Lines 106-107: It is not clear why age and sex of the subjects were treated as observed indicator variables for prediction. If the goal is to establish the factor structure of the GLSF-25 then these should not be included in the CFA. After the factor structure has been identified, invariance testing has been completed (to determine the scale is invariant between sex, age groups, etc.), then a predictive model can be tested. Age and sex should not be included in the CFA models; models must be rerun without and fit-indices reported.

Input data, model estimation, and potential model modification
Line 114-115: How were skewness and kurtosis calculated? What criteria was used? Please include a citation.
Line 118-119: Same as the previous comment
Line 124: CFI and TLI cutoffs are typically reflected as >.90. (previous standard) or >.95 (most recent standard); not ‘close to 1’.
Line 124-125: Although modification indices can be used as a guide, they should not be used alone. MI’s should be assessed but only applied/used if the relationship between the concepts makes theoretical sense.
Validity of the findings: General Comments: There are flaws that need to be addressed regarding analysis and findings. The results, discussion, and conclusions need to be rewritten after the analysis is rerun.

Specific Feedback:
RESULTS AND DISCUSSION
Results
Line 144-146: Cronbach’s alpha should not be calculated for all of the items in the questionnaire. There should be six alphas reported, one for each of the factors. If authors would like to include a Cronbach’s alpha for all of the items because they ran a model that included all items in one factor, it is appropriate however, there should be six alphas reported for each of latent variables. Additionally, the range for alpha should be between 0.7 - 0.9; an alpha above .9 is an indication that multicollinearity may be present.
Lines 154-156: It is not clear why the authors chose to add cross-loadings and residual covariances between latent variables rather than eliminating items. Assessing factor items and content for those items, along with Cronbach’s alpha for each factor would allow you to see the best items to keep/eliminate. Please elaborate on why these steps were taken instead of attempting to identify a more parsimonious model.
Lines 157-158: Although the alternate model has improved fit, it only slightly meets recommended guidelines (CFI and TLI >.95; RMSEA < .06).
Lines 159-166: Alpha should be run on the new factors using all items in the proposed factor.
Line 162: error – should read “as they showed high intercorrelation”
Line 165: error – delete ‘the’; should read “in light of” not “in the light of”
Line 166: error – delete ‘of’ and ‘also’ to read “the factor body pain was positively associated with Q25.
Line 167: error – delete semicolon (;) and start a new sentence with ‘Additionally, Q7…’
Lines 172-176: Although the number of factors was reduced from six to three, there are still issues with the model. Adding residual covariances is only appropriate when it makes sense theoretically. Before doing so, the researchers must look at each of the questions (e.g., are they double-barreled, do they make sense, etc.) and also run the appropriate alphas on the factors. The proposed alternative model included residual covariances that should not be correlated. The model also includes a substantial number of items with low loadings (<.4) and one item that is has a negative valence (when all of the other items are positive). The loadings from second-order factor ‘psychosocial’ to first-order factors ‘soc-daily act’ and ‘cog’ are very high, which is an indication of either multicollinearity or model misspecification.
Authors should seek to condense items and factors to make a parsimonious model. The use of modification indices to only find a statistically better model is inappropriate. Additionally, cross-loadings should not be allowed as this indicates items are not unique to constructs. The alternative model proposed (Figure 4) is rejected as is.
It is highly recommended that authors identify a more parsimonious model (with a reduced number of items) that: 1) theoretically make sense, 2) is psychometrically sound (meets the most up to date criteria), and 3) can be administered and scored with ease. The alternative model proposed does not meet those guidelines.

Discussion
Line 190-192: The sentence that starts “Although dimension” is not clear. I am not sure what the authors are trying to say. Furthermore, dimension and factor analysis are used to identify unique constructs, this might be worth mentioning.
Line 199-203: The goal of the dimension reduction should be to theoretically and statistically differentiate unique latent variables. Even when dimensions are related, the latent variables should be uniquely contributing to the variance of the higher-order construct but in this case, it is not. Constructs can be related but should also be unique. Additionally, the model proposed is confusing for clinicians to use and should therefore not be recommended for practice.
Line 219-222: Completely agree that the questions need to be modified or improved however, it is still possible to create a parsimonious model from the 25-questions. A review of the items should be used as a guide for removal.
Line 224-225: Although you could revise the scoring algorithm, it would be more advantageous to instead design a questionnaire that has three factors with items that uniquely contribute to the factors. The 25-model should be reduced.

CONCLUSION
The results do not support the 3-factor structure and the authors should also address the lack of feasibility for physicians to use the proposed alternative model. The alternative model proposed should not be recommended for use.
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: ASSESSMENT OF LOCOMOTIVE SYNDROME AMONG OLDER INDIVIDUALS: A CONFIRMATORY FACTOR ANALYSIS OF THE 25-QUESTION GERIATRIC LOCOMOTIVE FUNCTION SCALE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have corrected the requested comments.
Experimental design: The authors have corrected the requested comments.
Validity of the findings: The authors have corrected the requested comments.
Additional comments: I consider that the work is done presents great clinical applicability.


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: ASSESSMENT OF LOCOMOTIVE SYNDROME AMONG OLDER INDIVIDUALS: A CONFIRMATORY FACTOR ANALYSIS OF THE 25-QUESTION GERIATRIC LOCOMOTIVE FUNCTION SCALE
Review round: 2
Reviewer: 2

Output:
Basic reporting: 1) The introduction is more concise, but I think it could be set up a bit more effectively. The transition to the problem and purpose statement starting in line 84 is an abrupt transition. I might consider discussing previous research in a bit more depth (e.g., Tanabe et al. study) and then using that to set up the problem, rather than identifying the problem and then discussing the literature that exists.

2) Sentence starting with “The cutoff scores” on line 52 is a bit unclear with how it is currently phrased.
Experimental design: 1) Recruitment is described in more detail now, but the sentences describing this process have unclear phrasing. There are also a couple of typos:
     a) Line 97 and 99: “eligibility” should be “eligible”
     b) Line 98: “GLSF-25” should be “GLFS-25”
     c) Line 102: “analysess”

2) The model specification section is a bit confusing with all of the questions listed – is there a more concise way to present this information? Table 1 is helpful in clarifying this information. Is there a way to denote within this table which construct each question represents according to the original scale?

3) I am still a bit confused on whether or not theory was a contributing factor in making modifications to the specified model. It is discussed a bit in the methods section, but when more detail is given later in the manuscript, it feels like there is still a very heavy emphasis on the statistics and numbers in isolation. It is okay to rely on the numbers, but other considerations with theory need to be made. If theory was a contributing factor, I think it needs to be explained a bit more explicitly. If not, I think it needs to be considered when re-specifying the model. If we only use statistics and cut-off values to determine the changes that need to be made, we are likely to find a model that fits regardless. The question is really whether or not that model makes sense theoretically while having good model fit.
     a) Related to this, was there a theoretical basis for adding the second-order factor shown in Figure 4?
     b) There is one item with a loading of 0.22 under "Body Pain". Is there a reason this was kept? I am curious just because the cut-off given was 0.60.

5) A few typos throughout:
     a) Line 197: remove “factor”
     b) Line 198 remove “the”
     c) Line 201-203: Incomplete sentence
Validity of the findings: Generally, I would be careful of how conclusions are stated.

1) Line 179-181: The interpretation of Cronbach's alpha is a bit confusing as it is currently worded. Currently, it sounds like it is being interpreted as reliability with previous data, instead of the internal consistency within the scale for this present data set, and that it happens to be consistent with previous findings.

2) From a statistical standpoint, the model met cut-off values, so "accepting" it from this standpoint could be okay. But from a theory standpoint, do they hold up? If theory is used, would we end up with this model? (See comments in methods section)

3) It is mentioned that the reliability of the model was confirmed. I'm not sure this can be stated since the final factor structure was different than the original model. There was still a model with 3 factors, but the content of those factors was not consistent with what was originally proposed in the literature. The potential issues of the model are discussed more clearly now, but it feels like sometimes two contrasting ideas are being presented, which makes it a bit hard to follow.

4) Line 275-6: Yes, it could be beneficial to differentiate between these constructs, but the results do not necessarily let clinicians do this with the scale in its current form. I would just be careful in the way this information is presented, as it sounds like you are saying that the current scale with 3 constructs can help do this. As you mention, there are cross-loadings, etc. within the final model, but these make it difficult to differentiate between constructs.

5) Line 293-298: Valid points, but some of this information seems out of place. I would make sure to set up this point in your discussion more clearly.

6) Good discussion points overall in the paragraph on lines 300-320. A couple things to consider:
     a) Sentence starting on Line 313 with “Our analyses…” – I would be careful with this statement – Unless compared to other tools, this claim may be difficult to make.

7) Fourth limitation – this doesn’t necessarily feel like a limitations methodologically as much as it does a discussion consideration.

8) I might consider modifying the conclusion slightly in accordance with any other changes made.

A few typos throughout:
     a) Line 247-250: Incomplete sentence; needs revising.
     b) Line 255: "explanatory" should be replaced with "exploratory"
     b) Line 262: should be “3 different” instead of “different 3”
     c) Line 319-20: Comma splice
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: ASSESSMENT OF LOCOMOTIVE SYNDROME AMONG OLDER INDIVIDUALS: A CONFIRMATORY FACTOR ANALYSIS OF THE 25-QUESTION GERIATRIC LOCOMOTIVE FUNCTION SCALE
Review round: 3
Reviewer: 1

Output:
Basic reporting: Abstract:
Line 19: “have not” should be “has not”

Introduction:
Line 60: Sentence starting “The full version…” is a bit confusing as it is currently worded.

Methods:
Line 78-79: “500 samples in order of visiting” – phrasing is confusing here. Is this intending to say that questionnaires were distributed until a total of 500 had been completed and collected?

Line 94: “written consent form of the study” – phrasing is confusing.

Lines 122 and 124: Remove bold period after table numbers to keep consistent with rest of manuscript

Line 131-132: “CFI and TLI are both required to be…” – this phrasing is a bit hard to follow with the rest of the sentence structure. Could potentially just put (≥0.95) after CFI and TLI as with the previous fit indices.

Line 134: “is” should be “was”

Line 138: “are” should be “were”

Line 139: “will” should be “would”; “fitting” should be “fit”

Results:
General consideration – Be sure that factor names, capitalization, etc. is consistent throughout.

Line 154: Does “Their mean age” refer to only the females or the full sample? It is not clear given the previous sentence.

Line 165: “fitting” should be “fit”

Line 185: “on factor of…and factor of…” – phrasing is unclear.

Line 186: “fitting” should be “fit”

Lines 200-201: This sentence is unclear. Is this saying that Q6 loaded onto two factors?

Discussion:
Line 213: comma splice; consider starting a new sentence after “with aging”.

Line 224: “fitting” should be “fit”

Line 238: remove “the” before “psycho-social complications” since “and LS” is also listed afterwards.

Line 242: unclear wording – either needs “the” added before “full 25 questions” or could also say “all 25 questions” instead.

Line 280: “are suggested” is unclear here. Perhaps something like “should note that…”

Line 284-5: Wording is unclear – is this meant to say “as well as the items [that] should be included…”?

Line 287: “subject” should be “subjects”

Line 296: “answers quality” should be “answer quality”

Line 297: “maybe also responsible” should be “may also be responsible”

Conclusion:
Line 308: is the word “organ” supposed to be included?

Line 309: “enhancing” should either be “in enhancing” or just “enhance”
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The authors have made positive improvements to this manuscript.


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

Input:
Title: INTRASPECIFIC VARIATION IN THE COCHLEAE OF HARBOUR PORPOISES (PHOCOENA PHOCOENA) AND ITS IMPLICATIONS FOR COMPARATIVE STUDIES ACROSS ODONTOCETES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is written in a clear, concise manner that is easy to read and easy to follow. It uses professional and unambiguous english throughout. The references are complete and thorough, and no major references are missing. The data has all be shared and is accessible, and the figures and tables are complete. The article is self contained with clear hypotheses being tested and results that unambiguously shed light on those hypotheses.

My only suggestion would be pertaining to the data. The authors have made most of their raw data available NHM dataportal. This includes all of the landmark data and the landmarks themselves. However, I would really like to see the authors publish the actual 3D files of each cochlea, probably as an STL or a PLY. I understand that this data also appears in a Park et al MS that is in review, so I realize they may be unwilling to do this at this time. I do not think this should stop the MS from moving forward, but I do think the 3D files should be made available.
Experimental design: The others lay out a clear and well stated hypothesis and the experimental design explicitly tests it in a falsifiable manner. It is clear how the results address the hypothesis and it is clear why the results are relevant to the field at large (i.e. many other studies are limited to a single specimen). The methods section in particular is exceptionally well written, easy to follow, and easy to replicate, and should represent a gold standard for methods reporting.
Validity of the findings: I have no concerns as to the validity of their findings. Their conclusions logically follow from their results.
Additional comments: A few additional edits and comments for the others to consider during revisions:

Line 46: I agree with the overall point, but it is probably worth adding a small caveat. Using a single specimen as representative of a species shouldn’t be a problem assuming that all species show similar levels of intraspecific variation as harbor porpoises. Perhaps a simple “if the results are consistent across other species…”

Line 60: “this has not been extensively tested”. Do you mean for cetaceans specifically? For cetacean cochlear data? I would argue that it has been extensively tested in some taxonomic groups for some traits, but I would agree that it certainly hasn’t been extensively tested for cetacean cochlear morphology.

Lines 205–212: Generally, I think that plotting PC1 and PC2 with color to indicate the ecological variables is a good idea. I suspect the authors and I would disagree politely over some of the categorizations—specifically pertaining to what may or may not constitute a suction feeder—but I think the plots are interesting and informative and, especially as supplementary, not something I would scrutinize too closely. I would, however, like to see this broken down, perhaps in another supplementary table? For example, in figure S6, which taxa are the ones considered “raptorial/suction” or which taxa are considered “deep”. As a reader I would appreciate knowing which taxa belong to which category and the references on which that is based.

General: The authors primarily compare harbor porpoises to the rest of Odontoceti as a whole. However, I am curious whether the dataset allows you to compare (even in a limited manner) harbor porpoises to other species of phocoena. I noticed a few in the dataset, and I am curious if they specifically are closer in morphospace to the P. phocoena dataset? This could be relevant because it might indicate that, intraspecific variation is more impactful if the taxonomic scope of the study is narrow. I don’t think the authors need to do much more, just perhaps add a sentence or two about this to the discussion.


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

Input:
Title: INTRASPECIFIC VARIATION IN THE COCHLEAE OF HARBOUR PORPOISES (PHOCOENA PHOCOENA) AND ITS IMPLICATIONS FOR COMPARATIVE STUDIES ACROSS ODONTOCETES
Review round: 1
Reviewer: 2

Output:
Basic reporting: I cannot agree that the manuscript is written in a clear, unambiguous, professional manner. The coverage of literature is sufficient, but background lacks specific, focused insights, and contexts are unclear (the authors never specified what intraspecific variations are examined in the cochleae in the first place). The manuscript is structured professionally, except that supplementary figures and tables should be incorporated into the main article. The manuscript is self-contained, but there is no statement of a specific hypothesis.

See general comments for what specifically the manuscript failed to meet these standards in, and how to improve.
Experimental design: The manuscript is original, primary research, but did not define research questions (intraspecific variations as a confounding factor in taxonomic identifications or comparative analyses, as a correlate of echolocation, or... The narrative is vague and waddles between these different questions). I am not sure what knowledge gap the manuscript fills. Technical and ethical standards are upheld, and methods were described with sufficient details.

See general comments for what specifically the manuscript failed to meet these standards in, and how to improve.
Validity of the findings: The authors surely quantified variations in cochlear morphology, but they never put it in context (sex, age, size, population, etc.). Any trait varies within a species, but the key information is its correlates. The authors tucked this most relevant aspect of their analysis in supplementary information (where they looked at vaguely defined ecological traits), and even this was only interspecific and did not extend onto their discussion of intraspecific variation.

They are unclear about which data specifically derived from Park et al. (2019) or Martins et al (2019). It almost reads like a lot of data got transferred over from these papers, but they didn't detail which specimens, species, or measurements. It is not clear if 3D renderings are available in NHM Data Portal.

Conclusion is not clear. Implications are not clearly stated or discussed.

See general comments for further details on what specifically the manuscript failed to meet these standards in, and how to improve.
Additional comments: I carefully read “Intraspecific variation in harbor porpoise (Phocoena phocoena) cochleae and its implications for comparative studies across odontocetes.” In this manuscript, Martins and colleagues report results from geometric and linear morphometrics on the cochlea from harbor porpoise (n=18) and 51 other odontocete species. Intraspecific variation (as ambiguously defined by the authors) was smaller substantially than interspecific variation (also as ambiguously defined by the authors). I found the methods and results are overall competent, but the presentation requires massive improvement. My concerns fall into four major categories: 1) treatment of intraspecific variation; 2) tenuous rationales and overgeneralizations, and the lack of the sense of goals; 3) data presentation; 4) overall writing; and 5) specific technical comments.

1) Treatment of intraspecific variation
The authors should consider what “intraspecific variation” they are recovering in the cochleae of harbor porpoises. Intraspecific variation —any polymorphism in a species, however defined— is so broad that it means little without context. Sexual dimorphism, ontogenetic traits, allometric trends, developmental plasticities, population means, reaction norms, performance differences…. They are all intraspecific variations. Many of these contexts (such as sex, size, age estimates) are essential collections data and I assume they were available to the authors. At the very least, size can be easily taken from their own scans. There should be some effort to dissect what biological context the data speak to.

In terms of study design, I also wonder why they only picked one specimen from each of the other species. It is unlikely that only one each was available to the study. I wonder if they picked one from each for the sake of simplicity. I believe they should sample whatever small numbers available in at least two or three more species, and they could test whether the range of variations in P. phocoena is compatible with other odontocetes — which is potentially an important point they could have backed up with data.

Additionally, what collection bias might exist in those other odontocete species sampled for this study?

2) Rationales and generalizations
The authors should have a clear sense of goals, or what they want to accomplish in this manuscript. The lack of this understanding transpires through unclear rationales. The authors were unclear about how and why the harbor porpoise data inform us broadly about morphological variation of cochlear among and within odontocetes — only a vague, arm-waving explanation how common they are in the collections and how they distribute in wild. The authors argue that intraspecific variation may be a confounding factor. But they omit explaining how specifically (e.g., are cochlear characters frequently used for specific diagnosis of odontocetes, and, if so, what?). They do not seem to refer to parallel studies in other taxonomic groups they only cited in passing, such as Cerio & Witmer, and didn’t seem to incorporate the analytical pipeline or interpretations from such previous studies in their own manuscript. The authors quantified intraspecifc variation to understand how it is set in the odontocete background, but they did not care to consider or test for sexual dimorphism, ontogenetic variations, allometric trends, or left-right asymmetries. Overall, it gives an impression that the authors employed a wobbly narrative.

Related to this problem, they make many general comments, either out of context or without sufficient evidence. Examples:
-	Intraspecific variation as “key driver” of evolution by natural selection. (Line 50) Do they really mean a “driver”?
-	“There can be variation in survival defences (what is “survival defence”?), parasite resistance, resource manipulation and others, all of which can alter the number and strength of interactions shifting the dynamics of an ecosystem.” (Line 53-54) What do the authors want to accomplish here? The list is neither comprehensive nor pertinent to their discussion.
-	The authors’ key statement: Levels of intraspecific variation are lower than those of interspecific variation (Line 59-60). In what context? Intraspecific variations CAN be greater than the sum of means across species.
-	Intraspecific variation not considered or impossible to calibrate (Line 62-65). If this concern is really the motivation for the authors, they must justify why harbor porpoises and why cochlear morphology. If the availability and its importance in echolocation are their best rationales, then this motivation about the general nature of intraspecific variation is irrelevant. The authors should identify something like: echolocation is an important ecological trait -> then they should look into how different cochlear morphology correlates with what aspect of echolocation. If taxonomic misidentification is a concern -> then the authors should list examples of diagnostic characters in cochleae.
-	The focus of study is “hearing ability” (L 107). Then why no specific discussion on correlation between cochlear morphology and auditory function anywhere in the manuscript?
-	Semicircular canals not phylogenetically or ecologically informative (Line 107-108). Really?
-	They can be “interpreted biologically” (Line 136). This statement doesn’t make sense. Any biological measurements can be interpreted “biologically.”

The authors should consult other parallel papers (such as Cerio & Witmer, which they cited) for how they set up their analysis, and in what context the data should be analyzed and interpreted. These out-of-context, truistic general statements are not helpful because the authors are not discussing general nature of intraspecific variation at all. They are discussing some specific aspect of intraspecific variation (however defined) in a given structure of a given group.

3) Data presentation
I recommend the authors include as many 3D renderings as possible in main figures. This is: a) to give readers good idea of the cochlear morphology and metric traits (Fig. S1); and b) to give readers sense of variation in addition to PCA plots — especially if they mean to maintain PCA results are “misleading”. Also, PeerJ as an online venue has no physical limit to the number of figures. So there is no good reason not to do this.

I also encourage all supplementary figures and tables incorporated in main text and discussed extensively. Again, no limit on length provides an opportunity to be as comprehensive in your presentation as possible. Few choose to view every single supplementary material. A good way to make sure your data to be open is to include them all as main figures and tables.

4) Overall writing
The authors did competent analyses and produced valid results. This is confounded, however, by the lack of clarity or focus in overall presentation and writing. Please see attached pdf for specific comments. I was distracted by general discussion of intraspecific variation (most of which seems to require no introduction or discussion, and reads like reinventing a wheel; e.g., the first three sentences in Abstract) and the lack of focus in the topics they set out to explore (e.g., a rough sketch of potential ecological correlates in Discussion) or sometimes an entire neglect of it (e.g., no discussion about sex, size, or age correlates). This aspect requires massive improvement by using clear and focused narrative.

Also, some minor corrections:
-	Throughout the manuscript, it is not “18 P. phocoena specimens”. It is “18 specimens of P. phocoena.” Latin binomials should not be used as an adjective.
-	“As we expected” “As we might have expected” and the like (Line 284, 313, and throughout) — these phrases do not accomplish anything. If you made predictions, then state them specifically and test them.
-	Fairly variable (Line 286). What is “fair” variation?
-	Line 292 – “coefficient of variation values” should be “values of coefficient of variation.”
-	Line 300-306 should be in Introduction to justify the work.
-	“Were nested with” (Line 310) — No, simply “overlapped with”.
-	“Neatly” (Line 313) — please be more descriptive.
-	“Although this does not appear to be the case for these data” (Line 315) — why? I do not understand.

5) Some technical comments

The list of linear measurements included some non-linear traits, such as angles, areas, volumes, discrete counts, and ratios (Line 128-134). Then the authors stated that they log-transformed all metric traits (Line 153). Did they log-transform ratios? (and how for ratios < 1?) Angles? Counts?

Line 157-160 – The authors should clearly state whether 3D renderings are available in NHM Data Portal, and which specific data entries derived from Park et al. (2019) or Martins et al. (2019). All specimens of P. phocoena?

Line 214-225 – the authors discuss some sensitivity analysis, but I don’t see detailed results of this sensitivity analysis. Also, how are those specimens chosen? Strictly randomly or otherwise?

Line 286-290 – the authors argue a standardized protocol could reduce noise. But this shows that the authors had an opportunity to make that sensitivity test but did not bother to do it. Please show that if the standardized protocol could reduce noise.

Line 292-296 — “artificial variation”. If the authors are sure about artifacts, then why show deficient results that they know contain artifacts? What did the authors do to minimize this?

Line 315 “Plasticity” — I think “plasticity” here is taken out of context, and I don’t know what the authors really want to communicate with this term here.
Line 319 “Similar acoustic environments” — what environments are “acoustically similar”?

Line 328-330 “same limited morphospace” — This argument is unclear. The least it suggests is that there is no one dominant correlate that explains most of the shape variation. I'm not convinced that the authors can say any more than that given the data.

Line 330-333 and also elsewhere discussing or mentioning human errors — Why go look for these human errors, where (a) the variations can be reasonably interpreted in biological context and (b) the authors themselves reject these possible sources of error? Do the authors think that could explain some major patterns in data? And if so, why are they presenting this result?

Line 335-350 General discussion of PCA interpretations — I don’t find this entire paragraph helpful. First of all, the authors complain that these plots do not covey “true” results because the plots show distributions that are not perfectly aligned with their “expectations”. But, once again, the plots seem to me as reasonable distributions, and they can be reasonably interpreted. I don’t know what the authors want to accomplish here.  Are they suggesting there is some “true result” or “true interpretation” that they can’t visualize otherwise? For the sake of argument, assume that their disappointment has some ground. Then I would wonder why they chose to show those “misleading” plots anyway. I recommend that this whole paragraph be removed.

Line 355-356 “lower than expected” — the authors never showed what was the expectation.

Line 362 “we believe this is unlikely” — Why?    “As discussed above” — where?

Line 363 “likely to be more variable than most species making our conclusions more conservative” — I do not follow their argument here. Why can they claim that when they only looked at one from each of the other species?


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: INTRASPECIFIC VARIATION IN THE COCHLEAE OF HARBOUR PORPOISES (PHOCOENA PHOCOENA) AND ITS IMPLICATIONS FOR COMPARATIVE STUDIES ACROSS ODONTOCETES
Review round: 1
Reviewer: 3

Output:
Basic reporting: Martins et al. present a thorough and interesting examination of morphological variation in the cochlea of harbor porpoises, using the largest sample size of CT scans to date of an individual species of odontocete whale. They identified low amounts of intraspecific variation in the cochlea shape within harbor porpoises, much lower than that seen across Odontoceti as a whole. Although some variability was still inherent, the study suggests that the use of single specimens in comparative studies of inner ear morphology should not present issues in data interpretation.

This study is extremely well written written, and in fact is maybe one of most typo free drafts of first submission I have come across. The study also addresses the important topic of individual variation. Too many paleontologists and marine mammal specialists tend to discount individual variation when describing morphology, and I commend the authors for actually rigorously testing the importance of this aspect of morphology in inner ear data. The paper is well structured, and for the most part well referenced (see below).
Experimental design: The analytical methods and data all seem sound, and the analyses thorough. I don't really have any suggested edits on the methods they used. I do have several concerns with the data, which I will elaborate below.

First, what is the origin of the P. phocoena ears? P. phocoena has a wide distribution, and populations in different parts of their range have a significant degree of morphologic and genetic differences. The case in this paper is much stronger if these all derive from a single geographic region or population. Furthermore, if there are specimens from, say the Pacific and Atlantic, does some of the variation observed reflect those differences in population? This needs to be spelled out more clearly in the paper. I would also suggest the authors state how many specimens are right vs left, given that the paper mentions some evidence of bilateral asymmetry in these structures. Does this account for some of the variation observed?

My second major concern focuses on the interspecific variation, particularly the classification of odontocetes by habitat, diet, and feeding mode. Although definition for some of these classifications, such as diving depth and hearing type are explicitly described, classification of the prior categories is left vague.

There is an extensive degree of variation in habitat use, so what particular parameters are used to define an animal as nearshore and offshore. I will note that the authors seem to be aware of this particular issue, as unmentioned in the text but illustrated in the relevant figure are categories that combine multiple habitat types (for instance nearshore/offshore as a separate category.

Similarly, I assume fish specialists are taxa whose diets consist of more than 50% fish, while generalists have a more equal fish versus squid ratio. But those proportions should be spelled out in the paper.

The same vagueness can be seen in classification of prey capture. Many odontocetes are capable of both raptorial and suction feeding.

In addition to more explicitly spelling out how these animals are characterized, there also needs to be references given here. And if all of these categorizations are simply following   classifications laid out in a past paper, that paper should be cited as the source.
Validity of the findings: This is a well put together paper, and other than some tweaks suggested above, I don't doubt the overall findings. Everything is clearly written, structured, and spelled out, and the conclusions seem solid with no real speculation inserted within.

About the only extra comment here I would have follows from my above suggestions. There should be an excel file or word table in the supplementary material which explicitly states all  of the classifications for each taxa, ideally with citations. As it currently stands, I don't know where the classifications are coming from nor what whale is under what category, which hampers interpretations of the plots in the supplemental material.

Otherwise however this is great
Additional comments: I only really noticed two sets of typos worth mentioning. First, I would reduce the use of SSL as an acronym, especially as there is one sentence that uses it twice, e.g. "Length of SSL (6) was measured to calculate percentage of extent of SSL (9)...". It would be easier to read if this was just spelled out.

For Figure S6, divetype and hearingtype should be each two separate words, as well as verydeep in the key. Mid should be changed to middle depth or something along those lines. I find it also slightly distracting that the order of the key goes from deep, mid, shallow, verydeep, rather than shallow, mid, deep, verydeep (or the reverse).

Otherwise I didn't notice much in the way of typos or grammatical edits.

Ultimately I really enjoyed reading this paper, and I think the study is excellent. I commend the authors on their work, and I look forward to seeing this published.

Best,

Morgan Churchill


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: INTRASPECIFIC VARIATION IN THE COCHLEAE OF HARBOUR PORPOISES (PHOCOENA PHOCOENA) AND ITS IMPLICATIONS FOR COMPARATIVE STUDIES ACROSS ODONTOCETES
Review round: 2
Reviewer: 1

Output:
Basic reporting: I still cannot agree that this manuscript passes the standard for clear, unambiguous, professional language.  My comments follow.  Please see the referee report.
Experimental design: Nothing to add.
Validity of the findings: Please see the referee report.
Additional comments: I carefully read the revised manuscript “Intraspecific variation in harbor porpoise (Phocoena phocoena) cochleae and its implications for comparative studies across odontocetes.”  Firstly, I appreciate many changes the authors made in response to various comments from the referees.  Secondly, however, I was disappointed to see rhetorical devices the authors set up in the revised text and their rebuttal to avoid addressing fundamental issues with the paper.  This is puzzling — They did a competent analysis, but continue to refuse putting their findings in a context.

Example: A recent paper by the same team of authors “Convergent evolution in toothed whale cochleae” (BMC Evolutionary Biology 19, 195) states the following conclusion: “The extreme acoustic environment of the deep ocean likely constrains cochlear shape, causing the cochlear morphology of sperm and beaked whales to converge. This study adds support for cochlear morphology being used to predict the ecology of extinct cetaceans.”
This manuscript can build on this paper by discussing how “low” levels of intraspecific variation supplements the ecological constraint argument, predicting how their findings can be generalized within odontocetes based on the ecology of harbor porpoises, and even providing some counterpoint: the fact that variations within harbor porpoises can still overlap with some mainly deep-water species (L 388–398) suggests there is more to it than ecology. What more?  Do regions of the cochlea more variable within harbor porpoises match regions showing ecologically constrained convergent evolution elsewhere in odontocetes? Or do they differ?
Instead, the authors touch on Park et al. (2019) by simply mentioning the intraspecific variations in harbor porpoises overlap with some shallow-water species and some mainly deep-water species. No further discussion is provided (L 388–398).

	Now, I would normally keep it to the manuscript and do not cite rebuttal by authors to argue my points, but in this case it is necessary as the authors chose to refute suggestions rhetorically, not scientifically.

	For example, they refuted suggestions of including images of cochleae or supplementary figures mentioned in the text as main figures: “Other reviewers and the editor have not suggested moving supplementary figures and tables” or “People don’t need to see every single cochleae image to understand the results of the paper. If they really want to look at them they are available in our online data.”
Here is my point: How does a paper with “intraspecific (morphological) variation of cochleae” in the title obstinately refuse to illustrate the very variations (or subtlety thereof) picking from many examples in the reconstructions they have — let alone showing a single image of the structure they study in the main figure?  They could do this by showing two reconstructions, one each from male and female, or young and adult, or any demographic extremes, to give the readers an idea how a cochlea looks like, and what levels of morphological variations they are dealing with.  They could do this by showing extreme shapes at each end of the PC axes. They could do this by showing examples of cochleae from different ecological guilds of odontocetes alongside one from a harbor porpoise to show interspecific variations far greater than intraspecific.  They could do this in a separate figure, or add them in the current figure.  They could even simply move one supplementary figure to the main paper to show landmarks.  They have tons of data in reconstructions they made, and it seems as just a matter of pulling images from the portal they listed in the manuscript.
They did none of this, and simply suggest go look into supplementary files.  If they are genuinely interested in communicating their results with colleagues who do not look at dolphin cochleae all the time, they should not resort to such sloppy excuses regardless of what other referees endorsed uncritically.

	This is unfortunate.  The analytical results are defensible, but the authors keep refusing to make seemingly easily attainable improvements that could help the paper become more accessible and useful.  So I continue to argue that this paper needs substantial revision to meet the presentation standard.

Rebuttal letter by the authors
Again, this is highly irregular to comment specifically on a rebuttal letter. However, the authors tried in the letter to justify changes that they did not make. So I will comment on some aspects of the letter to urge them consider their revision efforts seriously.

“The comment “any polymorphism in a species, however defined— is so broad that it means little without context”  could easily be applied to interspecific variation given that interspecific variation  also includes many sources of variation that are not identified.”
—	A straw man argument. While they are at it, interspecific variations are, however defined, systematically meaningful because of its context in interspecies. Intraspecific variations may be discrete variations among populations, sexes, habitats, or any biological factors that the species interacts with, and its systematic significance is unclear until putting it in any of those contexts. So, again, if their purpose is to serve future taxonomists, there are many things I suggested initially and in this round that help them address that. If their purpose is to delineate interactions between echolocation and morphology, there are things they can do to make a clear statement to that effect. They are doing neither.

“Intraspecific variation can meaningfully be defined as variation between species that are not species differences.”
—	I have no idea what they mean by this. Intraspecific variations are simply any variations that are not accounted for by species difference.

“We are focussing on the odontocete context as the reviewer notes. It therefore was outside the scope of the paper to cover intraspecific variation across all other species too.”
—	But they do discuss how general their findings may be across tetrapods in the manuscript. (e.g., L 438-440)

“Here we are describing intraspecific variation as a general concept, to clarify why it is important in populations and why it is present. In the line the reviewer is querying we are referring to work by Bolnick and colleagues.”
—	Why don’t they list examples more relevant to cochlea and its function? How relevant are predator defense or parasite resistance to an inner ear?

“The motivation of the study and why harbour porpoises and cochlear morphology was used is mentioned repeatedly throughout the study. As such we don’t see any justification for completely changing the framing of the paper, especially when reviewers 1 and 3 praised the writing and clarity of the original manuscript. ”
—	The authors argued “intraspecific variations are important to characterize” and “cochleae serve important functions” but never connected the two, for which they need some context. By the same logic, they could very well have looked at intraspecific variations in the entire endocasts as they scanned the skulls. Would that be more important?  I suggested, as in my comment previously, to bring in examples of diagnostic characters in the cochlea, or link echolocation to specific aspects of variations in the cochlear shape/size. It does not “completely change the framing of the paper.” It’s a clarification that helps their paper.

“We asked the editor about this and they agree these should stay in the supplemental. We think maintaining a narrative in a paper is more important than bombarding readers with all possible figures.”
—	I made the recommendation precisely so they could maintain the narrative. The narrative read rather broken and confusing, and it was even more disruptive to drop where one was reading and go look for that supplementary figure or table.  They referred to the materials in the main text as supporting evidence, not just raw or giant data tables. Why including them would break up their narrative?

“3D cochlear models can be constructed in different ways and using different techniques. The shape of the fenestra cochlearis varies between taxa, with some having a more circular opening and others having a more elliptical opening. This study and previous ones have used the formulae to calculate the area of these shapes as approximations of the area of the fenestra cochlearis. However, the fenestra cochlearis of each taxon must therefore be designated as one of these two shapes. This means that taxa with a fenestra cochlearis that isn’t exactly the same as its designated shape will have an incorrectly estimated area value.”
—	I think this is precisely the information they should be discussing instead of making a hand-waving mention about “artificial variation”. They can paste this response right into the main text. Why not do that?

“This is the discussion, these statements are speculative and based on interpreting our results along with other research on cetacean cochleae.”
“Again this is a discussion, where it seems pertinent to lay out possible caveats and limitations of the analyses and results. Most discussions contain this kind of information without a requirement to fix the whole field.”
—	Sure, but those speculations should be realistic, practical, and citable. This is where they could have included the information like their previous comment about reconstruction techniques, which clearly delineate potential sources of such ‘human errors’. I am rather puzzled why they did not.

“We have changed the word “true” to “complete” to allay some of these concerns. However, we feel this is an important caveat of the methods we are using.”
—	It’s still there (L 410).

“Often a huge amount of emphasis is placed on clusters visible in plots of PCs 1 and 2, but for highly multivariate data, like our 3D analyses here, PC1 may not actually reflect much of the variation in the data. Why do we still show these plots? They are standard for the field so omitting them would be strange. If another way to represent multivariate data in more than two/three dimensions on a page we would be delighted to use this, but the human brain, and print media, are limited to low dimensionality representations.”
—	Again, they could have inserted this response to the text and cite examples they found. To me, these caveats are simply common sense, and common sense requires no repeat unless there are cases of violations. If they can provide citations where these concerns directly apply, it’s worth discussing. But if everyone follows green light, is it worth telling them to not ignore red lights?

“The end section of the discussion, like most discussions, is speculative. We are saying that theory suggests that P.phocoena should be more variable than other species with narrower ranges and niches.”
—	And I am saying it does not logically follow, unless the authors can link variations with geographic ranges. Why should one expect A follows B? There are many “theories” that could support this “assumption” of theirs: population genetics, heterogeneity in habitat preferences across the range, patterns of variations in other aspects of anatomy, etc., relative to the generally defined odontocete background.

Comments on the main text (major)

I will first list technical/conceptual comments to which I call the editor’s attention.

L23–29
This is casting way too broadly.  It belongs in Introduction.
Also, low intraspecific variations do NOT necessarily mean "studies can proceed with only a few individuals." Small variations can still be morphologically discrete, taxonomically significant, but seemingly "low" when only overall shapes are considered -- consider bone textures, sutural forms, histological features, presence/absence of carinae, denticles, or other minor features, and many others.
My point here is that this is a wrong extrapolation, and this type of information that the authors can't substantiate doesn't belong in Abstract. Delete L23-27. Replace “Meaning that studies can proceed…” with “but this assumption is not usually tested.”
In any way, this narrative doesn’t work unless cochlear characters are cited as diagnostic in odontocete systematics.

L49 Introduction
This is supposed to provide context and justification: why cochleae? Why not, for example, endocasts?

L64-65
At whom are the authors pointing fingers?  Do they really think intraspecific variations are not "considered at all"?  Most taxonomic diagnosis is written with a list of traits, with considerations about intraspecific variations (e.g., those known to be variable intraspecifically in relatives are usually carefully omitted).  Just because they don't use the term in text does not mean they didn't consider intraspecific variation.

L97-98
The authors in their rebuttal letter state that there are taxonomically diagnostic characters in the cochleae.  What are those traits, and can their geometric methods capture those traits?  This is an important point to justify their study, but I still do not see it.  All they have to do is to cite some examples from odontocete descriptions.
In addition, why do they not discuss in details what they themselves have done with odontocete cochleae recently?

L102 Data collection
It appears that the authors have used the same data source as other studies (Park et al. 2019).  They could make their life easier by explicitly stating this.  Why downplay it?

L113
Why do the authors not say they used the same data?

L179-182
So what did they took? I don't understand what "cochleae data" mean.  Reconstructions on which their measurements and landmark data are based exist in the data portal as Martins et al. (2019). Linear measurements and landmark data also came from this dataset, or got transferred from Park et al. (2018 or 2019)?  Then what data did the authors actually collect SPECIFICALLY and NEW for this study?  It is entirely fair to say they used the preexisting dataset, rather than to be vague about what data they collected firsthand for this study.
And I will repeat this.  DO NOT use Latin binomial as an adjective.  It's not P. phocoena cochleae. It's cochleae of P. phocona.

L264-268
But how can they test and rule out left-right asymmetry when there are only three specimens represented by the right cochlea against 15 from the left side?

L361 “may reduce variation…”
Or increase? It is also possible that the reconstruction methods somehow underestimates whatever 'true' variations the authors seem to be envisioning.  Is a standardized protocol actually better at capturing morphology? or simply time-saving? If you assume intraspecific variations in bone densities, or collection and curation somehow affecting the quality of the specimens, or natural standing variations affected by any other factors, for example, a standardized protocol could actually increase noise.
I really think the authors should focus on what is practical, and what are realistic improvements they might expect.  They do not have to create the narrative of false positives (or negatives).
Also: Is large variation bad? They seem to imply it in this paragraph.

L375-376
values of CV, or relative degrees or magnitudes of variations more generally? CV values are dependent on the dataset, so won't those be incomparable, strictly speaking?
L409-411
No.  This is a given.  If they are not communicating the 'true results of multivariate analyses" clearly in this paper, then it would defeat the purpose of the entire paper.  Why do they undermine themselves like that?
I think they are trying to say something, but are using wrong words to describe it and I cannot guess what it is instead.

L413-414
It's given for PCA. Again, they are basically implying here that there is more to their analysis than they show in Fig. 1.  If they cannot communicate exactly what, then they are not communicating their interpretations of their own results clearly.

L415-421
To what choir are they preaching as if they invented the method?  If they are to tell colleagues how to do PCA, they should cite where people failed to do this.  I cannot think of an example.

L421-424
Once again, PCAs based on different datasets are NOT strictly comparable with each other.  Did they sample identical landmarks/traits from an identical set of specimens?  This is not a valid argument because they misunderstand PCA. What extra care exactly do the authors argue we need to take?

L431-433
How can they say that based on the study of a single species?  Because P. phocoena is a broadly distributed species and expected to interact with different regimes, because it is morphologically conservative in other aspects of anatomy, because population genetics of the species, like other odontocetes, suggest the species has standing genetic variations comparable to other species of odontocetes... Or?  They really need to address the assumption they are making to extrapolate P. phocoena onto the general trend among odontocetes.

L435-438
Why do you expect broad geographic ranges to enhance intraspecific variations? Make the logical link clear. This expectation may not be reasonable if the species is homogeneous about habitat usage and proportions of time spent in different habitats.  Any evidence supporting that claim? or any other lines of inference can they make (as in my comment above)?
Also, “false optimism” is a poor choice of words.

L438-440
Really, these studies are about relative degrees of intraspecific variation against arbitrary systematic background.  The authors here compared morphological variations against odontocetes, but is that really comparable whey other authors might have tested against a genus, family, etc? Are there not others that report measure of intraspecifc variations, and can they not support and draw some general conclusion like "regardless of systematic levels to a certain point, cochleae tend to be morphologically conservative.

L442-443
I asked this before and didn't get the answer: Is there any example of cochlear characters in odontocete diagnoses, and where this came under the discussion of taxonomic distinction?  If there is, that would be a useful thing this paper can mention and provide insights for.

Comments on the main text (minor)

I will follow these comments with more specific, grammatical/stylistic corrections.

L25 “In most comparative studies…”
In most morphological traits

L29 “This assumption is yet to be tested…”
Are the authors saying that intraspecific variation of any sort has never been tested in cetaceans? I find that hard to believe.

L 31 “Studies of cochlear variation are common in odontocetes…”
Interspecific variation of cochlear morphology is well characterized among odontocetes

L31-32 “Because of its importance in…”
Because of the importance of the structure in…

L34 “cochlear variation”
Variations in cochlear morphology

L63 “It is assumed…”
For most morphological traits, it is assumed…

L63 “levels”
magnitudes, or degrees

L63 “lower compared to…”
smaller than those of…

L65-66 “or using multiple specimens…”
“this assumption is not (or cannot be) tested either because of logistical constraints”

L66 “more specimens simply do not exist…”
“samples are limited”

L75 “for feeding, communicating and finding a mate”
Is that all, and are these examples even parallel with each other? (finding a mate can be, broadly, communication.)

L78 “due to”
“because of”

L79 “scanning them takes time and money”
“scanning them is logistically unreaslistic”

L81-82 and throughout
Something is wrong with their citation manager. Separate entries of Ekdale and Racicot et al. There are many other examples throughout the text by those and other authors. Fix them please.

L89-91 “comparing variation within the cochleae of 18 specimens of harbour porpoise (Phocoena phocoena) with cochlear variation across 51 other odontocete (toothed whale) species.”
“comparing morphological variation among the cochleae of 18 specimens harbor porpoise…with those across 51 other species of odontocetes (toothed whales).”

L92 and throughout
I repeat this until it sinks in.  DO NOT use Latin binomial as an adjective, period. Cetacean cochleae, and cochleae of Phocoena phocoena. The authors repeat this error throughout the text, including in the title.  The authors appeared to use "Replace" to make changes for "specimens of P. phocoena" but did not correct others.  Search for the binomial and fix throughout.

L115-117 “Of these 15 are from the left-hand side of the skull, and three from the right-hand side. 17 are from the UK Coast, and one is from the North Atlantic, four are female five are male and 11 are unsexed (see Table S3). All specimens are adult animals.”
“Of these 15 are from the left-hand side of the skull, and three from the right-hand side; 17 are from the UK Coast, and one is from the North Atlantic; four are female, five are male, and 11 are unsexed (see Table S3).”

L123 “Figure S1”
What is their justification NOT to put it in the main figure?  Puzzling.

L254 “so on”
What on?  Until what? What they are describing here is pairwise comparison for GPA, PCA, and MANOVA, followed by every combination of three specimens, and SO ON UNTIL reaching every combination of 17 specimens?

L258 “other Phocoena species”
Either "other species of Phoena" or "other Phocoena spp."

L295 “basal ratio and extent of”
Extent of what?

L332 “speciemns of P. phocoena”
I noticed this elsewhere and am only making a note of this here.  I'm not a native English writer but don't they need "the" for this and some (many) of these elsewhere in the text, given context?

L337 “Variation in…”
Also, distinguish variation versus variations.  I think it should be plural here. “Morphological variations in the cochleae of P. phocoena were not…”

L339-341
"...was significantly correlated with XXX, but was significantly correlated with YYY..."  Something is wrong here.  Either: A is significantly correlated with B and C; or A is significantly correlated with B but not C.

L342 “0.038, although after…”
“0.038; after…”

L353 “cochlear variation”
“those”

L357
What is moderate variation? Moderate relative to what?

L366 “biggest”
greatest, or largest

L379 “within specimens of…”
“among the specimens of…”

L384 (but see below)
Why don’t they refer to Fig. 1 here?