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: DNA BARCODE-BASED SURVEY OF TRICHOPTERA IN THE CROOKED RIVER REVEALS THREE NEW SPECIES RECORDS FOR BRITISH COLUMBIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: 1. The initial paragraphs of the introduction lead the reader to understand the importance of determining the biodiversity in an impacted area. However, when describing the studies area, I consider that the information from line 53 until line 74 could be summarized in a couple of lines. This information, although interesting in general, lead to ambiguity. I would recommend condensing this information.

2. In line 78, The objective number 2, states that they want to explore the biodiversity of Trichoptera. However, biodiversity has several components (alpha, beta, gamma diversity, abundance indices, ecological diversity, functional diversity, etc) that were not analyzed in this study. They only analyzed species richness and that was stated in objective 1. The objective 3 is redundant since that is expected in objective 1. I would recommend being concise with the aims and the reach of this study.

3. the sentence on line 148-150 is very confusing. The idea between DNA and morphological species identification is not clear. Please clarify this sentence.
Experimental design: The corrections suggested were done and the methods look more clear and concise. There are objectives, they were developed and the results were totally within their framework.
Validity of the findings: This study as a baseline will be very important for future references, especially in isolated areas that are impacted by human activities.

The data collected and analyzed provide support to his conclusions and can be used as a reference in future studies.
Additional comments: The corrections made by the authors were key to give clarity and relevance to this study. There are minor corrections that should be done and I mentioned above, but I recommend this paper 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: DNA BARCODE-BASED SURVEY OF TRICHOPTERA IN THE CROOKED RIVER REVEALS THREE NEW SPECIES RECORDS FOR BRITISH COLUMBIA
Review round: 2
Reviewer: 2

Output:
Basic reporting: Ok
Experimental design: OK
Validity of the findings: OK, although I still think the record of C. hardwoodi should be presented with some degree of uncertainty.
Additional comments: Several typographical and other errors that should be corrected and the whole paper proofread very carefully.  Note comment on use of parentheses for species authors' names. Ensure bibliography is properly formatted to journal style.


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: ACHILLES HEEL OF A POWERFUL INVADER: RESTRICTIONS ON DISTRIBUTION AND DISAPPEARANCE OF FERAL PIGS FROM A PROTECTED AREA IN NORTHERN PANTANAL, WESTERN BRAZIL
Review round: 1
Reviewer: 1

Output:
Basic reporting: The study deals with an important issue in Brazil (feral pig invasion) and with an interesting ecological question (why did the specie disappear in a Protected Area?) with considered applicability to conservation strategies (invasive species control). However, the study failed to properly describe the situation (Specie disappearance), there were misleading use of concepts (Potential niche x occurrence of specie), the methods lack more details for evaluation (RDA and SDM), and the analysis and results could be substantially improved:

1 –Specie disappearance:
The manuscript is ambiguous and unclear for the situation about the disappearance of the species in the PA. It is plausible the concentration of S.scrofa population has moved from PA to the adjacent cattle ranch due to the land use change. This phenomenon is really interesting, novel and useful for decision making regards to specie’s control. However, the specie’s condition was not clear to the readers till the Discussion section. Is strongly recommend to be fair with the readers since the beginning.
Actually, the specie didn´t disappear from PA as pointed out along the text (Title, Abstract and Introduction). At "Study area" section, it was clear the species still there: "Park rangers report that visual records of feral pigs were extremely rare and the species is seldom recorded". The Results section unfortunately failed to inform information about the presence/absence. By the other hand, the Discussion section started with "The low number of records of feral pigs in the PA..." and gave the impression the specie’s abundance in PA was low but it has not disappeared. The specie´s disappearance is a key situation for the study and it must be properly describe for the readers and for better evaluation.
Moreover, the apparent specie´s abundance reduction was based on the informal observation in the past in the two areas (PA and the adjacent cattle ranch). However, there were no measure of abundance for spatial and temporal comparison between them and the population concentration could be superficial, especially by considering the distance between the areas. The two areas are very close for the biology of the specie and it is likely there is only one population with the same variation in both areas. The population reduction in PA could happen in both areas and the study was unable to detect and demonstrate it. In regards of high sampling effort with few specie’s records, it is plausible to considered the current low S.scrofa abundance in PA, but there is no such information to the other area for proper comparison. The so called disappearance could be an overall phenomenon within the region, the municipality of Barão de Melgaço, without relationship with the PA effect.

2 - Potential niche x occurrence of specie
The effect of PA in occurrence of specie is the key issue for the study goals: “(i) identifying the spatial distribution patterns of feral pigs and (ii) inferring about the effect of landscape change, due to the implantation of a Protected Area (PA), in the occurrence of the species”. To these goals, the occurrence must be somehow measured in the field like occupancy (e.g., Mackenzie et al., 2006 - “Occupancy Estimation and Modeling” ). However, the study used the potential niche for this goal instead. The occurrence was then an extrapolation of the niche theory and not the proper measuring in nature. The study considered potential niche as “probability of presence” (Figure 4), i.e., a kind of “potential presence”. Therefore, the study was reduce to a merely description of the potential niche variation in the study area and it had limitations to the inference about the true PA effect on the specie occurrence.
Furthermore, the potential niche was dependent on 69 current records of the specie and it can results in biased estimation to the present and past niche/occurrence. The method has the assumption of unreal perfect detectability and it can easily be violated by false absence (e.g., Mackenzie et al., 2006 - “Occupancy Estimation and Modeling” ).
The data base for the potential niche modeling also need more details for better evaluation of this method as described below.
For this case and goals, I suggest using proper methods for occurrence other than potential niche, like occupancy models.

3 – More detail need for RDA and SDM
Multivariate analysis like RDA are proper evaluated with the complete results of axis and not only percentage of explained variation by each axis (Fig. 2). The complete results can be provided as table in supplementary material but it is also interesting to plot the results against the explanatory variable and ordering them to highlight the main effect.
Species Distribution Models (SDM) used in this study was based in 69 records of the species without more details. It fundamental to provide more details for better of evaluation of this method as such its geography distribution (e.g., in the map, Fig. 1) and how they were collected (camtraps only or all data of field effort like the monitored natural licks and artificial pounds). I suggest providing this information on the text and, if it was the case, I discourage the use of data based on the monitored natural licks and artificial pounds because they can work as attractive site and biased the presence and then the potential niche estimation.

4 – Analysis and results improvements
As many other invasion biology case, the human dimension is an important issue. However, the study was limited by considering only ecological variables. The results can be very biased because the variable comparison is based on relative importance. I suggest including in the analysis a human variable like the distance of settlement or other one that represent the influence of human mediated invasion.
For PA effect, the cattle was removed as well as the human presence with their culture (wild pig management) and livestock (free range system of domesticated pigs). The feral pigs in Pantanal is reported and known as an abundant and old population, but it still unclear how much the real human presence conserve this population by local management with constant introduction  (free range of domesticated pigs) and cultural hunting (Desbiez et al., 2011). This alternative interpretation does not reject the Authors´ one, but the article could have interesting improvement by considering human influence in this invasion biology. So far, the analysis have the assumption this invasion is strong dependent of biology of the species (dependent of "changes in the landscape and vegetation structure"), but the indirect human influence can much stronger. The management of cattle changes the landscape, but it also means constant human presence with their externalities as such conserving the wild pig population in higher abundance with protection (captive pigs close to the house) followed by constant restocking (scapeing pigs) and  biased harvest (preferable male hunting and some female care). The Achilles heel of S.scrofa can be the amount of propagule and restocking. An extra variable considering the human influence can improve the analysis.
Experimental design: The Index of Use (IU) has several limitations for the analysis and it could be replaced by other index or analysis. The first limitation is the spatial dependence of the camtrap sites. The minimum of 600 m is not enough for S.scrofa, puma and jaguar because the species has wider home range in 15-28 days. The same animal can use several sites and overestimate the IU. An alternative is to test the dependence for each species reducing the intervals as it was done for shots intervals. I suggest at least justifying clear the reason to use the sampling interval in each site.
The other limitation of IU was the assumption of the perfect and constant detection within and among species. The Authors should consider this index (IU) has the naïve assumption of perfect detection, i.e. when the species are presence at the site, it is always recorded and it scores the index; otherwise when the specie are absent the specie is not recorded. Thus, there is no false absence. The detection is also equal for all sites and all species has the same detection probability. However, it is expected different detection probability among sites, i.e. difference between forest and open area, for example. In the same manner, jaguar sounds more difficult to detect than puma and S.scrofa. It is very important then to control the detectability for this analysis. For this issue, I suggest the use of occupancy models (Mackenzie et al., 2006 - “Occupancy Estimation and Modeling” ).
Validity of the findings: The findings were very interesting but dependent on the kind of variables (only ecological variable) and spatial dimension for the species.
It is important to consider human variable to balance the relative importance among ecological variable. Such variables can be justified by the conflict of interest and it has important implications for controlling the specie in other parts of Pantanal, as the Author justify in the Introduction section ("direct conservation decision-making"). The conflict of interest was an important reason to consider the S. scrofa among the 100 of the world’s worst invasive alien species (Lowe et al., 2004) and its control depend on the overcome of this feature (Choqnot et al., 1996, Lowe et al., 2004). Without controlling the human influence, it is difficult to eradicate feral population.
The findings (“strong relationship with pasture”) can also be biased by the spatial dimension of the study because it was very narrow for the species. The results can just be a local effect of abundance variation or reduction of the abundance in the periphery of the local population´s range. In wider geography scale, the findings was not expected because the invasion is very old (>200 year old) and the species had been restricted to the Pantanal biome for centuries even with land use change around to open area like pasture-like system. For some reason, the species have not invaded the rest of Brazil even with enough time and favorable land use change.
These considerations don’t compete with the original propose. They are just a complement.  The suggestion can change the analysis but improve the interpretation, match the real invasion situation of the species in this country and provide more insights for decision making.
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: ACHILLES HEEL OF A POWERFUL INVADER: RESTRICTIONS ON DISTRIBUTION AND DISAPPEARANCE OF FERAL PIGS FROM A PROTECTED AREA IN NORTHERN PANTANAL, WESTERN BRAZIL
Review round: 1
Reviewer: 2

Output:
Basic reporting: The study deals with feral pig invasion, a relevant problem worldwide and an important issue in Brazil . The authors, properly describe the past and current situation at the study area, and  try to answer very interesting ecological questions applying proper research methods and analysis. Adittionaly, the study is very important for conservation strategies and invasive species control.
Experimental design: Like in most biological invasions, in the studied case, the human dimension is an important topic. However, the study was focused only in ecological variables. The importance of invasion history is also underestimated.  It would be relevant to include in the analysis historical data about the micro invation within Pantanal, and a human variable like the distance of settlement or other one that represent the influence  of human assisted invasions in the modelling.
Also, I recommend that, whenever feasible, similar macro-scale approaches to the species distribution modeling are pursued to capture the extent of conditions that support the species populations and generate hypotheses about species limitations or invasion potential that can be tested in combination with this type of finer-scale research.
Validity of the findings: Although long-term movement data for wild pigs is lacking in South America, social factors such as value of wild pigs as a recreational hunting resource or as farmed species are at least as important as natural dispersal in driving the current distribution of wild pigs. As such, we recommend that future research investigating the distribution and invasiveness of wild pigs should include social factors in addition to biological factors (what biotic and abiotic factors limit wild pigs populations?) to address competing hypotheses and generate effective management solutions.
Despite of this, I strongly recommend the publication of this very interesting 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: CRUSTACEAN AMPHIPODS FROM MARSH PONDS: A NUTRITIOUS FEED RESOURCE WITH POTENTIAL FOR APPLICATION IN INTEGRATED MULTI-TROPHIC AQUACULTURE
Review round: 1
Reviewer: 1

Output:
Basic reporting: - The English language should be improved throughout the manuscript to ensure a clear understanding of the information by an international audience.
Some examples where the language could be improved include lines 20, 24, 28, 35-36, 49, 51, 60-70, 74,78, 103, 105, 123, 324, 327, 332, 339, 345, 385, 433, 437,443, 682, 689, 696, 703, 708.
Phrasing employed and sentence construction in the following lines makes the comprehension difficult. 16-18, 51-53, 80-82, 336-337, 341-343,367-372, 389-391, 422-425,443-445.
- The structure of the introduction as well as the background description does not clearly demonstrate how the work fits into the broader field of knowledge. Moreover the literature referring specifically to the field of study is limited and should be further developed to include references related to various aquaculture species nutritional requirements.
- The structure of the article is conform to an acceptable format of ‘standard sections’
- Figures are relevant to the content of the article, of sufficient resolution, and appropriately described and labeled.
- The raw data provided does not appear as machine-readable format as it appears as table and figure.
Experimental design: - The manuscripts describes original primary research within Aims and Scope of the journal.
- The research hypothesis is relevant & meaningful for the development of sustainable aquaculture practices, however it is not clearly defined and does not clearly state the aims to fill a given knowledge gap.
- Ethic statement is not provided and might not be applicable considering the field of study.
- The biochemical analysis and statistical analyses methods are clearly described, however the general experimental design is questionable to reach the proposed conclusions taking into account the restricted sampling period (1 week) and the number of replicates (n=2).
Validity of the findings: - The data on which the conclusions are based is robust and statistically sound within the restricted limits of the study, however it can be considered incomplete to reach the proposed conclusions given the limited time during which the samples were collected. Considering the recognized effects that environmental parameters and seasons have on the characteristics and specificity of the species studied, analysis of various replicates at different sampling periods would be required to support discussion, conclusions and recommendations about the species to be intensively cultures as alternative feed sources.
- Part of the discussion focusing on the general field of study is limited and should be further developed to illustrate diverse potentials of alternative sustainable feed sources for aquaculture production.
-Generally the discussion is referring to studies performed out of the scope of the field of study of the research undertaken making the global comprehension difficult.
- Part of the discussion referring to IMTA is not plainly justified considering that it is not clearly stated that the experimental samples were collected within IMTA systems.
- L 311: Please indicate the larval species the text is referring to.
- L 362-363: Please provide the references.
Additional comments: The manuscript is of interest considering the quest to provide sustainable alternative feed sources for the further development of aquaculture, however it requires significant major revisions and various points (indicated in the review) which should be improved upon before acceptance.


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: CRUSTACEAN AMPHIPODS FROM MARSH PONDS: A NUTRITIOUS FEED RESOURCE WITH POTENTIAL FOR APPLICATION IN INTEGRATED MULTI-TROPHIC AQUACULTURE
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is in general well written.
Experimental design: The mean values are a result of only two measurements (n=2). However since there are no experimental treatments (this is just a decription of the composition), and each sample consists of many individuals I consider this acceptable.
Validity of the findings: The authors present the idea as a novelty, however this is not new. In pond culture (often freshwater), this is an often used technique in extensive culture systems. Whether this will be a realistic scenario for large scale production remains to be seen however that is not in the scope of this article. The data seems to be robust and is discussed in the light of previous studies.

The PCA plots are mentioned in the results, however do not come back in the discussion. I do not see the clear purpose of these plots and suggest to only include the tables.
Additional comments: Major comments:
The authors use the terms ‘trace/major metals’, ‘trace elements and metals’ trace and major elements’, etc. I would recommend to use elements for both the trace and the major ones. Many of the elements mentioned are not metals.
The authors describe that the prey collected in these ponds are lower in heavy metals than prey caught in other locations. The abundance of Ulva sp. could be a reason for this as this green algae is known to readily accumulate heavy metals and thus might lower the concentration in the water. (This is just a comment and does not have to be included in the article).

Minor comments:
Keywords
I am not sure what ‘major metal’ as a keyword means

Abstract
Line 33: change ‘alternatives preys’ into ‘alternative prey’
Line 38: Calcium should not be written with a capital, just ‘calcium’

Introduction
Line 51: change ‘Sothern’ into ‘Southern’
Line 62: change ‘optimum’ into ‘optimal’
Line 62: remove ‘high’
Line 75: ‘depends on limited and overexploited fisheries’. The fisheries is finite (limited) but it is not reasonable to call all the fisheries overexploited. Moreover, a substantial part of the fish meal and fish oil is now coming from fish slaughter waste.
Line 94-96: Furthermore, ….in aquaculture. In this senctence ‘elements’ would be a better word than ‘metals’. Also, the suitability of the prey is not evaluated, it is their nutritional composition that is evaluated. Please change.

M&M
Line 123: I presume the samples were weighed before and after burning so include ‘gravimetrically’ before determined.

Statistical analysis:
Lines 190-191: Sentence can be taken away

Discussion
The discussion starts with the argument of overfishing, but that FAO report does not distinguish between fisheries for human consumption and for fish meal production. The argument of fisheries having (over)reached its limits and fish meal being a finite resource, meaning that if we want to increase the fish feed production we have to find alternatives makes a scientifically more correct argument.

Lastly, the authors suggest this as a possibility for extensive fish farming. It would be nice to see a few lines on the possible environmental impacts of this type of farming when it will find a market since it will put more pressure on the marshlands (or not?).


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

Input:
Title: A NEW SMALL-BODIED ORNITHOPOD (DINOSAURIA, ORNITHISCHIA) FROM A DEEP, HIGH-ENERGY EARLY CRETACEOUS RIVER OF THE AUSTRALIAN–ANTARCTIC RIFT SYSTEM
Review round: 1
Reviewer: 1

Output:
Basic reporting: The ms is well writen and provides good new and relevant information on both the geology of the site and anatomical characteristics of the specimens. The ms is supported by relevant and complete references from the available literature.
I would recommend further elaboration and discussion about the phylogeny of the new taxon.
Figures of osteological elements should have the same standarized scale bars in all of them. I recommend using a single bar, without subdivisions, indicating the scale (1 mm, 1 cm, 10 cm, etc).
Experimental design: The new taxon should be supported within a phylogenetic context. There are several data matrices that the authors can use. The diagnosis based on authapomorpies is ok but it is important that combination of other characters be supported by a phylogenetical analysis.
Validity of the findings: As said above, a phylogenetic analysis of the new form within the Ornithopoda clade is mandatory. Some of the putative autapomorphies proposed by the authors could be unveiled as homoplasies or ambiguously distributed features.
Authors need to provide data sets of characters, with the new taxon properly scored, and a posible phylogenetical position of it.
Additional comments: The ms is an important contribution about the poorly known ornithopod diversity from Australia. I encourage the authors to work a little deeper on the phylogeny of the new taxon.


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

Input:
Title: A NEW SMALL-BODIED ORNITHOPOD (DINOSAURIA, ORNITHISCHIA) FROM A DEEP, HIGH-ENERGY EARLY CRETACEOUS RIVER OF THE AUSTRALIAN–ANTARCTIC RIFT SYSTEM
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is clearly written, professional and unambiguous it its language.  The introduction and context for the article are sufficiently developed, and the appropriate literature is cited.  The body of the description is very thorough, and the quality and number of figures exceeds normal requirements. The measurement raw data are shared (when possible), with exceptions where ratios are provided without the raw data. The CT scan data/3D models do not appear to be included in the submission. The paper is self-contained and does not contain extraneous information. Hypotheses are not clearly laid out or tested, but given that it is a taxonomic description this is not expected.
Experimental design: This represented original research, and falls within the Aims and Scope of the journal.  The research questions are defined and of interest to the pertinent scientific community.  The investigations performed were thorough and rigorous. The anatomical description is very detailed and of high technical standard. There are minor issues with the limited quantitative analyses performed. It would have been helpful to see the specimen/taxon placed in a cladistic context, and while this is not required its absence should at least be explained/justified. For the most part, documentation of the mythologies is sufficient for replication (and I was able to replicate several of the results), but more details on CT scanning an measurements would be useful.
Validity of the findings: The conclusions are clearly stated and backed up by the body of the paper. The data presented are accurate (with a few minor exceptions). Speculations do not over extend past those supported by the data.
Additional comments: General comments:

This is a very thorough anatomical treatment of interesting small-bodied ornithischian material from the Early Cretaceous of Australia. The anatomical description is very thorough, and I was surprised by the amount of description given the limited nature of the specimen.  I am very happy with the separation of the description from the comparison (although this slips up in a few places - especially the end).  The number and quality of the illustrations is excellent. It is a good contribution to the field and will be a very useful paper and resource.

While I do not doubt that this is a distinct and diagnosable taxon, I do have some concerns over the diagnosis.   There are a large number of proposed autapomorphies for such limited material, and for material that is often not regarded are being overly diagnostic for related taxa. While some of these are autapomorphies, and many of them are strong and likely to be robust in future analyses (e.g., 2, 3, 7), the bulk of these features are not apomorphic.  For these other features, a list of taxa that share this feature should be provided, and would be greatly beneficial.  Some proposed autapomorphies (e.g., 4) are actually several features that are grouped together to form and ‘autapomorphy’. Rather than one large list, it would be more useful to break it down into two categories: firstly proposed autapomorphies and secondly other characters which can be used to differentiate from taxon XX.  I do prefer the discrete autapomorphies over those based on relative proportions, especially when considering the effect of size/growth on these features.

While I appreciate the use of quantitative data to show differences in proportions between taxa (Figure 28, S5, S7, S8) I do not believe the simple comparisons of ratios is the most useful test. A ratio has two components, the numerator and denominator, but when two ratios are different you do not know if that is due to a difference in the numerator or denominator (or both). Likewise when two ratios are the same, you have no context of the absolute size of the elements. Since you need both the numerator and denominator to calculate a ratio, it is far more informative to simply plot these against each other in the graph.  If you log both axes, any line with a slope is 1 represents a constant ratio.  To illustrate this, I have taken the raw data (where available) from Table S3, and quickly plotted it up as series of ratios, and also in a bloxplot (colour-coded for taxa) (see attached).  This allows for an examination of relative size (position along a line of slope = -1) and absolute size (position along a line of slope = 1)  to be observed at the same time(I realized I switched the axes, but the point is the same). All points falling along the diagonal lines (slope of 1) in the figure will have the same ratio. Boiling down a biplot of numerator/denominator sets into a series of ratios is the mathematical equivalent of projecting the 2D data of a graph onto a 1D line (specifically a line with a slope of -1).  While I appreciate the need to reduce the number of axes when that number is greater than three, our minds are very good at teasing out relationship in 2D space, and there is no reason to simplify these data into 1D space. Doing so removes a lot of the useful data, specifically absolute size, and which of the ratio components is changing.  That being said, I do not this that this is a huge issue with the paper, it is just a better way to present the data, and can hopefully be incorporated.

The original data for the described specimen are provided (Tables 2-5) which is very good. Some of the data for the other taxa used for comparisons are presented (Table S2, S3, S4) which is great, but the majority of the data presented are not the raw data, but the ratio between two metrics. The raw data cannot be back-calculated from these ratios, and (as argued above) ratios have limited use compared to plotting up the raw data. Including the raw would both allow for better current analyses, and will serve the science better moving forward.

There are several errors in the tables, which are either math errors or typos (I can’t tell which).  For example, the ratios for two of the seven taxa (Mattaburasaurus and Parksosaurus) in table S2 cannot be obtained from the supplied raw data.  I only really checked out this table (because it has the most raw data), but a thorough check of the remaining math should be done.

The lack of cladistics analysis is confusing.  I am not suggesting that one should always be required when a new taxon is described - there are several reasons why this may not be the case. However, if one is discussing potential relationships of the new animal in both the abstract and conclusion, it is reasonable to expect a cladistics framework, or a justification as to why this was not done. In this case I suspect the analysis will result in a low resolution, large polytomy, due to the nature of the material and poor character scoring in these anatomic regions in related taxa. If this is the case, explain why and it may help convince others to look for characters in these areas. If one is planned, indicate that as well.

As far as I can tell the CT data and/or resulting 3D digital models are not included in the supplementary materials. Inclusion of these data may be required to be consistent with PeerJ data sharing policies. I will leave that decision to the editor.

All in all, a great paper about an exciting specimen/taxon. I am looking forward to seeing it published.

Specific comments:

Throughout the document “zygopophysis”/”zygapophysis” are used seemingly interchangeably. There may a reason for this, but if not, use a consistent spelling.

Line 85 – “hyperextended” is this mean to indicate ‘elongate’?

Line 97 – the first usage of “Eric the Red West” should include the abbreviation ‘ETRW’ that is used in the rest of the paper

Line 130 - One minor omission to the methods is the details as to how the measurements were obtained. Where they obtained by calipers, tape, or digitally from the CT scans?

Line 135 – What voltage and amperage were the CT scans performed at?

Line 147 – the 11% intervertebral gap that was added needs more explanation. Presumably this was added to more accurate reconstruct the length lost due to intervertebral disks? Since the tail is still largely articulated, I have a hard time understanding how the disk lengths could be lost while retaining articulation (since the soft tissue is what is holding it all together).

Line 397 – It is unclear what is meant by a “linear” spinal process.  Are these not all linear?  Does this mean thin? Straight? Of  constant thickness?

Line 445-446 – There is an apparent conflict.  The first line suggests that the sutures are difficult to distinguish past Ca8, yet the second line discusses the position of the sutures on Ca10 and ca13?

Line 471 – “The centrum OF the referred…”

Line 487 – “… the anterior and posterior margins of the spinal processes are parallel AND OF CONSTANT ANTEROPOSTERIOR WIDTH…..”  This this is intended meaning?  If so it should be clarified more.

Line 488 – I do not understand the intended meaning of “The dorsal tips of these spinal processes are convex and their ventral tips, angular”

Line 490 – “Proximately narrow” do you mean “proximally constricted”

Line 501 – “linear” is this meant to indicate straight?

Line 512 – I think the incorrect figure is referred to here.  Do you mean Figure 12?

Line 514/5 – Here is the first comparison in a so far comparison free description.

Line 565/5 – Other comparisons. I am not overly bothered by this, but is does break down the nice discrete sections you have established.

Line 599 – The term “restoration” is unclear. Would “digital 3D model” or similar work better?

Line 630 – “The distal (‘dorsal’) margin is obtuse”  I am unclear what this is trying to say. How can the distal margin of the tarsal element also be the dorsal margin?

Line 681 – It is unclear what is meant by “less-derived ornithopods”.  This is a vague and imprecise term. Do you mean ‘non-iguanodontian ornithopods”?

Line 819 - “length centrum” should be “centrum length”

Line 857 and 861 – “Parksosaurus warreni”

Line 865 – “C. browni”should be italicised.

Line 984 – two successive periods

Line 1193 – It is unclear what is meant by “linear along their length”.  Does this mean straight?

Line 1275 – It may be helpful to end this section with a statement similar to… “Future cladistic analyses may help to test these hypotheses of relationships.

Line 1334 – The Anderson et al 1985 is a bit out of date.  It may be good to also refer to the updated Campione et al 2014 (Meth in Ecol Evol) paper.

Figures 9, 10, 20, 21, 22, 23, 24, 25, 26, 27,  31A , 33 – Rather than simply describe these as “virtual” I would suggest “Digital 3D models” or similar. It is just a more specific description of what they are.

Figure 16 – Label “C” is in the wrong position. I think most people will be able to figure out that it pertains to the image on the left, but an arrow may help.


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

Input:
Title: A NEW SMALL-BODIED ORNITHOPOD (DINOSAURIA, ORNITHISCHIA) FROM A DEEP, HIGH-ENERGY EARLY CRETACEOUS RIVER OF THE AUSTRALIAN–ANTARCTIC RIFT SYSTEM
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: A few speculative statements in the anatomical descriptions should be moved to the discussion or removed. These are discussed in my comments below.
Additional comments: This paper presents a thorough description of a specimen that is important in understanding the taxonomy of Australian ornithopods. I particularly appreciate the thorough description of the geological context (at both a macro scale and at the quarry level), and the many figures showing the details of the anatomy of this specimen.

The descriptions of the anatomy would be improved by remaining focused on features that can be directly observed and refraining from speculation about things like the location of muscles. This can be included in the discussion section of the paper, but clutters the description section. There are also some features that are discussed, notably the tprl and the abductor groove on MT II, that are not clear in the figures. The models created from CT scans have low resolution, and while these are still useful in showing certain features not visible in the photographs, small features are not clear in these images. There are still clear autapormorphies of this specimen that can be discussed: I would advise emphasizing these to clean up the description section and make it more focused.
Additionally, lists of proportions can clutter a description with superfluous information. An example here, from the description of pedal digit I-1: “The proximodistal length of pd I-1 is 47% that of mt I and 27% that of mt III. The transverse width of pd I-1 at its proximal end is 56% that of proximal pd II-1 and the dorsoplantar depth, 50% that of proximal pd II-1.” These measurements are all available in Table 5—unless a particular proportion is something that is diagnostic or will be highlighted in the discussion in comparison to other taxa, it need not be listed in the written description.

Based on the evidence presented, I’m unconvinced by the pathology section. I would want to see either close-up photos or histological sections of the affected areas—this is something where surface texture is important, so CT imagery is not a useful figure to demonstrate this. In short, I would like to see a more convincing figure demonstrating the pathology. Otherwise, I would simply remove this section.

In terms of phylogeny, it would be worth mentioning or considering the analysis of Boyd (2015), in which many of the taxa referred to in this text as basal ornithopods are in fact recovered as basal neornithischians outside of Ornithopoda. While you can certainly disagree with those findings and continue referring to these taxa as basal ornithopods, this alternative phylogeny should at least be mentioned.

On the topic of terminology, there is a mixture in this manuscript of the terms anterior/posterior and cranial/caudal. While either set of terms is fine, please pick one and stick with it for consistency and clarity. There also seems to be no abbreviation of genus names—after the first use of a binomial, the genus can be abbreviated.

When multiple references are cited, they should be put in chronological order.

Again, I applaud the authors’ thoroughness in describing and illustrating this specimen, and I look forward to the publication of the manuscript. Following is a list of specific comments and suggestions for improving the manuscript. Attached is a pdf containing further edits—these are simply minor grammar/spelling/punctuation errors.

Line 97: insert (ETRW) after first use of the full name “Eric the Red West”
Line 269-78: The Interpretation of the Anchor Sandstone says paleosol deposits overlie the lake deposits, but the caption of figure 5A says the Anchor Ss has “shallow lacustrine at top”.
Line 384: I realize this is a diagnosis, not a phylogenetic systematic analysis, but I think that breaking features down in a systematic way can be instructive. Features 4 and 5 are each three different features, with some overlap between them. Feature 4 deals with (a) shape of the spinal process, (b) length of  the spinal process, and (c) orientation of the spinal process. If each of these features are unique and useful in diagnosing Diluvicursor, they should be listed separately. Feature 5 is about the height of the neural arch, which is tightly tied to length of the neural spine already covered in feature 4. You compare it here to three different measurements, but each of these can also vary between species (thus, they are separate characters). I would stick to one reference point, probably centrum height, as a comparison. Comparing the height of the neural arch to the length of the transverse process is a different feature, since that number is highly dependent on the length of the transverse processes (which is covered in feature 6). There are similar issues with feature 11.
Line 398-9: You need to be more specific in your shape descriptions. What, precisely, is the difference between “boot-shaped” and “hatchet-shaped”?
Line 578-82: The terms “hatchet-shaped” and “boot-shaped” aren’t defined here. It would be helpful to describe the discrete features here: are the proximal and distal edges of the hemal arch parallel? Does either edge diverge from the other? Is it symmetric or asymmetric? These are much more useful descriptions. Things like hatched-shaped and boot-shaped are fine as short-hand descriptions for continued discussion of the features, but they need to be defined in a more rigorous way at some point in the manuscript.
Line 613: “The fibula is anterolaterally positioned relative to the tibia.” But you note later that the fibula is displaced. Because of that, I would avoid discussing the relative positions of the tibia and fibula, unless there is other evidence of their anatomical relationship.
Line 614: You refer to a condyle on the fibula, but previously discussed malleoli on the tibia. If using the term malleolus, you should use this for the lateral malleolus of the fibula as well.
Line 630: “The distal (‘dorsal’) margin…” I don’t understand how a feature on the astragalus is both distal and dorsal. Inserting a sentence at the beginning of the description explaining the orientation you will use for your description of tarsal/metatarsal/phalangeal elements would be useful.
Line 656-7: “The metatarsus is compact, elongate and roughly cylindrical in shape.” I would describe this as an elliptical cylinder, as the cross section is oblong.
Line 660-5: This could all be shortened to something like: “Despite diagenetically imposed imbrication of the metatarsals, all elements are here described in life position.”
Line 675-7: “The M. extensor hallicus longus (e.g., White et al., 2016) that would have located within the extensor groove on the distal condyle, likely extended proximally along the medial margin of mt I and mt II.” This seems entirely speculative—I’m not sure what value it adds to the description.
Line 681-2: “…as in less-derived ornithopods”. Less-derived than what? I would use the term “basal ornithopods” here, or more technically, “basally-branching ornithopods”. But also see Boyd 2015: some of these taxa may not be ornithopods, and are better referred to as basally-branching neornithischians.
Line 728: “Adductor and abductor tendons could also have located within the medial and lateral grooves” (of mt III). This is rather speculative. In addition, interior digits are abducted and adducted by interosseous muscles and lumbricals. While these could be termed “abductors” and “adductors” based on function, the muscles themselves are not generally referred to this way.
Line 754-5: “The plantar portion of the cotyle is split in the axial direction (Figs 19A, 23B), which could be pathological.” Why not taphonomic? Is there any evidence either way?
Line 769-70: “Placement of Diluvicursor pickeringi in the Ornithischia is supported by the combination of a distally tapering mt IV…” Is this supposed to be distally curving? I don’t really see (nor is there a description of) it tapering.
Line 796-7: “The triangular intervertebral processes developed on the posterior-most caudal vertebrae of Diluvicursor pickeringi (Fig. 17) are similarly unique.” I’ve actually seen something similar in Gasparinisaura, specimen MCS-Pv 001 at Museo Cinco Saltos, which has a nearly complete and articulated tail. The intervertebral process is only present on two or three vertebrae, but they are quite similar to what is shown in this paper. To my knowledge, this specimen hasn’t yet been described, so I’ll leave it to the authors’ discretion whether to make this comparison or not, but I thought you might like to know about it—it certainly strengthens the case for a close relationship between Australian and South American ornithopods. (The ventral grooves on posterior caudal vertebrae are also present in this specimen.)
831,3,5: Spell out the full names of the lamina, at least the first place they are mentioned in the description, rather than sprl, tprl, and prsl.
839-41: “A prominent prsl on the caudal vertebrae of theropods, such as the abelisaurid Majungasaurus crenatissimus (O'Connor, 2007), suggests this feature is also plesiomorphic in dinosaurs, although variably expressed among taxa.” Or it arises frequently due to parallelism. Either way, it’s not diagnostic.
847-55: Again, I’ll refer to the undescribed specimen of Gasparinisaura MCS-Pv 001. While it has some hemal arches with rounded distal ends, just two vertebrae distal to this and still within the middle caudals are hemal arches with asymmetric triangular ends similar to those seen in NMV P185992/NMV P185993. It is important to remember in these discussions that the shape of hemal arches changes quite drastically based on position even within middle caudal vertebrae of one individual. Drawing conclusions about taxonomy or systematics based on these bones is dangerous unless comparisons can be made between fairly complete series.
885-8: “…suggesting that the position designated Ca 3 in Diluvicursor pickeringi is close to correct. It is reasonable to suggest that up to four caudal vertebrae could have been present on the Diluvicursor pickeringi holotype anterior to that designated Ca 1.” Based on what? How did you arrive at the number four?
968-70: “Similar features of the hallux in the early ornithischian Lesothosaurus diagnosticus (Thulborn, 1972), suggests this condition may be plesiomorphic for ornithopods.” While it’s true that Lesothosaurus has an “early” temporal range, in the context of describing its features as plesiomorphic, the better term here would be “basal” or “basally branching”.
970: “However, the halluces of the early ornithischians…” see above.
973-4: “indicating that the plesiomorphic condition of the hallux in ornithischians is presently not understood.” Well, what about outgroups? What would they indicate?
996-7: “…within a dorsolaterally oriented extensor groove (Figs 31A–B, S6E–F).” Figure 31 does not show an extensor groove on any of the specimens—or at least nothing is labelled as such. Figure 24A and 24F show the extensor groove clearly for D. pickeringi.
1020: “coerzeei” Should be coetzeei
1028: “Anti-mortem”: I think you mean antemortem?
1152-4: “a protuberance is also developed on each of the paired spinoprezygapophyseal lamina (sprl), between which, the transprezygapophyseal lamina (tprl) extends dorsally to both the neural canal and the prezygapophyses”. I don’t understand this description. The protuberances on the sprls appear to be dorsal to the prezygopophyses. How does the tprl then extend dorsally from the protuberance of the sprl to the prezygopophyses?
1267: “coerzeei” Should be coetzeei
1384-9: “Investigations on disparity in dental and cranial features between both co-occurring dinosaurian and ancient mammalian herbivores have addressed questions of habitat preferences within these groups…. However, the palaeoecological implications of cranial, dental and postcranial disparity between small-bodied ornithopods have yet to be investigated.” You say these disparities have been investigated in dinosaurs previously, but not in ornithopods. Maybe the first sentence should specify “some dinosaur groups” or “non-ornithopod dinosaurs”.

Figure 1: The color of water in figure 1C is very similar to that of land in figure 1A, and the background land color in 1C matches the water in 1B. This makes it difficult, at first glance, to discern where the coastline is in 1C. It’s overall a lovely figure, but consider making the color schemes consistent across all parts.
Figure 5A: I’m a little confused by the parenthetical “(top only)” in the description of the Anchor Sandstone. The description says it is a channel deposit with shallow lacustrine sediments at the top. But you have more than the shallow lacustrine sediments in your section. If you are trying to indicate that the site doesn’t include the full thickness of the Anchor Sandstone, this could be indicated by dashed arrows continuing downward in the schematic cross section.
5B: Just for the sake of clarity, it might be useful to change “intertidal zone” to “modern intertidal zone”, and “shore platform” to “modern shore platform”.
Figs 9, 10, 20: Perhaps this is a difference in Australian vs. American English, but describing a vertebra as “virtual” sounds to me as if there is something reconstructed or not quite real about it. I would describe this as a three-dimensional model or maybe “CT imaging of anterior caudal vertebra”.
Figure 10: “tprl, intraprezygapophyseal lamina” should be transprezygopophyseal lamina to match descriptions in the text.
Figure 19: The description of the views would be better if the elements were indicated, e.g., 19A: Tibia, fibula, and tarsals in anterior view, pes in plantomedial view. I would also argue that the tarsals seen in 19B are in something closer to a distal view than anterior.
Figure 20: “pd #, pedal digit number and phalanx position”—since you only point out metatarsals in this figure, why not use something like “mt” (or at least shorten the description to “pedal digit number”).
Figure 24: It would be nice if the parts of this figure were realigned so that MT I and its phalanges were aligned. They can remain as separately labelled parts of the figure, but aligning them such that a lateral view of MT I is next to a lateral view of the phalanges would make their relationship easier to understand.
Figure 30C: why is the schematic reflected while the photograph is not? If the purpose is to compare with the right limb of Diluvicursor, just reflect both the photo and schematic.
Figure 31: what view are these seen in?
Figure 33: As mentioned above, the CT imaging is not the best way to demonstrate pathologies. Consider a close-up photograph here instead.
Figure 35: “Extent of viscera (brown shading) ventral to hypaxial musculature (dashed lines) not shown.” If the cloaca extends this far posteriorly, it would be located more medially then ventrally (for a nice illustration of this in Alligator, see Mallison et al. 2015). Honestly, I think you could ignore viscera, since this is such a schematic view, and since this isn’t relevant for most of the tail. However, if you want to include viscera, they should be properly placed medial to the left and right hypaxial muscles.

Table 1: What sources are you following for this nomenclature? What do the asterisks mean?

Refernces
Boyd, C. A. (2015). The systematic relationships and biogeographic history of ornithischian dinosaurs. PeerJ, 3, e1523.
Mallison, Heinrich & Pittman, Michael & Schwarz, Daniela. (2015). PrePrint Version: Using crocodilian tails as models for dinosaur tails. PeerJ PrePrints. 3. e1653. 10.7287/peerj.preprints.1339v1.


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: POSITIVE SELECTION ON HUMAN GAMETE-RECOGNITION GENES
Review round: 1
Reviewer: 1

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: I have read the paper by Hart et al. The authors have tried to identify specific sites under selection that could account for previously discovered linkage disequilibrium (LD) between human C4BPA and ZP3 and extend the analyses to include human ZP2. I find that the paper is interesting and it is generally well-written. However, I have several comments which can help improve the paper.

Why rs2286428 and rs200481427 are no in Table 1?

Page 14, line 293, middle, Table 2 should be Table 1.

Page 15, bottom paragraph, the authors list the test methods for selection, but only Vitti, Grossman & Sebati 2013 is referred. To me, the references of Tajima’s D, the composite likelihood ratio test (CLR), and Fay and Wu’s H, as well as xp-EHH should be given too. Although Vitti, Grossman & Sebati 2013 was published in 2013, it missed the latest method EHHST and xp-EHHST developed in

1. Zhong M, Zhang YW, Lange K, and Fan RZ (2011) A cross-population extended haplotypebased
homozygosity score test to detect positive selection in genome-wide scans. Statistics and
Its Interface 4:51-63.

2. Zhong M, Lange K, Papp JC, and Fan RZ (2010) Extended homozygosity score tests to detect
positive selection in genome-wide scans. European Journal of Human Genetics 18:1148-1159.

EHHST and xp-EHHST has a better feature of easy to calculate and easy to interpret results than xpEHH. Hence, the authors should add the results of these better methods to Table 3. The related software can be found on https://sites.google.com/a/georgetown.edu/ruzong-fan/about

The plots of Figure 3 are not clear to me. I wonder if the mean or median allele numbers can be provided to make it easy to understand.

In Table 3, the p-values should be provided in addition to the test statistic values.

Minor issues: in references, there are some problems. For example, the tauthors of following ref

Wang H, Choi Y, Bamidele T, Xuefeng W, Morris N, Zhang X, Broeckel U, Hanis C,
Iardia S, Redline S, Cooper RS, Tang H, Zhu X. 2017. Genome-wide survey in African
Americans demonstrates potential epistasis of fitness in the human genome. Genetic
Epidemiology 958 41:122–135.

should be:

Wang H, Choi Y, Tayo B, Wang X, Morris N, Zhang X, Broeckel U, Hanis C, Kardia S,
…


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: POSITIVE SELECTION ON HUMAN GAMETE-RECOGNITION GENES
Review round: 1
Reviewer: 2

Output:
Basic reporting: Overall, this report reads well with professional English, well thought out hypothesis and supporting evidence for them. Although I am not entirely familiar with the field, the included references appear to be correct and overall attribution seems appropriate.

My only suggestion is to include significance values in Fig. 3 and to more clearly delineate their findings from previous reports, especially in the discussion.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: No additional comments


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

Input:
Title: POSITIVE SELECTION ON HUMAN GAMETE-RECOGNITION GENES
Review round: 1
Reviewer: 3

Output:
Basic reporting: Overall well written and referenced, see general comments for some specific suggestions for improvement.

It would be helpful to provide a link in the fertility data supplementary file to the location of the previously published values for individual families, on which the summary stats are based.
Experimental design: Questions are clearly defined and methods appropriate. See suggestions for some additional statistical tests in general comments.

I particularly appreciate the acknowledgment of 'researcher degrees of freedom' and possibility for inflated false positives. The authors do a nice job clearly showing the 'story' of their study.
Validity of the findings: The authors are clear about the relative robustness of their findings and which should be treated with caution.
Additional comments: Hart and colleagues investigate evolution of egg and sperm binding proteins in humans. They test for evidence of positive selection on two egg coat proteins ZP2 and ZP3, consistent with findings reported in other mammals. Furthermore, they test for positive selection on C4BPA the sperm protein which is the putative human homolog of mouse Zp3r, which binds to the egg coat. They find evidence for positive selection on one or more amino acid sites in each of these proteins, but not in the egg coat protein ZP1. Moreover, they report associations between the candidate selected sites in ZP2 and C4BPA with fertility in a Hutterite population.

This is an interesting study testing implications of the pattern of rapid adaptive evolution of fertilization proteins in mammals (and other taxa) - usually viewed in the context of reproductive isolation and speciation - for reproductive compatibility within humans. The authors do a nice job explaining the limitations of the methods employed for within species data, and are clear that their findings are suggestive and should be treated with caution - but are exciting leads for future research.

1. I found the manuscript well written and easy to follow, with the exception of the abstract - the framing of the question was somewhat muddled. I suggest rewriting the beginning of the abstract and streamlining the description of results. For example the intro focuses on co-evolution between egg and sperm proteins, but that's not clear from the abstract - which starts focused on egg proteins.

2. population genetics analysis
A. it is unclear to me why it was not possible to perform analyses on the ZP3 site using downloaded variable sites. Most/all of the test statistics can by computed using other programs or calculated directly. Was the author/administrator of the 1000 genomes selection browser contacted to correct the error in order to run analysis?
Please include analysis for ZP3 using other software (at least Fst, TajD, Fay & Wu's H, CLR) or explain in more detail why this wasn't possible.
B. I suggest adding McDonald-Kreitman (Nature 1991) tests. While conservative, this test is commonly used to distinguish high amino acid polymorphism due to balancing selection vs. relaxed purifying selection. As other great ape sequences were used to identify ancestral vs. derived mutations, appropriate outgroup sequences are available for MK. πR and πS (replacement and silent diversity) values should be reported for each gene.
C. It would be useful to add popgen tests for the combined sample, in addition to individual populations, to evaluate the hypothesis that divergent alleles are maintained over time in humans. (although I agree with argument from L379 that this may be problematic for LD-based tests)
D. Fst is not a test for selection - change in description of tests and results (beginning  L348) to indicate evidence is only for population differentiation not selection

3. positive vs. diversifying vs. balancing selection - Unfortunately, this terminology is not used consistently among different people in the field and some clarification is needed here. It seems in the MEME paper, "diversifying" and "positive" selection are used interchangeably (and for interspecific comparisons). Diversifying sensu Murrell et al 2012 is not the same as balancing selection, but it seems in this manuscript the authors suggest that significant results in MEME are evidence for balancing selection. Be careful to distinguish exactly what the test shows - i.e. rapid & adaptive amino acid substitution at a site - particularly for this intraspecific analysis.
- Title, L13, L16 - change 'selection' to 'positive selection'

Add haplotype tables including variable amino acid sites for each gene as supplementary.

Table 2 - add #s of nonsynonymous and syn polymorphisms for each gene.

Minor comments:
L16 - there have been many papers on sperm proteins too - e.g. reviewed in Turner & Hoekstra IJDB 2008

L18 - change to "selection the human egg-coat genes ZP3 and ZP2. We also found evidence for positive selection on C4BPA, which encodes a repetitive..."

L22 "Several additional lines..." this sentence is confusing right after saying no selection on ZP1 - re-word

L55 - is this the right reference? title still calls it sp56

L140 "one candidate site under diversifying selection" to "one candidate site each under"

L178 - caveats about applying these models within species are explained clearly later in the manuscript. It would be helpful to either move them here or add "(but see caveats below)" or similar.

L706 could add mention of parallel amino acid changes at same sites in ZP3 in multiple rodent taxa and mammals, reviewed in Turner & Hoekstra IJDB 2008

Fig 1 - add x axis with aa positions

Fig 2 - add colors to indicate % alleles from different populations

Fig 3 - smaller, jittered points; add P vals to graph or legend


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: POSITIVE SELECTION ON HUMAN GAMETE-RECOGNITION GENES
Review round: 2
Reviewer: 1

Output:
Basic reporting: good
Experimental design: good
Validity of the findings: good
Additional comments: I am satisfied by the changes made in response to my comments and those of other reviewers, or the clear and thorough explanations why they were not possible/advisable. I appreciate in particular the extra work necessary to run selscan to run haplotype tests for ZP3.


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

Input:
Title: A STREPTOMYCIN RESISTANCE MARKER IN H. PARASUIS BASED ON SITE-DIRECTED MUTATIONS IN RPSL GENE TO PERFORM UNMARKED IN-FRAME MUTATIONS AND TO VERIFY NATURAL TRANSFORMATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is not organized well. For example, there is no connection between section "3.4" and "3.3".
Experimental design: The experimental design is strange. I don't know why the author using EMS to induce mutation. In addition, the author did not tell us how many mutant they have gotten and what are they.
Validity of the findings: The authors claimed that they have developed a new novel development of EMS-induced SM-resistant method.  But I do not think so.
Additional comments: Some experiment details should be described in the methods section instead of in the results section.


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

Input:
Title: A STREPTOMYCIN RESISTANCE MARKER IN H. PARASUIS BASED ON SITE-DIRECTED MUTATIONS IN RPSL GENE TO PERFORM UNMARKED IN-FRAME MUTATIONS AND TO VERIFY NATURAL TRANSFORMATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1 Writing of a scientific article should be concise and clear. However, the logic of this paper is vague. Numerous grammatical errors also hinder understanding of the paper.
2 Lines 50-52, “A prerequisite for this process includes a marker-containing strain (Reyrat et al., 1998); a streptomycin resistance marker based on rpsL or rrs mutations is one of the most frequently used phenotypes (Tsai et al., 2014).”
The authors mixed up the concepts of positive selection marker and counterselectable marker. Streptomycin sensitivity is one of the most-used counterselectable markers in allelic exchange as described in the papers that the authors cited. To this end, a streptomycin-resistant strain and a suicide plasmid containing a wild-type rpsL gene are required. When the suicide plasmid is used to deliver an inactivated allele of the target gene in the chromosome, expression of the wild-type rpsL gene on the integrated plasmid confers a streptomycin-sensitive phenotype upon streptomycin-resistant strains and allows for selection with streptomycin to detect loss of the vector. However, in this study, the authors used sucrose sensitivity, which is conferred by the sacB gene on the suicide plasmid pK18mobSacB, instead of streptomycin sensitivity in the selection of the deletion mutant (lines184-201). Streptomycin-resistance only served as a positive selection marker for the wild type strain. In fact, any antibiotic to which the SC1401 strain is resistant but E. coli S17-1 is sensitive can serve as a positive selection. Did the authors analyze and compare drug resistance profiles of both strains before starting the study?
Experimental design: 1 Lines 168-170, “ The cells were screened by TSA++ containing 25 μg ml-1 of SM. The visible single colonies were propagated and the DNA extracted and sequenced for further identification.”
Did the authors identify the mutants with genomic DNA sequencing?!! The corresponding data were not presented in the section of Result. In this experiment, streptomycin selection is not enough for allelic exchange because the frequency of double crossover events may be low and illegitimate recombination may occur. Addition of 10% sucrose to the selection medium is appropriate.

2 Lines 221-222, “The visible single colonies were identified by PCR and western blotting.” Why and how did the authors identify the colonies with western blotting assay?
Validity of the findings: 1 Lines 320-323, please describe the assay of Western blot in the Section of Material and Methods.
2 Lines 326-327, “Point mutations in rpsL which don't confer negative effect on growth were assumed to be more effective in verifying natural competence.” Did the authors compare the growth rates of the wild type and the mutants?
3 Lines 334-336, “Genomic DNA of HPS32 and HPS32 couldn’t confer SM-resistance to SC1401, which also in support of our elucidation highlighted in “Introduction” that spontaneous mutations in this species occur at a fairly low level.” Why? Is transformation the cause of spontaneous mutation?
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: A STREPTOMYCIN RESISTANCE MARKER IN H. PARASUIS BASED ON SITE-DIRECTED MUTATIONS IN RPSL GENE TO PERFORM UNMARKED IN-FRAME MUTATIONS AND TO VERIFY NATURAL TRANSFORMATION
Review round: 1
Reviewer: 3

Output:
Basic reporting: The level of English is acceptable. I found a few spelling errors and non-idiomatic expressions.

The Introduction and background sections will have to be improved. The references from line 41,42 below
should be substituted for the relevant original sources.

40 producing significant mortality and morbidity in pig farms and leading to serious economic losses
41 in the pork industry throughout the world (Yue et al., 2009;Zhang et al., 2016b).

Structure conforms to PeerJ standards as far as I can judge. Abstract is within the specified limits.

The manuscript has six figures which seem a bit excessive as I think the manuscript lacks an important figure.
This figure should be a scheme that shows how the so called "in-frame" deletions happen. This figure should
contain relevant plasmids and primers. I think figure 2 could be put among the suplemental figures to make room for this new figure.

All relevant raw data was supplied.

Experimental design is adequate and the findings are valid.

# Specific line by line comments

27 Combined with natural transformation-based knockout system and this
28 genetic technique, multiple deletion mutants or attenuated strains of H. parasuis can be easily
29 constructed

correct to:

Combined with a natural transformation-based...

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38 pleomorphic, NAD-dependent opportunistic bacterium

Please explain what a NAD dependent bacteria is? Is it auxotrophic?

---

58 2011). To generate SM mutants by using

correct to:

58 2011). To generate SM resistant mutants by using

---

61 et al., 2014). However, spontaneous or UV-induced mutants of streptomycin resistance in H.
62 parasuis probably occurs at a fairly low rate in H. parasuis; SM mutant generation in this organism
63 is very inefficient using these strategies (data not shown).

correct to:

61 et al., 2014). However, spontaneous or UV-induced mutations leading to streptomycin resistance in H.
62 parasuis probably occurs at a fairly low rate; SM mutant generation in this organism
63 was very inefficient in our hands using these strategies (data not shown).

The statement is too strong give the lack of experimental detail.

---

The lines 65 - 85 do not belong in the materials section. Some should go to introduction and some to results.

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90 S2. Plasmids were propagated in E. coli DH5α or S17-1 (λpir) and grown in liquid Luria-Bertani

LB means Lysogeny Broth and NOT Luria-Bertani.
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118 growth. Moreover, the MIC-S of EMS induced SC1401 derivatives were also determined using
119 above method.

correct to:

118 growth. Moreover, the MIC-S of EMS induced SC1401 derivatives were also determined using
119 the above method.

---

138 Wild type SC1401 (deposited in GenBank under the accession NO. NZ_CP015099.1), which

The strain was not deposited, what was depositied was the genomic sequence.

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The sections
2.7. Construction of Plasmids pkTLR and pkALR and
2.8. Construction of Unmarked In-Frame Targeted Mutant 1401D88ΔtfoxΔarcA of H. parasuis

Would benefit from the extra figure that I mentioned previously. It is very hard to follow the details of the genetic designs.

---

210 The genomic DNAs of H. parasuis SC1401 derivatives 1401D88 and 1401D43 via site-
211 directed point mutation were used to verify natural transformation capacity of H. parasuis strain

This is a mix of concepts that is hard to understand. What was done vis site-directed mutagenesis?
Rephrase to clarify.

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255 we used a discontinuous induction method in our experiments. The culture in a 10mM of EMS-

Please correct spaces between dimension and units here and possibly throughout the manuscript.

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The section between lines 271 - 289 needs to be split up to introduction and results or discussion

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357 In this study, we found that EMS has a characteristic dual function in H. parasuis. High
358 concentration of EMS inhibits growth (20mM) or even exhibits a bactericidal effect (30mM),
359 whereas low concentration introduces random somatic hypermutations in genome.

Although, this is not directly my field this must surely be something that is observed every time
EMS is used. I remember performing experiments as an undergraduate to demonstrate that the a cmpound
would be bacteriostatic at low concentration and bactericidal at higher. Please consider removing this.

---
Experimental design: Experimental design is adequate. See above for more details.
Validity of the findings: Findings are valid. See above for more details.
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: A STREPTOMYCIN RESISTANCE MARKER IN H. PARASUIS BASED ON SITE-DIRECTED MUTATIONS IN RPSL GENE TO PERFORM UNMARKED IN-FRAME MUTATIONS AND TO VERIFY NATURAL TRANSFORMATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript still needs a thorough proofreading to improve the English language used.
Experimental design: In my comment that “In this experiment, streptomycin selection is not enough for allelic exchange because the frequency of double crossover events may be low and illegitimate recombination may occur. Addition of 10% sucrose to the selection medium is appropriate.” I mean the experiment of “2.6. Site-Directed Mutagenesis”, not the experiment of “2.8. Construction of Unmarked In-Frame Targeted Mutant 1401D88ΔtfoxΔarcA of H. parasuis 1401D88”. In 2.8, 10% sucrose was added into the selection medium. However, In 2.6, the sucrose was not used in the selection medium. Why?
Validity of the findings: No comment
Additional comments: No additional comments


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

Input:
Title: STAT-TRACKS AND MEDIOTYPES: POWERFUL TOOLS FOR MODERN ICHNOLOGY BASED ON 3D MODELS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This paper introduces the term 'mediotype’, which incorporates a multitude of digital 3D data files relevant to the field of (fossil) track research. The word is enclosed by inverted commas in the title and is a practice that should be continued throughout the body of work. I have no further comments to add to their Basic Reporting as are very well structured and of publication quality.
Experimental design: The authors identify a significant gap in palaeoichnology, that is how to obtain track data that can be utilised in quantitative comparative studies (albeit in a series of paired analyses). They succeed in their approach by utilising the powerful, innovative, and newly developed DigTrace software. The authors provide a series of case studies that are relevant for the application of the method, by which the findings are very clearly documented. This approach is of very high significance for this research field (particularly dinosaur tracks, and is one that I am confident that progressive palaeoichnologist are/will be eager to employ.

As clearly stated by the authors, this is not a methods paper. The aim of the paper is to introduce ‘mediotype’ as a term for use by the wider palaeoichnological community to incorporate as range of ‘statistically-generated three-dimensional track models [SG3D]’. While ’mediotype’ is a pleasant term that is simply to use, I do not think the term will be received unfavourably by palaeoichnologists for the following reasons :
	•	Etymology implies a type specimen: ‘Mediotype’ adds to now a growing list of ICZN non-formalised terms (e.g., ‘digitype’, ‘plastotype’). Issues of repositories and accessibility to ‘type’ specimens will also come into play. Line 423 "unlike conventional palaeontology finding a 'morphologically-perfect' specimen is almost impossible" I am of the opinion that there will be strong resistance for the digital construction of an 'ideal' by any means. The authors "argue that the use of 3D data may assist in correcting this omission" which may be appropriate in for analyses but I disagree that type specimens should be a chimera of track data, nor would this be acceptable for type specimens for other research fields.

	•	Etymology implies ‘averaging’ of data: In practice, ‘average’ data sets (mean, median) appear to be the preferred documentation source for use in this paper (supplied figures, raw data). While I am in agreement that such track data are perhaps the most useful data sets for palaeoichnologists, the fact that their term encapsulates non-averaging statistical data makes use of the term non-inclusive and potentially misleading.

	•	Implies a single specimen: Even ‘digitype’ and ‘plastotype’ inferred specimens limited themselves to single representation. ‘Mediotype’ include six csv file types are generated with the DigTrace software (mean, median, maximum differences, minimum differences, standard deviation, point-to-point comparisons) most of which are not elaborated further after their mention in the paper.

	•	Implies that only type specimens can be used in the generation of SG3D track data whereby limiting application (e.g., just as ‘digitype’ is limited to type specimens), a restriction that is almost certainly not the intention of the authors.
Validity of the findings: The placement of landmarks can be problematic for tracks that are, by their very nature, highly variable abiotic structures. Although While the software the authors show preferences for using (Digtrace) displays significant robustness around this issue.

One aspects that is confusing it the greyscale visualisation and interpretations of the standard deviation ‘mediotypes’ shown in figures 1D, F; 5C; 6B, D. Here, white indicates low deviation and black indicates high deviation. Yet in each example that the authors state in-text that there is low deviation the plantar impressions are darker than the surrounding surface. In the example that the authors state in-text as high deviation (e.g., figure 6 B) most of the plantar impression is white and surrounding surface is darker. In these cases, the data contradicts the authors claim. This is particularly important to resolve as readers that become users of the Digtrace software may face the same issues.

Otherwise very well structured.
Additional comments: This is an important, well-written paper for dinosaur palaeoichnology and has the potential to be a very positive and broad influence for future research in this field.
The use of the term 'mediotype' is with significant problems that can be resolved, for the most part, by substituting the non-ambiguous and more accurate term 'statistically-generated three-dimensional track model' (SG 3D) of 'statistically-generated digital surface model' (SG DSM).

For further comments see attached annotated pdf.


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

Input:
Title: STAT-TRACKS AND MEDIOTYPES: POWERFUL TOOLS FOR MODERN ICHNOLOGY BASED ON 3D MODELS
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: Dear all,

I should emphasize that I am conservative regarding the use of 3D imaging in vertebrate ichnology. Therefore I would probably be categorized a ‚traditionalist‘ following the terminology of the authors.  I do not refuse the application of 3D imaging in vertebrate ichnology, but I just do not see any use of hitherto suggested methods in order to solve the main problems of studying fossil tetrapod footprints.
The morphology of tetrapod tracks is the result of the superimposition of anatomy, gait and substrate. A majority of vertebrate ichnologists prefers an ichnotaxonomy highlights anatomically-based characters of the imprint morphology and trackway pattern. Therefore, the main challenge to these researchers is to distinguish anatomical input of tracks and trackways from extramorphological characters (= influence of gait and substrate conditions).

In which way a ‚mediotype‘ sensu Belvedere et al. may help anatomically-focused vertebrate ichnologists? As far as I understand the authors, the ‚mediotype‘ is mainly a tool to quantify the differences between two or more tracks. The result is a number which nothing helps to interpret the reason for the calculated difference(s). I definitely see that I could introduce tresholds such as a similarity index, e.g. two tracks should be similar by 90% in order to assign them to the same ichnospecies. However, I do not know how much of the similarity/dissimilarity is based on anatomy, gait, and substrate. Thus, where is the progress? I totally accept that the ‚mediotype‘ is one out of several tools for vertebrate ichnologists but I doubt that it has the potential to revolutionize this paleontological discipline.

What to do with this manuscript? It may be worth to describe the ‚mediotype‘ method and its application as examplified by the authors. But I feel that the importance of the paper is overstated. My suggestions: I would go along with the proposal to introduce tetrapod ichnotaxa at the base of long and well-preserved trackways, only. Thus, the introduction of ichnotaxa (diagnosis, description, measurements of track and trackway parameters) could be completed by data from 3D imaging in a way that the similarity of tracks within each specimen of the type series is calculated separately. This might result in useful values for other workers who want to quantify the similarity of their own specimens to the type material. By calculating discrete specimens the authors avoid the accusation of arbitrary selection as they base their models (‚mediotype‘) on type specimens exclusively (that are used by ‚traditionalists‘ as well). I do not see any use to extend the data base of the ‚mediotype‘ beyond type material (according to the requirements on quality and quantity of new ichnotaxa).

I think it would be a good paper to describe and illustrate the process of introduction a new ichnotaxa including a ‚mediotype‘ in most detail (documentation of the type material, traditional diagnosis, measurements, description, 3D model, ‚mediotype(s)‘ production). In addition, it would be helpful to apply the ‚mediotype‘ to similar specimens from another locality to examplify the tool. Certainly, my suggestions are not so far from the content of the author’s manuscript. However, I feel that the manuscript and its ideas would probably find more acceptance when the methods are demonstrated at a single example and in most detail. A good example would be Robledopus macdonaldi Voigt et al., 2013, small reptile tracks from the Early Permian oft he New Mexico as the ichnotaxon is based on a type series and there is ambiguous material from other localities of the same or similar age in New Mexcio.

Finally, I welcome the idea of the ‚mediotype‘ if it will be restricted to type material. The authors should think about my suggestions to focus on a discrete and fully elaborated example. At the present stage, I do not see that the manuscript will be of much use to the vertebrate ichnology community.

Sebastian Voigt
2017-08-17


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: STAT-TRACKS AND MEDIOTYPES: POWERFUL TOOLS FOR MODERN ICHNOLOGY BASED ON 3D MODELS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: I am a supporter of the use digital methods to evaluate the 3D topography of track surfaces, and view such approaches as providing much needed quantifiable data to a field of science that is prone to much subjectivity.

One of the main aims pf this paper is to provide information of a recently developed tool for quantifiable comparative track analyses. I feel biased in my desire to have methods, like those employed by these authors, to be widely used by dinosaur ichnologists, and while the paper provides some new results from previous published examples, it is unclear as to its novelty.  The authors explain the use and strengths of the approach very well, but this is not methods paper that would be of benefit to a wider audience and facilitate the adoption of this method by researchers. Shortcomings. The quantifiable aspects of this approach can be made much clearer in the examples the authors use. For example, the values of standard deviation should be stated within the text for the respective ‘stat-tracks’, as well as shown as a calculated range of standard deviation along the figured grey-scaled 'stat-track'. Inclusion in track figures of digit impression number are features currently absent and would facilitate ichnological assessments. Currently the statistical variants are comparative via grey-scale colouring of tracks yet lack numerical data.

My earlier appraisal of this work expressed confusion associated with author interpretation of grey-scaled 'stat-tracks’. While the authors have now elaborated their explanation further the point I wished to raise has been lost, that I hope to clarify here. In regard to the grey-scaled 'stat-tracks’, it  is repeatedly stated that lighter-to-darker colours indicate less-to-more deviation (respectively), yet appear to not adhere to this criterion in interpreting the data. For example: in assessing sauropod tracks the are “pronounced similarities amongst the tracks. The resemblance is so similar that, …all these tracks could fall in the range of intraspecific or even intra-trackway variation”. Yet the ‘stat-track’ (Fig. 1D) shows very light colouration outside the track region and dark grey-black within the track region, the latter indicating areas very highly variants and can contradicts the statement within the text. But this is not in isolation, occurring in figures 5 and 6. In regard to the figure 6 theropodan tracks, “the standard deviation stat-track (Fig. 6B) shows only few similarities” which contradicts the very light colouring of the impressions of the digits II and IV and metatarsophangeal pad. The authors explanation of these similarities as “highly biased by the completely different preservation of the two specimens”. It is not made clear to the reader whom may wish to employ the tool outlined in the paper how to distinguish topographical similarities/differences as ichnologically significant/insignificant. A more comprehensive evaluation is wanting.

The second aim of this paper is to introduce new terms for potential future use in ichnotaxonomy. In considering neologisms for a very specific discipline of science, I question if it would be preferable to seek a more specific journal for the publication of this paper. This may be within either a palaeoichnological journal, or preferably a bulletin specific for nomenclature, where the validity of their proposal can be more definitively evaluated.
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: STAT-TRACKS AND MEDIOTYPES: POWERFUL TOOLS FOR MODERN ICHNOLOGY BASED ON 3D MODELS
Review round: 2
Reviewer: 2

Output:
Basic reporting: No complaints.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: Dear all,

the revised version of PJ_18800 addresses most of my former cautions with this manuscript. I especially welcome the separation of „stat-track“ and „mediotype“.

It is still my opinion that the importance of paleoichnological studies is first of all limited by the quality of studied tracks and traces and only subsequently affected by the applied techniques.

In the end, however, application in other studies will be the best way to decide about the utility of the author’s concept. Therefore I recommend this ms for publication.

Sebastian Voigt
2017-11-27


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: REFINING AMINO ACID HYDROPHOBICITY FOR DYNAMICS SIMULATION OF MEMBRANE PROTEINS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Figure 3. PMF insertion profiles for mass centers of sidechain analogs relative to the bilayer
center.

The letters (w, g, o, c, etc.) at the plot are very confusing, please use a different mark.

Figure 5. Linear regression, please show a small mark, and then the letter next to the mark, otherwise is hard to understand the data presented here.

Figure 6. CgProt PMFs for one and two-residue backbone moieties. Again, the letters overlap and they are difficult to see. Please add a different mark.
Experimental design: Methods are well described, the results and findings are relevant and interesting.
Validity of the findings: It would be interesting if the authors present how their hydrophobicity force field refinement address the protein-protein interaction in a  transmembrane helix dimer.
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: REFINING AMINO ACID HYDROPHOBICITY FOR DYNAMICS SIMULATION OF MEMBRANE PROTEINS
Review round: 1
Reviewer: 2

Output:
Basic reporting: While the literature cited is failry complete, for the reader to get a complete picture of the field, I suggest to adding the reference to the recent paper by Pawlowski et al who developed a continuous lipid model for coarse-grained simulations of membrane proteins (W Pulawski, M Jamroz, M Kolinski, A Kolinski, S Kmiecik
Journal of chemical information and modeling 56 (11), 2207-2215)
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This is a very good paper that sunstantially advances the development of coarse-grained simulations of membrane proteins. The parameters of the CgProt force field were refined to reproduce the peptide-insertion PMFs calculated by all-atom simulations and experimental hydrophobicities. The resulting force field was shown to perform significantly better regarding the insertion of peptides into lipid membranes.


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: REFINING AMINO ACID HYDROPHOBICITY FOR DYNAMICS SIMULATION OF MEMBRANE PROTEINS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript by Hills reports on the refinement of the CgProt 2.4 coarse-grained force field for proteins. This is one of several force fields for protein simulations.

The text and the figures are reasonably clear, with a few exceptions. The graphical quality of Figure 1 is rather poor, I suggest using molecular models instead of chemical formulas.

Literature references are not always appropriate; for example, in the introduction, when writing about other coarse-grained force fields for proteins, the author mentions the MARTINI force field but provides incorrect citations. At line 92, the author refers to himself the idea of temperature coupling to separate heat baths, and to Arnarez the idea of implicit solvent for CG simulations. Bizarre.

The text is far from self-contained, particularly in the methods section:
- the description of the force fields is completely absent; one would need to dig out one or more previous papers to understand the meaning of acronyms for different particle types and the shape of the potential energy function.
- I did not find a description of bonded interactions (except for the restraints on helices).
- How was the position of the CG particles calculated?
- which structural properties of proteins are reproduced? which dynamic properties?
- what is the speedup compared to an atomistic simulation?
Experimental design: The goal of the research is well defined: to correct the flaws present in previous versions of the force field. Based on the results presented, the goal seems to have been achieved.
At the same time, it is not very clear what is the general goal of the force field; what are the pros and cons compared to other force fields available in the literature?

The design of the simulations has no original point. All of the simulations seen here have been done before by others, using other methods and/or force fields.

The description of the methodology is insufficient to reproduce any of the calculations: no mention of the algorithms used for thermostats and barostats, nor the cutoffs (if present).
Validity of the findings: The technical quality is difficult to assess because a description of the force field is missing (see above for details) and the simulation parameters are rather incomplete: no mention of the algorithms used for thermostats and barostats, nor the potential energy functions used, nor the cutoffs (if present).

Methods and figure 3: the AA data has been calculated or extracted from the figures by MacCallum et al.?

Line 218, “The favorable attraction of basic residues for the ester bilayer region has been dubbed snorkeling.” Why would it be valid only for basic residues?
In fact, in a real system, snorkeling does not have much to do with the supposed attraction for the ester group, but rather with the tendency of a charged side chain to remain hydrated. The ester region in a lipid bilayer is generally hydrated, hence the proximity of charged side chains with lipid ester groups. The real physics of the system is hidden by the implicit solvent.
Additional comments: The general philosophy of the force field is not described: what are the target properties? what kind of problems should be tackled by this force field?
Does this force field make progress with respect to other similar, available methodologies?


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: REFINING AMINO ACID HYDROPHOBICITY FOR DYNAMICS SIMULATION OF MEMBRANE PROTEINS
Review round: 2
Reviewer: 1

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


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

Input:
Title: USING UNDERWATER VIDEO TO EVALUATE THE PERFORMANCE OF THE FUKUI TRAP AS A MITIGATION TOOL FOR THE INVASIVE EUROPEAN GREEN CRAB (CARCINUS MAENAS) IN NEWFOUNDLAND, CANADA
Review round: 1
Reviewer: 1

Output:
Basic reporting: This article, addressing the trapping efficiency of the Fukuii fish trap, is a very important study that should be of great interest to those biologists who use this trap to monitor and control the European green crab.  Green crab researchers in Australia and on both coasts of North America are using this trap because it is light and can be folded. However, no one has ever questioned its trapping efficiency.  Knowing that the efficiency is only 16% is especially important to programs designed to “eradicate” newly discovered satellite populations.  It is important to note that poor catches may not mean that a population has been reduced to a low enough level to prevent self-seeding.
The article is well written and easy to follow. The introduction includes all the relevant references and clearly states the context of this study.
The figures are clear and well described.  I wonder if Figure 6, showing catches with and without the camera can be left out.  All that would be needed is a statement that there was no significant difference in the catches.
Experimental design: The experimental design is rigorous and well described. The fact that the authors used of a no-camera control treatment and deployed the traps at various sites and various conditions is very impressive.
Validity of the findings: The data are robust and the analysis is sound. From this rigorous study we learned that most meaningful data can be obtained at sites with high crab densities, during daylight and with good visibility.  Knowing these parameters will make it easier to test modifications to the Fukuii trap that will increase catch rate. The number 1 modification for increasing catch rate would be to work on “difficulty in completing entry”.  I am suggesting that the authors describe some modifications that could be tested to achieve this goal.  Even though the authors did not test any of these modification, they are in the best position to advise fellow green crab biologists for getting better catch rates.
Additional comments: This is a very needed piece of information for all researchers who use the Fukuii trap.  Knowing the traps limitation needs to be incorporated in any monitoring and control studies.  It would help if the authors made some suggestions for improving the design of the Fukuii traps.  Researchers using new traps with tight fitting openings may not trap as many crabs as researchers using older traps with sagging mesh openings. That could lead to a difference in CPUE.