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: MODELED LARVAL CONNECTIVITY OF A MULTI-SPECIES REEF FISH AND INVERTEBRATE ASSEMBLAGE OFF THE COAST OF MOLOKA‘I, HAWAI‘I
Review round: 2
Reviewer: 1

Output:
Basic reporting: The language used throughout the manuscript is clear and professional. Figures are generally of high quality, and well described. The structure in conform PeerJ standards. However, there are still a number of style inconsistencies and typo’s for which the text should be checked and some aspects may need further clarification or could be rephrased for clarity. I have provided my suggestions and comments in more detail in the ‘comments for authors’.
Experimental design: The study consists of original research and, by answering well-defined questions, provides insight that is relevant for spatial management. The methods are described in much detail. There are some aspects that may need further clarification, such as whether or not the model includes tides. I have provided my suggestions and comments in more detail in the ‘comments for authors’.
Validity of the findings: The results presented in the study appear valid and the authors have discussed the results in much detail. The authors have included an additional paragraph to stress the importance of considering the model resolution when interpreting results from model simulation as used in this study.
Additional comments: Dear authors,

kindly find herewith some detailed comments and suggestions to be considered:

Sometimes X km, sometimes Xkm (spacing); Sometimes X-Xkm, sometimes X – Xkm (hyphen type); Sometimes Xd, sometimes X days

L124-125: “(…) which is designed for the study of
 dynamical processes in the ocean on a horizontal scale.” The way this is presented feels a bit odd. Consider removing this part of the statement and rephrase as follows: “The hydrodynamic model selected was the MITgcm, which is designed for the study of
dynamical processes in the ocean on a horizontal scale. This model solves incompressible
Navier-Stokes equations to describe the motion of viscous fluid on a sphere, discretized using a
finite-volume technique (Marshall et al., 1997).”

L124-125: I am wondering if the MITgcm solution includes tides? If so, it would be valuable for the reader to explicitly state this, as for this type of systems, tides constitute an important process in shaping simulated coastal and near-shore trajectories, and hence, influence dispersal distances and long distance dispersal potential. If tides were not considered, I think it’d be valuable to include one or two sentences that cover the potential implications of not having considered this process in simulating trajectories and connectivity patterns. Given that the authors have a paragraph on limitations already (L517), the authors could consider to group all information on ‘Model limitations and future perpectives’ in one section.

L158-159: Consider rephrasing as follows: “Vertical velocities (w) were not implemented (…)” to enhance readability.

L160-161: “an Eulerian method” instead of “a Eulerian method”

L160: replace ‘time-step’ by ‘timestep’ for consistency

L194-195: “At each time step, a larva’s depth was checked against bathymetry, and was assigned to the deepest available layer if the species-specific depth was not available at these coordinates.” This statement is not fully clear and would benefit from further clarification. I wonder what the justification is for assigning to the deepest available layer. Is this fully arbitrary of based on field-based knowledge/literature?

L198: “occurs May-July” should be “occurs in May-July”

L234-237: “To calculate (…), by scaling (…).” This sentence seems incomplete. Could rephrase as “We calculated the forward settlement proportion, i.e. the proportion (…), by scaling (…).” Note: ‘the’ forward settlement proportion (L234) and ‘a’ specific settlement site (L235).

L267: This statement seems to define a strongly connected component (SCC) rather than a weakly connected component (WCC). A WCC is a subgraph in which all nodes are not reachable from other nodes. Hence “A weakly connected component (WCC) is a subgraph in which all nodes are not connected, either indirectly or directly.

L299-302: It is interesting to wonder how the timing of spawning events relative to the semi-diurnal tidal range variations would influence dispersal and connectivity patterns in these species.

L305: “showed the highest XXX at 8.1%”. Kindly consider rephrasing as follows: “Local retention was lowest for Caranx spp. (<1%) and highest for O. cyanea and P. sexfilis (8.1% and 10%, resp.).

L493: “(…) along the eastern half of the island, These (…)”; replace comma by point.

Table 1: This table is very informative! For consistency, consider using same hyphen in all cells.


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: MODELED LARVAL CONNECTIVITY OF A MULTI-SPECIES REEF FISH AND INVERTEBRATE ASSEMBLAGE OFF THE COAST OF MOLOKA‘I, HAWAI‘I
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors replied to all the comments and edited their manuscript as suggested by all the reviewers. The manuscript is clear and the main results are highlighted. I recommend this manuscript for publication after some minor reviews.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Line 33: reveal
Line 93: Replace biophysical model by individual-based model. The individual-based model is coupled to the oceanographic model. Both IBM and oceanographic model define a biophysical model.
Lines 152-161: I noticed that you moved this paragraph from the Discussion. I don’t think it should be located at the end of your Intro. Because you do not mention Graph Theory in the Intro, you should move this paragraph in the “Graph-theoretic analysis” paragraph in the Methods. And maybe you can shorten a bit the paragraph.
Line 1077: IBM instead of “individual-based model”

Figures 3 and 5: On both figures, the x-axis is the same color as one of the PLD length for Figure 3 and location for Figure 5 which is confusing. Just change the x-axis color (black for example).


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: MODELED LARVAL CONNECTIVITY OF A MULTI-SPECIES REEF FISH AND INVERTEBRATE ASSEMBLAGE OFF THE COAST OF MOLOKA‘I, HAWAI‘I
Review round: 3
Reviewer: 1

Output:
Basic reporting: Following previous revisions, I have no further comments.
Experimental design: Following previous revisions, I have no further comments.
Validity of the findings: Following previous revisions, I have no further comments.
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: MODELED LARVAL CONNECTIVITY OF A MULTI-SPECIES REEF FISH AND INVERTEBRATE ASSEMBLAGE OFF THE COAST OF MOLOKA‘I, HAWAI‘I
Review round: 3
Reviewer: 2

Output:
Basic reporting: The authors have answered to all the comments and edits. I recommend this manuscript for publication.
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: META-ANALYSIS OF NORTHEAST ATLANTIC MARINE TAXA SHOWS CONTRASTING PHYLOGEOGRAPHIC PATTERNS FOLLOWING POST-LGM EXPANSIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This is on the whole a solid meta-analytical study of mtDNA marine population genetics that is aware of its limitations, but works appropriately within those bounds. It is well written and presented and will be of utility to anyone hoping to gain insights into patterns of connectivity and recent demography in populations of NE Atlantic marine fauna. Below are some areas that could be improved however:

1) The formula used to estimate the timing of population expansion assumes an exponential expansion and produces a single date for the expansion. Is there a reason why you haven't considered using bayesian skyline plots (e.g. in Beast) which provides an age bounded within a 95% CI to complement your estimates of demographic expansion? This might offer more nuanced results.

2) In the methods, you haven't made clear with which software the Tau parameter was calculated.

3) On line 90 you state that the "British-Irish ice sheet led to a drastic drop in sea levels in the English channel". Are you saying that the lower sea level in the English channel is a local effect? One would presume that lower sea levels at the LGM were a global response to the glaciation.

4) On lines 233, 234, 235 you appear to differentiate between unimodal and skewed unimodal mismatch distributions with the former associated with sudden population expansions and the latter associated with recent expansions or bottlenecks. I'm not aware of this - can you provide a reference to the relevant research that demonstrates this? My understanding of mismatch distributions is that at best they can indicate either recent expansions/bottlenecks or the lack thereof - but not how sudden this expansion was.

5) On lines 240-248 you appear to suggest that bimodal mismatches indicate two or more distinctive lineages. This may be true, but those lineages do not necessarily mean that you're dealing with separate cryptic species or "inter-clade" differences necessitating dividing up your datasets in the demographic analyses. As mitochondrial DNA can be considered a single locus with effectively no recombination, divergent lineages can still be produced in large, panmictic populations - as I think you state later on lines 291-293. The only real indication that the divergent lineages may be indicative of cryptic diversity, thus warranting separate demographic analyses is where these lineages are geographically separated and not sympatric. Nevertheless it doesn't hurt to run the analyses with the separate lineages where there is a reasonable expectation that they may have separate demographic histories.

6) Lines 262-263 belongs in the discussion - i.e. "suggestive of population expansions as the ice started to retreat from its maximum positions"

7) Lines 269-270: The sentence - "Cases of species-specific unique haplotypes were evident at certain locations across the sampling range" could be written more clearly. Are you saying that in some species, certain regions exhibited unique haplotypes?

8) Lines 312-313: Is there circular reasoning here: "given that many species/lineages in this study showed a pattern consistent with demographic expansion, it seems likely that a large proportion of them did indeed experience a rapid population expansion...". I think you mean that a generally similar pattern in mtDNA diversity across a variety of species points toward demographic changes associated with the end of the LGM, rather than elective sweeps. That being said - dramatic climate changes could also be a trigger for selective sweeps - which would also be interesting...

9) Line 317: I think "have" should be inserted between "may" and "survived".

10) Line 330: There are also other things that could explain the result, such as your sample of genetic diversity for this species/lineage not being representative (see Karl et al. 2012) - or that mutation rate estimates are wrong or too conservative for this species, for example.


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: META-ANALYSIS OF NORTHEAST ATLANTIC MARINE TAXA SHOWS CONTRASTING PHYLOGEOGRAPHIC PATTERNS FOLLOWING POST-LGM EXPANSIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: In general, I found this manuscript clear and concise with a well-explain aim to achieve, and interesting conclusions. In addition, the manuscript is clearly written in professional, unambiguous language throughout. It is clear, coherent and used a professionally presented format. The manuscript is has a very good structure and show context of the current knowledge and question of interest. However, I do have some suggestions for the authors, which they may wish to consider including and that would strengthen the paper. If there is a weakness, it is in the statistical analysis (as I have noted below) which should be improved upon before acceptance.

Tables and figure are relevant and well explained. In addition, I found the Figure 4 is really informative and well-describe the main conclusion of this manuscript. The inclusion of some examples of the different haplotype networks shapes and mismatch distributions are very useful. I suggest use the same species name order in both tables (Table 1 and 2) which will make easier the comparing between both.

Line 93-95 : It would make easier for the reader to make a reference to the map and include the names in the map (Hurd Deep/Iberia) to clarify which refugia are pointed out.

Your introduction covers the state to date knowledge of comparative phylogeography but it may need more detail about the importance of this field. For example in Para 1: It would be good to have a sentence about the importance of using comparative phylogeography also in terms of management and conservation purposes. (Toonen et al. 2011; Villamor et al. 2014; Liggins et al. 2016; Pelc et al. 2009; Von der Heyden et al. 2014).

Line 96-100 : Reference to this part, there are many approaches for multispecies analysis. It would be interesting to add some references to support this point.
I thank you for providing specifically details on how to access to the raw data and the inclusion/exclusion criteria that you used. I have a few questions that may be worth to also explain in the methodology section.

References:

Liggins L, Treml EA, Possingham HP, Riginos C (2016) Seascape features, rather than dispersal traits, predict spatial genetic patterns in co‐distributed reef fishes. Journal of biogeography 43, 256-267.
Pelc RA, Warner RR, Gaines SD (2009) Geographical patterns of genetic structure in marine species with contrasting life histories. Journal of Biogeography 36, 1881-1890.
Toonen RJ, Andrews KR, Baums IB, et al. (2011) Defining Boundaries for Ecosystem-Based Management: A Multispecies Case Study of Marine Connectivity across the Hawaiian Archipelago. Journal of Marine Biology 2011.
Villamor A, Costantini F, Abbiati M (2014) Genetic Structuring across Marine Biogeographic Boundaries in Rocky Shore Invertebrates. PLOS ONE 9, e101135.
Von der Heyden S, Beger M, Toonen RJ, et al. (2014) The application of genetics to marine management and conservation: examples from the Indo-Pacific. Bulletin of Marine Science 90, 123-158.
Experimental design: The research question and main goals are defined and well-introduce. However, I include below some suggestions about where it may be worth to improve the introduction of your research question.

Line 96-100: Reference to this part, there are many approaches for multispecies analysis. It would be interesting to add some references to support this point.

Line 103-105: This point is clear in the first paragraph of the introduction. In this paragraph, it would be more interesting to see some hypothesis or expectations based on previous findings in the Atlantic ocean (Marko et al. 2010) or other similar studies around the world, to emphasize the importance of your question.

Line 105-106: It seem that there are previous studies on the western part of the Atlantic ocean but nothing in the Northeast Atlantic. It would be good to expand upon the knowledge gap being filled.

One of the strengths of this study is the wide literature searched and data reanalysis performed which are really well described and able to replicate. The literature search and the inclusion of the final studies is a considerable piece of work. I have a few minor comments about the species information included in the analysis that it may need to be clarify (from line 126 to 138):
-	Are they all covering the whole distribution range of the species? If you only include the sampling locations in the area of interest (northeaster Atlantic) you may need to clarify.
-	Have you include only endemic species?
Validity of the findings: The rationale and the benefit of using the literature for this meta-analysis are meaningful and well explained. It is clearly beneficial the used the existing genetic dataset to study the main question of this manuscript. I commend the authors for their extensive literature review and work in reanalysing the genetic dataset with a standardised methodology to uniform the wide range of methods used in previous studies.

On the other side, I have a major comment about the statistical methodology used. In this study, a mismatch distribution approach have been used and it seem to be useful in order to estimate the time of expansion in case it was detected. However, in order to examine the historical demography, there are many other studies supporting the used of Bayesian inference to improve the precision of the results (e.g Crandall et al. 2010; Villamor et al 2014). It has been found that the mismatch analysis provide only analytical approximation of substitution patterns expected from a spatial expansion, without considering genealogy, therefore it may yield less precise estimation. I would recommend considering the use of Bayesian Skyline Plots (BSPs) using the software BEAST v. 1.7.5 (Drummond and Rambaut (2007).

I thank you for providing the mutations rates references in the supplementary material, however the divergence dates used for the Carcinus maernas for example, were based on Crandall et al. 2012. And there are considerably higher than the ones reported by Roman and Palumbi 2004 (1.4-2.3% per Mya). Please can you develop why you used this mutation rates instead.

Discussion is well stated, linked to original research questions and limited to the supporting results. I have some minor comments about your first (Line 111) aim but I want to highlight that the other two aims are neatly discussed and linked to the original questions. I really appreciate the discussion about the possible limitations and future directions.

One of the aims in the introduction was (1) to identify commonalties (or otherwise) in contemporary genetic structure and you discuss some finding in the first paragraph of the discussion. I suggest that you clarify with a starting sentence in the paragraph (Line 268) if you did find some commonalities or not. In addition, in your report, you included interesting information about the pelagic larval duration for the studied species (Table 1). However, this information is not incorporated in any part of your manuscript and it would be worth developing some ideas. It would be interesting to mention if you observed the level of population structure (Fst/Djost) or/and the haplotype network found were related to the pelagic larval duration or otherwise, there was no relation. Speculation is welcome, but should be identified as such. Several studies have shown that PLD is a weak predictor of the genetic differentiation (Weersing & Toonen 2009;Kelly & Palumbi 2010; Riginos et al. 2011).

References:
Kelly RP, Palumbi SR (2010) Genetic structure among 50 species of the northeastern Pacific rocky intertidal community. PLOS ONE 5, e8594.
Riginos C, Douglas KE, Jin Y, Shanahan DF, Treml EA (2011) Effects of geography and life history traits on genetic differentiation in benthic marine fishes. Ecography 34, 566-575.
Weersing K, Toonen RJ (2009) Population genetics, larval dispersal, and connectivity in marine systems. Marine Ecology Progress Series 393, 1-12.
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: META-ANALYSIS OF NORTHEAST ATLANTIC MARINE TAXA SHOWS CONTRASTING PHYLOGEOGRAPHIC PATTERNS FOLLOWING POST-LGM EXPANSIONS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Well-presented and clearly written, with appropriate background / context and use of the literature, although a short summary of possible refugial areas for NE Atlantic species would have made the Introduction more complete.
Experimental design: Within scope of the journal.  Good meta-analysis of NE Atlantic phylogeographic studies on animals.  Approach clearly described.
Validity of the findings: Findings valid (if mostly unsurprising), and handled well in the Discussion.  Could possibly have included a comparison with findings from non-animal taxa (mostly seaweeds), which may present different patterns.
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: META-ANALYSIS OF NORTHEAST ATLANTIC MARINE TAXA SHOWS CONTRASTING PHYLOGEOGRAPHIC PATTERNS FOLLOWING POST-LGM EXPANSIONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: I have little to write here. The authors have been thorough, clear and concise. The paper is well structured, the analyses appropriate and the figures are good.
Experimental design: The study fits within the scope of the publication, with a relevant and timely assessment of past climate changes on the genetic demographic structure of a variety of marine fauna in the NE Atlantic. The authors have taken onboard suggestions by the reviewers to use a bayesian approach to estimating demographic history.
Validity of the findings: The authors conclusions are appropriate and reasonable given their findings. They provide useful new evidence filling a regional gap in our understanding of how past climate changes have influenced marine populations.
Additional comments: I have little to comment here, given that my queries and comments appear to have been adequately addressed. This is a good paper. The only thing I would note is that the figure caption for Fig. 5 (the BSP plots) does not clarify what the y axis is, nor what the dotted and solid lines are. Thus I recommend accept with this one minor revision.


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: META-ANALYSIS OF NORTHEAST ATLANTIC MARINE TAXA SHOWS CONTRASTING PHYLOGEOGRAPHIC PATTERNS FOLLOWING POST-LGM EXPANSIONS
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This meta-analysis of marine taxa in NE Atlantic is a very interesting piece of work with interesting results that help to understand patterns of connectivity and the influence of historical events in the spatial genetic pattern of the marine fauna. Well-written and presented and good definition of the limitations of the study.

One of my major concerns in the previous revision was the formula used for the time of expansion. The inclusion of bayesian skyline plots gives an important statistical support to the methodology.

I am more than satisfied by the authors' responses and I recommend this manuscript to be accepted. I appreciate the inclusion of the suggestions and the clarity in the responses and congratulated the authors for the work undertook.


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: CELLULAR PRODUCTION OF A COUNTERFEIT VIRAL PROTEIN CONFERS IMMUNITY TO INFECTION BY A RELATED VIRUS
Review round: 1
Reviewer: 1

Output:
Basic reporting: See below
Experimental design: See below
Validity of the findings: See below
Additional comments: This study demonstrates that exaptation of a non-retroviral RNA virus capsid gene by yeast can provide immunity to the cognate virus.  On the whole, the manuscript is clearly written and the results seem unambiguous.  However, the manuscript would profit from consideration of
1.	precedents of related phenomena provided by retroviruses (JSRV – Mura PNAS 101:11117, 2004; Fv1 – Goff Cell 86:691, 1996) and retrotransposons (Ty1 – Tucker Mobile Genetics Elements 6:e1154639, 2016).
2.	How many copies of cp are there in D.hansenii (line 93)?  What is cp1 (line 105)?
3.	In Fig1 it looks as though pG3cp1m is reduced compared to PC847.  Can these data be quantified?  How many repeats were performed?  How do levels of mRNA compare in mutants with ORFs (note – I couldn’t open SF1)?
4.	How do levels of cp1 expressed from pYES compare with those seen in D.hansenii? Can one demonstrate an effect from integrated “endogenous’ cp1 Do the results presented here really go further than those reported in Yao & Bruenn?


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: CELLULAR PRODUCTION OF A COUNTERFEIT VIRAL PROTEIN CONFERS IMMUNITY TO INFECTION BY A RELATED VIRUS
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: The authors focused one the interaction between introduced viral protein DhVcp1 and viral coat potein ScVcap, and they concluded that the introduction of DhVcp1 interfered the asembling of virus particles, and subsequently affect the persistence of SsVL1 in yeast.
I have some comments for cosideration
1. It will be much fine if authors delete the viral gene that intergraded on the genome of Debaryomyces hansenii, and then carry out transfection test with ScVL-A. If ScVL-A could replicate in the cp1-deleted D. hansenii, this study will be much convince.
2. The expression of cp1 in D. hansenii and in Saccharomyces cerevisiae may not be comparable. At least, authors need provide the expression data.
3. May S. cerevisiae have strong response when a viral gene is introduced in cells? Why did authors use a strain PC847, in which ScVLa is absent? I read the Materias and methods and I was told that PC847 were infected by ScVL1, ScVLa and ScVM1? If authors use the strain which carried both ScVl1, ScVla and satelite virus ScVM1, and perform this study, it will be much convince.
Validity of the findings: This finding is very interesting; it will significantly help us to understand the functions of NIRVs in eucaryotic organisms. But the presented data is shortage of enough convince by my own judgement.
Additional comments: 1. The hypothesis in this study is the D. hansenii virus NIRV (DhV) cp1 might cure ScVL1 but not ScVLa due to similarity of the target proteins (coat protein), thus, this study should present the data that DhVcp1 could not cure ScVLa.
2. If authors did not use strains PC4391 and CBS767 in the current study, delete the infomation of these two strains.
3. The dsRNA bands of ScMV1 should appear in Figure 1 (top pane ).


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: CELLULAR PRODUCTION OF A COUNTERFEIT VIRAL PROTEIN CONFERS IMMUNITY TO INFECTION BY A RELATED VIRUS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Clear and unambiguous, professional English used throughout: fair

Literature references, sufficient field background/context provided: fine

Professional article structure, figs, tables. Raw data shared: basically fine (see comments to authors)

Self-contained with relevant results to hypotheses: sufficient but additional confirmation is welcomed (see comments to authors)
Experimental design: Experimental design is fine.
Validity of the findings: Findings in the study is important and has great impact. Conclusion and hypothesis was all based on obtained data from in-vivo, in-vitro and in-silico experiments.
Additional comments: The manuscript of Warner et al. reports the first example of contribution of an endogenous non-retroviral RNA virus element (NIRV) on immunity against a yeast RNA virus in the Saccharomyces cerevisiae pathosystem. The authors proposed a hypothesis of mechanism how the NIRV conferred the immunity that an NIRV product originated from probable ancient totiviral capsid protein gene integrated and interfered virion assembly of present virus ScVL1. Although the evidence supporting the hypothesis is not so strong, the finding is very interesting and worth disseminating to researchers as it stands. Followings are minor considerations for improving the paper.

Some fluctuations found: (His-tagged, his tagged) and (6xHis tags, 6xhis tags), ‘His-tagged’ and ‘6xHis-tag’ may be better?
L113: ScVL1 capsid protein (cap) N terminal fragments...
L118: caps means capsids?
L157, L282, L421: Western(s) may be Western blotting
L159: Mouse anti PENTA Histidine Tag:HRP (BioRad)?
L183: the resultant sequence was cloned into...
L203-L210: this paragraph needs more explanation about obtained data; the yeast/virus materials are also deferent from ones in the former paragraph, please describe
L224: give a space after COOT
L242: pYEScap
L251: proteins were analyzed
L255; ScVL1
L233-260: (comments) In my understanding, physical interaction of proteins is usually examined and evidenced by two or three different approaches because of potential false positive output. I guess the authors tried several approaches but suffered from a problem that cp1 expression resulted in degradation as shown in Fig. 3. Yeast two-hybrid system may be useful and easy to confirm the interaction between DhV-cp1 and ScVL1-cap.

Legend to Fig. 1: the upper panel shows electrophoresis of dsRNA fraction
Fig. 1: quality of the figure may need increased especially the middle panel; spaces need between number and kbp/bp; L1 on the right may be ScVL1
Legend to Fig. 4: (ScV int.); figure title and explanation are hard to follow, please restate clearly in a form consistent with description in L249-253
Fig. 4: there is no labeling on X- and Y-axis parameters
Supplementary Fig. 1: this figure carries important data and could be moved to main body of manuscript


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

Input:
Title: SIZE DIMORPHISM AND SEXUAL SEGREGATION IN PHEASANTS: TESTS OF THREE COMPETING HYPOTHESES
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This manuscript reports the testing among several hypotheses that have been proposed (primarily based on studies in ungulates) to explain sexual segregation in the non-breeding season. Using pheasants hatched in captivity and then released to the wild, patterns of attendance at feeders relative to predator observations, gut contents of hunted birds, and activity patterns were assessed for individuals in their first year (prior to first reproduction) to provide data that should test among the three proposed hypotheses. The sample sizes are reasonable, though they found no support for any of the three tested hypotheses. However, each hypothesis does have a unique prediction that is testable, the authors are appropriately cautious in interpreting their results, and the manuscript is largely easy to follow.

1. I found it of interest that all of the hypotheses are explained, at least in part, by acquisition of food (males have exposure to greater predation risk to obtain higher quality food resources, males may need to exploit different food resources, males have greater activity due to need for greater energy acquisition). This might suggest that there could be many situations where sexual segregation may be due to a combination of all of the hypotheses, rather than just one (as the authors allude to) rather than to any single hypothesis. This raises the question about whether an analysis that might look at the hypotheses collectively could explain this behavior. I wonder if there might be more sophisticated analytical approaches that might look to see if a model that incorporates all of the data could potentially explain sexual segregation (I admit I am not certain whether there are appropriate analyses that would be suitable, but possibly some sort of structural equation modeling?).

2. No mention in either introduction or discussion is made about whether any aggression is known to occur between the sexes outside of the breeding season, either from published studies or from data collected as part of this study. This might be of interest to mention, as it could get at whether segregation is due to each sex preferentially seeking the same sex, or whether it was in part due to one sex excluding the other.

3. In the discussion, the authors raise some reasons why these hypotheses might be applicable to mammals, but I think this could also be raised in the introduction as a reason to evaluate this in a different type of taxa (e.g., taxa where much of the dimorphism is dichromatic, and less so for body size).

4. Lines 83-84: Do female birds have a smaller gut? Later on this is tested, but at this point you might indicate this is not known for birds (or if it is, what taxa and/or that it is variable across taxa).

5. I found some of the methods hard to follow, particularly the differences among years (they were raised slightly differently, data from some years used for some tests, etc.). Perhaps a table or flow chart that might include what was done with what birds raised in what year would help readers better follow what was done.

6. Lines 411-414: I think this is an important point that I am glad you brought up. I agree that they segregate at this stage, so this is only relevant to the hypotheses if selection for segregation at older ages drives segregations at this earlier age.

7. Line 435: In line with the previous comment, if aggregation behavior gets stronger as they age, then potentially future studies should evaluate this behavior in after hatch year birds rather than hatch year.

8. The discussion brings up the social preference hypothesis. However, from the introduction, it sounded as if there might be additional hypotheses that have been suggested to explain segregation. Although they were not tested, if these exist it might be nice to bring up in the discussion the ones that might be applicable to pheasants and discuss whether they are likely given the data and what is known about pheasants (or birds in general).

9. Figure 2 - why not show males versus females (since that is relevant to the hypothesis)?

10. Table 1: You already indicate that all of these hypotheses are for sexually dimorphic species, so I think that the column saying "yes" on this is not necessary. Indicating that you would not expect something to occur when taxa are monomorphic also seems unnecessary (particularly as this study ONLY included a species known to be sexually dimorphic, and you justify using that species partially due to that).

11. Table 1: The number of predictions based on information in the introduction is much longer than what is shown here. If these are just the predictions used in this study, then the monomorphic comments (given that the species is dimorphic) is not relevant. If it is more general, then I would include more in this table (possibly indicating those traits you studied).

12. Table 7: What does "Sig" mean? In my version, some of these values go on two lines and I am not clear what this means as the values are not what I might expect (e.g., in table 5, it is clear what Sig means as you indicate a p-value for each trait).


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: SIZE DIMORPHISM AND SEXUAL SEGREGATION IN PHEASANTS: TESTS OF THREE COMPETING HYPOTHESES
Review round: 1
Reviewer: 2

Output:
Basic reporting: While the MS is generally well written throughout, there are a number of issues that could be improved, outlined below:
1.	There are a number of different datasets used, in terms of birds sourced and raised under a range of different conditions. While I believe that this is handled OK during the analyses, it can at times be difficult to follow. I suggest putting the rearing conditions listed in the methods in under the methods for each hypothesis to be tested. That way the reader knows the history of the birds for a given hypothesis, without needing to recall what happened in year X.
2.	The results could be improved through clarification of the language in regards to statistical outcomes. For example, lines 343-5, and again on line 364 and Line 372 -  did these groups differ significantly? Line 353 what was the actual proportion here? Clarification for all results presented in this manner would improve readability immensely.
3.	Line 488. Negative results can be difficult to interpret, but the newly proposed hypothesis should be dealt with prior to introduction during the conclusion section. Deal with likely interpretations, potential new hypotheses and so forth in sections prior to the conclusion, which should be a concise summary of the paper's findings.
Experimental design: This is comprehensive and a great use of multiple sources of data to test several hypotheses. No specific comments, looks sound.
Validity of the findings: No comment.
Additional comments: 1.	It would be helpful to know the scope of the project in terms of the monitoring methods. For example, we know how many birds were released and how many were detected, but this is not easily obtained for all birds. For example, Line 38 states 2400 birds released, then Line 40 that the authors 'determined their fate', however not all birds were recovered. It would be very useful to know how many individuals were detected on camera, observed in the field, measured gut etc for the relevant hypotheses at the start of the methods.
2.	Line 50. This conclusion re: flight doesn't follow the data presented, and is particularly strange for a game bird that spends so long on the ground. Some of the most dimorphic species (e.g. large raptors) have superb flight capability, so this conclusion doesn't appear warranted based on data presented for mine.
3.	Too often the paper refers to unpublished material, or another paper for key results. For example line 129 – how did social preferences drive this segregation? How natural were the rearing conditions? Line 175: the details are pertinent in this paper and should be summarised for the reader here, rather than requiring them to go to another paper for the information. I suggest that the authors search for all of their self-citations and include some base detail where the reference is not currently available, and/or it is key information for this paper.
4.	Line 157. State the prediction here specifically.
5.	Line 170-3. Be specific here: release notes lower numbers that was an unnaturally high density – which is it and what was the actual density to begin with? This whole paragraph could be reduced in length for the introduction – much of this is methods.
6.	Line 315: Again, be specific, what distance, and how was it ascertained that this was not disturbing the birds?
7.	Single sentence results with a new subheading for each is very difficult to read – suggest restructure.
8.	Table 1 is not required and could be text. Table 2 could be supplemental material. Give degrees of Freedom for F statistic in Table 5.


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: SIZE DIMORPHISM AND SEXUAL SEGREGATION IN PHEASANTS: TESTS OF THREE COMPETING HYPOTHESES
Review round: 1
Reviewer: 3

Output:
Basic reporting: No comment
Experimental design: No comment but see my General Commnents to the Author
Validity of the findings: No comment but see my General Commnents to the Author
Additional comments: This is a generally well written paper where authors try to disentangle the importance of various hypotheses to explain sexual segregation in the pheasant. My main concern is that all conclusions are based on artificially reared chicks, and thus the sexual segregation as adults could be influenced by a number of factors derived from the artificial setup. This artificial setup does not only affect the imprinting and socializing processes prior to release of the birds into the wild, but also the period during adulthood due to various causes, notably: (a) a possibly non-natural sex ratio at release could affect the behaviour of immature and adult birds when integrating into flocks; (b) the abnormally high density at release could also affect the behaviour of the birds in the wild; (c) the artificial feeders, and the perception of risky environments based on just the previous presence of foxes at them, ignoring raptors and hunting, does not emulate a natural situation.
At least I think the authors should discuss all these issues, and include a critical statement where they clearly admit that their study is based on artificially reared birds, and that the behaviour of released pheasants could have been critically influenced by the artificial setup and might not be extrapolable to a wild population.

A second main concern is that if the authors did not specifically test for the Social Preference Hypothesis in this study (see their own assertion in lines 497-498), then they cannot take that SPH is the most relevant as a conclusion of the current study.

Other important comments:

Introduction:

Second paragraph: There are more than three hypotheses to explain sexual segregation (Ruckstuhl & Neuhaus 2005 pp 15-19). Why do you reduce this number to three? Why not introducing here the Social Attraction and Social Avoidance Hypotheses as well? And what about other 'minor' or less studied hypotheses like the Weather Sensitivity or Physical Condition Hypotheses? If you exclude them here you should justify why.

lines 128-131: I do not agree that during adulthood social preferences may not be as important as other factors to explain sexual segregation.

lines 117, 128, 140, 176, 388, 435.....: I am not sure whether it is justified to cite here a submitted ms? There is no guarantee that this paper will be published, and I would suggest omitting reference to all these results from the present paper. The only section I would perhaps admit citation of this paper is the Discussion.

How could have the 8-10 week rearing period in captivity affected the biologically natural tendency to sexual segregation?

Methods:

line 199: Were the 30-individual groups mixed-sex groups? In which proportions were male and female chicks mixed in these groups? What was the sex-ratio at release? Please explain and discuss possible consequences of these factors for the social segregation hypothesis.

lines 206-207: What do you think could be the effect of feeding chicks on commercial chick crumbs on their possible sexually differential Forage Selection as adults?

Results:

To test the PRH you just used feeders, but you could have also used the time spent at other natural sites estimating the predation risk through other variables, e.g. presence of raptors, horizontal visibility of the foraging spots, etc.

lines 379-383: The Activity Budget Hypothesis test is not convincing. I can hardly believe that males and females spent the same time foraging/resting, and suspect that the absence of a difference is due to sample size and inappropriate parameters measured. For example, you could have compared the pecking rate of males and females, which I would expect to show some differences.

Discussion:

lines 391-393: Here you cite several examples of mammals, but since your study species is a bird, you should include some examples of birds showing SSD, at least great bustards which show the strongest SSD among birds (Alonso et al. 2009: The Auk 126:657-665), but maybe also others like González-Solis 2004: Oikos 105: 247-254, or the review by Payne 1984: Ornithological Monographs 33.

lines 398-406: These conclusions to me are not very convincing. First, the time taken to visit an artificial feeder is clearly not the best way to estimate risk-sensitivity. Second, it is very improbable that mortality rates do not differ between sexes in a species showing clear SSD.

lines 470-477: To exclude the Activity Budget Hypothesis as a major cause of sexual segregation, you only measured foraging, resting and walking, but not other social behaviours like interactions related to dominance and mating, which might also be very relevant in determining sexual segregation. I would expect males spending more time performing these activities than females. Thus, I am not sure that excluding the ABH as a relevant hypothesis is justified.

The conclusion about "avian systems" in lines 506-508 is not justified with just your example with pheasants. Other avian species show clear SSD and sexual segregation (great bustards are the most remarkable example, see e.g. Bravo et al. 2012: Bird Study 59: 243-251, Bravo et al 2016: The Auk 133: 178-197).


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: MOLECULAR ANALYSIS OF ORAL MICROFLORA IN PATIENTS WITH PRIMARY SJÖGREN’S SYNDROME BY USING HIGH-THROUGHPUT SEQUENCING
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors have provided a clear unambiguous and professional manuscript, that has been well researched and appropriately referenced.

The article is appropriately structured, including correctly labeled figures and tables. The authors have made all data available, however the accession number submitted in the manuscript, reads SRP133569 instead of SRP133529.

The authors have clearly reported a number of appropriate results in the results section however some results not mentioned in the results section are reported in the discussion. It would be appropriate for the authors to report all results within this section, specifically their investigation of differences in specific bacteria, namely Streptococcus and Veillonella in the results.

The authors aimed to reveal any connections between the oral composition and dental caries. Data shown in previous studies was backed up by comparing pSS patients to healthy controls, however, data includes the severity of dental carries in the form of DMFTs and DMFSs, it would be important to explore how the bacterial community changed with the severity of dental changes not just the changes between the 2 groups of patients. This would also allow the validity of Veillonella to serve as a biomarker for disease.
Experimental design: This article is within the aims and scope of the journal and the authors clearly define the knowledge gap they are investigation.

The authors were careful in patient selection however no mention was made of controls being included in sequencing. The inclusion of negative controls or mock communities would be important to confirm there was no contamination. If this was performed, please include the data.

The region of the 16S rRNA gene sequenced was longer than usual for paired end sequencing of 16S, information on how the forward and reverse reads were paired would be useful.

Which chimera checking algorithm was used through mothur?
Validity of the findings: The authors have thoroughly researched the literature and appropriately sited appropriately throughout the paper. No previous publication appears to have investigated the microbiota in SS and its association with dental carries. This appears to be an interesting area as the authors show significantly more decayed, missing or filled teeth or surfaces were observed in those with pSS compared to healthy controls.

The authors carefully explored differences between the pSS patients and healthy controls, however failed to further investigate any correlation between the bacterial community and the dental carries. In order to further added to the field and answer the hypothesis, it would be important to explore how the bacterial community changed with the severity of dental changes not just the changes between the 2 groups of patients. This raw data is presented in the attached demographic and clinical data however this investigation does not appear to have been performed.

It is hypothesised that Veillonella may serve as a biomarker in pSS, is Veillonella increased in pSS patients with more severe carries? A box plot or other appropriate diagram to show the range of Veillonella abundance within the groups would be useful.
Additional comments: 1.	Line 313-315: The authors assume that an increase in Veillonella increases dental carries, does the data back this up within the pSS group?

2.	Please clarify line 284 – 289, It is unclear which study you are referring to.

3.	Previous studies have measure oral dryness, was this examined in your patients

The discussion of pH was extremely interesting and would be very interesting to investigate further. This may not be possible for the current study but is a very useful and important point.


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: MOLECULAR ANALYSIS OF ORAL MICROFLORA IN PATIENTS WITH PRIMARY SJÖGREN’S SYNDROME BY USING HIGH-THROUGHPUT SEQUENCING
Review round: 1
Reviewer: 2

Output:
Basic reporting: Methods are not described to the detail that allows others to repeat the study. some parts, eg, lines 117-119, are incomprehensible due to lack of explanation (in this case, which females, SS patients?) and placement in the text (right after the description of the control group).
Figure legends not complete (eg, fig 1 misses description on what is CR and RR group). Supplementary table on demographic and clinical data - no explanation on what is reported in all those columns starting with C. Figure 4 legend is unclear and should be improved.
Experimental design: Regarding methods, more detail is needed in the part about subjects.
Caries prevalence should be defined. Does this mean only decayed, or the entire DMFS index, thus including filled and missing surfaces?
Was power analysis performed? How is sample size justified?
Validity of the findings: lines 172-173: referring to the question about caries prevalence, in supplementary table on demographic and clinical data, there is one individual in the SS group (assuming that 0 stands for SS group, which again, is not clear) who has 0 decayed surfaces. Nevertheless, the results part in lines 172-173 states that SS group had 100% caries prevalence. Do authors account fillings and missing teeth as caries? That is called 'past caries experience' (assuming that the extractions were performed due to caries, and the same goes for the fillings).
Throughout the results part (and also in the abstract), authors should avoid using terms as 'much lower' , but, instead, report, if the difference was statistically significant, and report the p value.
The same goes for descriptions such as 'relatively concentrated tendency' (line 216 -  'the structure was more conservative' (line 409-410). Please use more scientific descriptions.
Avoid using terms suggesting that this was a longitudinal study, eg, 'clear change in microbial ecology was present' (line 269), 'there was a sharp decline in diversity..' (line 345) etc.
Figure 3: thisfigure does not add any useful information for the reader. Instead, variation in the data (standard deviation per taxon) should be presented.
lines 381-386: here the low sample size should be discussed as a potential reason for lack of difference. Judging from the supplementary figure S3, the beta diversity is quite different, just the groups are too small to get this statistical.
Discussion on Veillonella should be carefully revised - the metabolic products produced by Veillonellae are less cariogenic than lactate (higher pK acid than acetate or propionate) - the energy source and substrate for their metabolism. Increase in lactate production by streptococci is accompanied by increase in Veillonella population and lactate reduction. Most likely link with higher caries prevalence is that absolute numbers of these organisms are higher, thus also the streptococci, resulting in more total acids. Salivary role in clearance of acids has not been mentioned, but is a known reason for caries.
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: MOLECULAR ANALYSIS OF ORAL MICROFLORA IN PATIENTS WITH PRIMARY SJÖGREN’S SYNDROME BY USING HIGH-THROUGHPUT SEQUENCING
Review round: 1
Reviewer: 3

Output:
Basic reporting: Article “Molecular analysis of oral microflora in patients with primary Sjögren's syndrome by using high-throughput sequencing” study the microbiome in Sjögren's syndrome compared to healthy subjects. The topic of the work is interesting and well-balanced disease and control subjects using 16S molecular techniques. However, some improvements should be addressed
Experimental design: Introduction
The author mentioned line 67 “Researchers have performed several experiments to study oral bacteria in pSS patients” however they didn’t cite the most relevant articles in the last years regarding oral microbiology and Sjögren's syndrome.

Material and Methods
Authors indicated received radiotherapy or treated with drugs. Due to the low number of disease subjects, should be clarified the clinical data. I suggest including a table by subject following info: drugs, chemotherapy treatment, dmfts, oral lesions present during the sample collection, salivary flow rate and demographics such as gender and age.

Bioinformatics analysis was not reported the software used. If the authors used R, should include the packages used (e.g., vegan, ape…) in the methods and the references sections.

I didn’t find negative controls to discard contamination during experimental procedures. Did the authors collect samples for negative control evaluation? Please, indicate and submit the sequences of the negative control samples (extraction and PCR controls)
Validity of the findings: Results
Section 3.1 and 3.2 should be compressed in one, excluding the paragraph line 188-198 (first paragraph of the microbiome analysis section).

Table 1 should include more clinical info relevant to the results such us, flow rate, drugs or radiotherapy treatment.

The authors could start the results describing the cohort selected and explaining the specific clinical characteristics related to the goal of the study, justifying the relevance of caries in the disease cohort.

Paragraph lines 183 to 187 and Figure S1 are not necessary to evaluate the results. I suggest removing the paragraph and Figure S1

Sections 3.3 and 3.4 starting from paragraph line 188-198 should be compressed in one describing the bacterial composition of the cohort.
I suggest revaluating figures to be more informative and precise for the reader to understand.
-    The authors could include as Figure 1 Heatmap including individual samples might show the cluster of the most abundant genera in healthy or disease (as they mentioned Veillonella after).
-    Figure 2 could be boxplot grouped by Healthy vs. Sjogren for Fig. 2A Richness and Fig. 2B Diversity that would be a more clear visualization of the data to evaluate the differences among study groups
-    Figure S3 should be part of Figure 2 as Figure 2C using PCoA plot. Please, evaluate using PERMANOVA the groups CR and PR centroids to reanalyze the statistical significance of the groups, and indicate the percentage of the axis PC1 and PC2

Next section is the most relevant of the study should be developed in more detail, due to the authors found Veillonella as the most pertinent genus related to the disease. Did consider the authors to have a more in-depth analysis of the genus, by species level (e.g., OTUs of Veillonella found or qPCR of the main spp.)?

Section core microbiome could be shown by the heat map (suggested as figure 1) and do a 16S hierarchical clustering of the samples. Some of the genera are related to contamination in other studies, please evaluated by negative controls those findings are real taxa of the samples.

Discussion
The first paragraph should include a resume of the cohort, findings, and conclusion of the study. Please add the section.

Caries is related to some bacterial species, but the authors highlight S.mutans. However, one of the significant findings of this study is Veillonella. Sample chose to rinse not a plaque, so others oral niches could be represented as gingival, mucosal, tongue among others, implying multiple oral manifestations beyond caries that the authors didn’t evaluate.

Lines 333 to 335 is not clear what the authors were claiming. Please, rephrase.

The authors mentioned pH (line 338), decreased saliva (line 354) and medication (line 357) as a possible explanation for the disease microbiome. Did the author measured the pH, salivary flow rate and collect medication info on the subjects? If they did, please include as part of table 1.
Additional comments: They have a good potential in their study, but the authors should consider reanalyze the micriobiome data to cover better their conclusions.


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: MOLECULAR ANALYSIS OF ORAL MICROFLORA IN PATIENTS WITH PRIMARY SJÖGREN’S SYNDROME BY USING HIGH-THROUGHPUT SEQUENCING
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have successfully addressed the issues raised in the first review.

There are some very minor errors that should be corrected prior to publication:
157: "reads were underwent paired-end *reads merging using Mothur" *extra reads not required
161: OTU - operational taxonomic unit
216: should read "matrix"
Fig1: "Heatmap *that all samples" *of

Fig2: Diversity measures do not correlate with higher or lower alpha diversity they indicate or describe the community.
Higher Simpson index (D) does not correlate with lower alpha diversity, it indicates or describes lower alpha diversity. Some researchers find it helpful to use 1-D (Simpsons index of diveristy) or 1/D (Simpsons reciprocal index) to prevent confusion.

"Box plots of alpha diversity measure using Ace (A), Chao1 (B), Pielou (C) and Shannon (D) and Simpson's index (E) show a decrease in diversity in the rinse samples from pSS patients."
Legend should indicate the PCoA was carreid out using weighted UniFrac distance.
Experimental design: Could you please indicate what length of overlap you used to pair the reads.
Validity of the findings: Thank you for adding in the extra analysis, this makes the manuscript much clearer and more informative.
Additional comments: Thank you for your clear response and addressing the issues raised by the reviewers.


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

Input:
Title: MOLECULAR ANALYSIS OF ORAL MICROFLORA IN PATIENTS WITH PRIMARY SJÖGREN’S SYNDROME BY USING HIGH-THROUGHPUT SEQUENCING
Review round: 2
Reviewer: 2

Output:
Basic reporting: The changes made the article clearer. The authors changed all based on my suggestions. I Think the paper is very relevant.
Experimental design: Negative controls, clinical data, and bioinformatic analysis details provide more reproducibility and clinical significance of the work
Validity of the findings: Robust Microbiome findings and statistically supported
Additional comments: I appreciate the authors made the changes that I suggested


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: DYNAMICS OF NITROGEN AND ACTIVE NITROGEN COMPONENTS ACROSS SEASONS UNDER VARYING STAND DENSITIES IN A LARIX PRINCIPIS-RUPPRECHTII (PINACEAE) PLANTATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: Basically, it is easy to read and understand. But I have hard time to know exactly the meaning of some sentences. “Dissolved organic nitrogen … nutrient availability” (at Line 53-56) might be problematic in grammar. Line 227-229 is confusing. Please ask the English native writer to help modify the whole paper if possible.
I am not sure if I understand your third question right (at Line 83). Do you mean how the environmental factors influence the N pools?
Some typo errors: Line 19, 146, 152, 209, 235, 249-250.
It is very vague to say “more and less severe thinning treatments”? (Line 216) Could you please provide a clearer way?
Since the authors want to compare the N components at two aspects - treatments and seasons, I would suggest the authors to illustrate the comparisons in order, that is, effects of treatments first and effects of seasons second; or vise verse. It might be clearer and easier for reader to follow and compare.
For a clear frame of paper, I might suggest the authors to list sub-titles in Discussion which could correspond the sub-titles in Result.
At Line 358, you mentioned “enhance the soil N pool”, did you mean to enhance the accumulation or transformation of soil N pool. It is better if you give a clear point here.
I was confused by your labels on x-axis in the figure 1, so please double check the labels.
Experimental design: Could you provide the descriptive characteristics of the background information (e.g. altitude, grade, slope direction and soil condition, etc.) of the stands you chosen for quadrats?
What is the scientific or empirical criterion to set the ratios of thinning?
I am confused by your quadrat design. As I think you have 3 quadrate which includes 12 study treatments, but you said “three sample area (which equals to quadrat) was designed for the 15% thinning (Line 103-104). Could you please explain it? Or could you please provide plot design graphs to illustrate?
For the measures of light environment, could you please explain why you choose July? What was the time in a day as you measured? And how many times did you conduct the measures in 2015 and 2016, respectively?
As many factors, besides the main interest of thinning, would impact the soil N and C cycles, so I might suggest the authors to consider some other statistical methods to identify the importance among those factors, like redundancy analysis (RDA).
Validity of the findings: Why the soil temperature was higher in MT in 2015? Do you have a reasonable explanation? (Line 197)
How did you calculate the total biomass at Line 197?
For the understory, did the local clear the weeds or understory? If yes, do they use herbicide or other ways?
Did you apply fertilizer to the plantation? If yes, what is the amount and kind of fertilizer?
What is your purpose to add figure 6? What are the potential impacts of runoff and sediment concentration on your current results?
In table 2, it looks like the soil respiration shows obvious difference between 2015 and 2016. Could you use paired t-test to examine if these environmental factors statistically differ between 2015 and 2016?
I would suggest you enhance your results interpretation and discussion based on table 4. Because table 4 is actually the core to support your research and findings.
Additional comments: No additional comments


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

Input:
Title: DYNAMICS OF NITROGEN AND ACTIVE NITROGEN COMPONENTS ACROSS SEASONS UNDER VARYING STAND DENSITIES IN A LARIX PRINCIPIS-RUPPRECHTII (PINACEAE) PLANTATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors reported on how the process of thinning in forests could positively or negatively impact the soil nitrogen and carbon profiles. The literature cited within this research project is sufficient for the objectives and clearly states the requirement of thinning within agricultural forestry practices. The research rational is very applicable to the forestry industry and the hypotheses regarding thinning and soil interactions have been established. The structure and visual elements of the manuscript is acceptable. Authors should consider their figure legends to be of international reporting standard (figures labeled at the bottom, tables at the top). Some figures are of poor quality which hinders the readers ability to clearly distinguish. Within the review manuscript, tables are incomplete (it is cut off toward the end of the page). Figures should be re-submitted in higher quality format.

However, there are some grammatical errors within the document and it would be advised to send the manuscript for English grammar correction. Authors should also note that there are clear differences in font size throughout the manuscript and line spacing is inconsistent, which needs to be addressed. Authors should also consider placing their equations within a text box, or at least in the centre of the page.
Experimental design: The primary research objectives fits within the scope of PeerJ and the authors stated their research rational. This rational is relevant within the agricultural forestry industry and could potentially have a positive impact on future ecological and conservation ventures. The process of thinning (and how the authors compared the various degrees of thinning) and its impact on soil nitrogen and carbon flux provides a meaningful contribution to the knowledge within the specified field. The experimental design addresses all the necessary components (including microbial) which could influence soil nitrogen and carbon content and the experimental process has been given in enough detail to reproduce.
Validity of the findings: This study looked toward potential strategies for the improvement of soil nitrogen and carbon assimilation, by looking at thinning processes within plantations. It was concluded that moderate thinning could potentially be of great value, when applied, to species diversity and assisting in the growth of a variety of organisms above- and under-ground. This interaction between species is very important in maintaining the soil nitrogen and carbon content.

The authors clearly stated their conclusion and this study could hold very meaningful outcomes for future forestry practices. Findings are valid and, the authors acknowledge the need for further research within their hypotheses.
Additional comments: No general comments. I wish for the above-mentioned review comments to be sent to the authors.


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: DYNAMICS OF NITROGEN AND ACTIVE NITROGEN COMPONENTS ACROSS SEASONS UNDER VARYING STAND DENSITIES IN A LARIX PRINCIPIS-RUPPRECHTII (PINACEAE) PLANTATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: General comments: I have read the manuscript “Dynamics of nitrogen and active nitrogen components across seasons under varying stand densities in a Larix principisrupprechtii (Pinaceae) plantation” (Ma et al). Undoubtedly, the present manuscript has been improved significantly after careful revision. Authors conducted measurements of soil nitrogen and its active components during the growing seasons and corresponding environmental variables with four treatments, and performed appropriate statistical analyses. This study indicates effects of forest management (thinning) on soil nitrogen pool in a larch plantation and the moderate thinning exhibits more important role for the accumulation of soil nitrogen pool by adjusting a series of factors. The manuscript is well organized, the results are interesting and fits to the scope of the Journal.

Specific comments:
Line 19: soil respiration?
Lines 27-28: I think these conclusions should be rewritten, because the conclusion is based on your findings rather than inference
Line 135: Why did you conduct only one day’s measurement of soil respiration?
Line 268: affected
Line 294: and
Line 307: There should be a blank before and after “=”, just like before, and this should be consistent throughout the manuscript
Line 328: delete the comma
Line 343: unclear, is that mean the environmental factors in moderated conditions would be better for microbes and plants?


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: FUNCTIONAL RESPONSES OF A COSMOPOLITAN INVADER DEMONSTRATE INTRASPECIFIC VARIABILITY IN CONSUMER-RESOURCE DYNAMICS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a well-written piece of research that aims at comparing the role of different populations of an invasive crab species in several areas, both native and colonised, concerning predator-prey functional responses. There are however some points, noted below, that need clarification.

The authors have a good background and the references used are relevant. There are however some points, that need to be further developed.

The structure of the article is correct. The section on Results is however rather short when compared with the rest of the sections.

SPECIFIC COMMENTS
Abstract
-	Line 28: the acronym is not necessary here.
-	L 30 I would change the sentence by something like: The European Green Crab Carcinus maenas is a northeast Atlantic intertidal and shallow water species which has become invasive in several regions around the world (it is not a globally invasive predator "per se". It's not its fault, but probably ours).
-	L40: "Type II functional response". Not adequate in the Abstract. This is specialist jargon; not many readers may know what this means (myself, for example). It should be explained in a more intelligible way.
-	L42: A more precise meaning of "higher attack rates" should be presented here. By itself, I could not visualize what an attack rate could be.
-
Introduction
-	First sentence, L59: As indicated above, species are not invasive per se. Some of them have become invasive in some areas.
Experimental design: The experimental design is simple and robust, but it probably would need a larger number of replicates.

Both C. maenas and C. aestuarii are present in South African waters. This should have been taken into account and could modify conclusions reached. No reference at this "problem" is found in the manuscript.
-	The sample size used (a minimum of 18 male crabs) by study area is not that large. A slightly larger sample size should not be that difficult to obtain for Carcinus. Sample sizes larger than 25-30 individuals have been shown to strongly diminish overall variability in means and proportions in many population biology studies. I recognize the effort done to sample and run the experiments, but this point should be clarified.
-	Given the importance of handling time and of the success rate when running the experiments, information on moult stage of the crabs used should be given. Information on "red" vs "green" morphotypes, which is a proxy of the time spent since the last moult could perhaps be obtained from pictures of the individual crabs used, if they are available.
-	L227: I have some doubts on the grouping /combining of British Columbia (Pacific) and Nova Scotia (Atlantic) into a single group for further comparisons (even though results are not significantly different). The study areas are so different and separated that I think this is not necessary.
Validity of the findings: There is one main problem concerning the experimental design. I assume that the authors have identified correctly the crab species they are dealing with. There are two species in the genus Carcinus: C. maenas, and C. aestuarii, sometimes somewhat difficult to morphologically identify, and can be identified through genetics analyses. Both species, especially C. maenas, have shown invasive characteristics and are, or have been present in at least one of the study areas, South Africa. There is no reference to this fact in this manuscript. Some of the differences found may be related to the use of, at least some, crabs belonging to C. aestuarii.

Discussion

-	Calcification differences with temperature,both in predator and prey, as well as  co-evolution between predator and prey, are points worth of being discussed.
Additional comments: No further 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: FUNCTIONAL RESPONSES OF A COSMOPOLITAN INVADER DEMONSTRATE INTRASPECIFIC VARIABILITY IN CONSUMER-RESOURCE DYNAMICS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Some of the figures are difficult to read. For example, for Figure 1 native and invaded ranfes are difficult to identify due to the selected colours (black and dark gray).
Same proble for figues 2 and 3. No clear and "clean" distinction beteween blacka and darke grey.
Figures 2 and 3 offer redundant information. Keep only one of them. I suggest to keep Figure 3.
A more professional aspect for figure 5 should be great

All other aspects are fine for me.
Experimental design: The comparison between invaded and native range is flawed. Three different regions are used for invaded but only one for native range (Ireland). No formal comparison is possible. The native region is un-replicated and this lead to confounding (or pseudoreplication). With the described design, the interpretation should be limited to compare differences among 4 regions, but formal discussion van be done on the differences between native and invaded range.
In general, I don’t not like feeding experiment made in the laboratory. At best, they have difficult interpretations. In most cases, animals are forced to consume the preys that may be unfamiliar for the consumer. And it is done under environmental conditions far from natural conditions. Extrapolation to the field may be flawed. Of course this is a very biased point of view.
Starvation is not a very good idea in feeding experiments, as it can artificially influence the response of the consumers
I also have serious doubts on the validity of single choice experiments as it may force unnatural behaviours in the consumers. This is relevant for the exact shape of the functional response. Assuming that a handling time exist, only a type II response should be expected. With a single food item, Type III responses cannot appear if they arise as a consequence of density dependent predation.
The experiment might be of limited value if mussels are not the exclusive or most common food item in the diet of the crabs (as it is suggested in lines 358-361).
Validity of the findings: Lines 257-262: You must give a justification for the Kruskal-Wallis and the Welch tests. There are more efficient alternative to those tests.

It is not clear to me how handling times were obtained. Were they estimated or directly calculated?
Main results are a bit disappointing: (i) increasing prey density results in a decreased proportion of animals killed (expected if handling time is relevant); (ii) the proportion killed increases with claw size (expected if claw size influences handling time); and (iii) in one region mortality is larger than in other regions, but this cannot be related to the difference native-invaded range (due to the pseudoreplicated design).
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: FUNCTIONAL RESPONSES OF A COSMOPOLITAN INVADER DEMONSTRATE INTRASPECIFIC VARIABILITY IN CONSUMER-RESOURCE DYNAMICS
Review round: 2
Reviewer: 1

Output:
Basic reporting: This second version of the manuscript has been modified taking into account my main comments and suggestions included in my previous, full, revision.

I therefore consider that it is now ready to be approved for publication.
Experimental design: This second version of the manuscript has been modified taking into account my main comments and suggestions included in my previous, full, revision.

I therefore consider that it is now ready to be approved for publication.
Validity of the findings: This second version of the manuscript has been modified taking into account my main comments and suggestions included in my previous, full, revision.

I therefore consider that it is now ready to be approved for publication.
Additional comments: This second version of the manuscript has been modified taking into account my main comments and suggestions included in my previous, full, revision.

I therefore consider that it is now ready to be approved 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: FUNCTIONAL RESPONSES OF A COSMOPOLITAN INVADER DEMONSTRATE INTRASPECIFIC VARIABILITY IN CONSUMER-RESOURCE DYNAMICS
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: Dear Editor/Authors
I still see problems with confounding. Despite the claim of the authors that they do not try to compare native and invasive ranges, that comparison is still implicit in the paper. At several places authors talk about invasive ranges when referring to North American and South African populations and native range when referring to Northern Ireland population. Just to mention three of them: lines 263-264; line 290; lines 338-339.
The authors are right in their rebuttal than native range is not replicated. There is only one range. But a very large one. The native distributional range spans from northern Scandinavia (within the Polar Circle) to northern Mauritania (Fig. 1 in the ms). I have serious doubts that the Northern Ireland population is representative of the whole native range. Any comparison involving native and invasive ranges should consider replicated native regions. Taking more localities in N. Ireland does not solve the problem.  Authors say in their response that the N. Ireland population is the baseline population. They are implicitly assuming (i) that populations all along the native distributional range show the same consumer-resource dynamics or, (ii) that the source of North American and South African invaders is the N. Ireland population. Obviously, no evidence for any of these alternatives is presented.
But even in the case that the native range was very limited (for example, restricted to N. Ireland), there are sampling designs and analyses of data which allow for that formal comparison. Asymmetrical designs are commonly used when one of the treatments is un-replicated. Careful thinking is required to enunciate the sequence of tests to detect differences but formal, un-confounded comparisons are possible. Sampling designs used to detect impacts when a single impact locality exists are a good example.
The spatial scale of sampling within regions is also different: probably a few of ten of km for N. Ireland and South Africa and hundreds of km for American regions. No surprise that American localities differ more within regions than the others.

I can recommend publication only if the result of the study is interpreted in terms of geographic variability and not in terms of distributional ranges.

I have two additional comments:
When comparing functional responses (lines 258-268) among regions, inference is done by inspection of overlap of confidence intervals. While this procedure allows for correct inference when intervals do not overlap, when intervals overlap visual inspection might lead to erroneous conclusions. Slope of the initial part of the response curve or asymptote might be formally compared using the bootstrap. Regional differences in functional responses can only be demonstrated if the observed differences among regions are significantly larger than differences among localities within regions. Visual inspection is not enough to conclude. Particularly when localities in some regions exhibit large differences.
I suggest to delete comments on functional responses in the discussion (lines 321 to 331), as a type II functional response might have appeared as an experimental artefact. Authors recognize that in lines 324-328.
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: E-CIGARETTES VERSUS NICOTINE PATCHES FOR PERIOPERATIVE SMOKING CESSATION: A PILOT RANDOMIZED TRIAL
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper reports on a small pilot/feasibility study conducted 2 years ago. It is well-written in clear English to high standards in a professional style. The authors commendably and correctly adhere to reporting guidelines (CONSORT). The references are appropriate and relevant; there is one figure (CONSORT trial flow chart) and 7 tables; raw data is provided.
Experimental design: This is a RCT pilot study. It has been well conducted as a pilot trial, with the study Methods reported in line with CONSORT guidelines, with each of the key CONSORT items addressed specifically.

However, the aims are less than clear - as a pilot trial, it was not powered to detect an efficacy outcome: the concern with estimating a likely effect size with which to help calculate the sample size for a future adequately powered efficacy and safety trial is to the fore. However, it is stated that "The study was designed to test the feasibility and acceptability of the use of e- cigarettes (versus nicotine patch) as a smoking cessation aid in the perioperative period." but many unanswered questions that relate to assessing the feasibility of key study processes (recruitment, blinding, follow up and loss to follow up). are now specifically addressed. And then "We attempted to determine the acceptability of e-cigarettes as a smoking cessation aid and add to the limited existing data on the safety and efficacy of e-cigarette use in smoking cessation, specifically in the perioperative setting where the risks of continued smoking are great and the motivation to stop is high."  The acceptability of the study treatments was assessed, but the a one-dimensional scale with a non-validated question about product satisfaction seems weak methodologically.

From a feasibility perspective, it would be helpful to have sought the perspectives of participants and clinicians via complementary qualitative work, such as through focus groups or key informant interviews.

A major design feature that is not clear in the article is the time period exposed to the products pre-operatively - it is unclear how much time each group had using the different study products; analysis of the raw data shows this varies quite widely.  This should be reported.

There are other areas that lack clarity and require explanation:
 - It is unclear why there was a 2:1 ratio used to randomised (ENDS: patches) and why were patches chosen as the NRT product , rather than a short acting NRT such as the inhalator, which is more analogous to ENDS.
 - It is unclear why tapering was used in the dose of nicotine.
 - Why was a 1st generation ENDS used when the ability these devices have to deliver nicotine reliably at doses likely to substitute for conventional cigarettes and mitigate withdrawal syndrome symptoms is known to be limited?
 - Why were both eCO and cotinine measured if this was a feasibility study?
 - What were Lung Function tests done if this was simply a pilot or feasibility study?

The pragmatic approach to accessing counselling support is a design strength in a pragmatic trial but in this situation should have been explored further in the analysis as a key feasibility issue to help decide what to do in the future trial.
Validity of the findings: Validity is limited by the varying time periods of participant exposure to the products prior to surgery.
Could the FEV1 differences be due to the higher prevalence of COPD (30%) in the ENDS group?
Additional comments: Some minor corrections:

Lines 105-106 are redundant
Reference 15 is to a trial that involved a now obsolete e-cigarette. ENDS have improved since in terms of nicotine delivery and reliability so one would expect efficacy for cessation to have improved.
Reference line 341 spelling should be 'Benowitz'
Table 1 use the same font throughout
Table 4 p value 'from'


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: E-CIGARETTES VERSUS NICOTINE PATCHES FOR PERIOPERATIVE SMOKING CESSATION: A PILOT RANDOMIZED TRIAL
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: In general the experimental design is OK. I have some specific comments that i will submit below and ask for some clarifications and additional discussion by the authors.
Validity of the findings: No comment
Additional comments: This is an interesting research subject. I agree with the authors that it should be further studied. I fully understand the limitations of the small sample size which makes statistical comparisons difficult. These limitations are adequately addressed by the authors.
I have some comments, mentioned below, that the authors need to comment on in the manuscript.

The authors should provide more detailed explanation on why they chose to taper the dose, gradually reducing the levels of nicotine in both groups.

Abstract, Results section, line 55: “30 patients were recruited”
There is no need for this sentence since you already mention in the previous section that you randomized 10 people in the patch and 20 in the e-cigarette group.

Lines 141 and 143-145.
While the authors mention that participants were asked to use the e-cigarettes ad libitum, they seem to have provided limited nr of devices, based on the nr of cigarettes the participants were smoking. I don’t think this can be considered ad libitum use.  Also, although this may have been done to follow the same procedure as with NRTs, I don’t think this is appropriate for an e-cigarette trial because it deprives participants from using them as they prefer and based on self needs. Unlike medications, e-cigarettes do not have a recommended dose. Additionally, factors such as depth of inhalation, and puffing patterns may affect nicotine intake from the e-cigarettes, while such factors are absent when NRTs are provided. Please provide some explanations for these issues and perhaps mention some limitations. I believe a less conventional approach is needed when assessing e-cigarettes in clinical trials, with more freedom of choice for flavors and nicotine strengths, as well as true ad libitum use. Perhaps the authors could make some brief statements about these issues in the discussion section.

6-month follow-up.
Were participants instructed to use (if they wanted) or refrain from use of NRTs or e-cigarettes after the 8-week period of providing the products?

Lines 204-206
While smoking cessation and reduction was assessed at 6 months, nothing is mentioned in the results section. There is some information in tables, but I suggest to add a sentence about the 6 months data in the text too.

Line 255.
The authors present the difference in cigarette consumption separately in e-cigarette users and NRT users. I think it would be interesting to compare the % change in cigarette consumption in the two groups and whether there was a statistically significant difference in the % change between groups.

Lines 317-320.
The changes in FEV1 and FEV1/FVC were much more pronounced in e-cigarette users. The authors should try to explain this. For example, e-cigarette users had worse baseline spirometry values indicating more adverse respiratory effects from (the heavier) smoking. Thus, they had more prospects for improvement, while no improvement can be expected in participants who already have good respiratory function at baseline. I noticed there were many more patients with COPD in the e-cigarette group. This would perfectly explain the improvement in respiratory function observed in this group, based on my previous statement. I think this difference in COPD prevalence should be specifically mentioned in the text, and also present whether there was any statistical significance. Also, the higher rates of smoking cessation and reduction in the e-cigarette group, although not statistically significant due to the small sample size, could be another reason for these findings. I don’t think e-cigarettes have any direct beneficial effect on respiratory function, it is smoking cessation and reduction that probably contributed to these findings.

Table 2. I think it would be useful to add rows evaluating the combined smoking cessation/50% reduction rates in both groups and the statistical comparisons.


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: E-CIGARETTES VERSUS NICOTINE PATCHES FOR PERIOPERATIVE SMOKING CESSATION: A PILOT RANDOMIZED TRIAL
Review round: 2
Reviewer: 1

Output:
Basic reporting: The revised article is much improved: it is self-contained, with good clarification of previously inadequately explained elements to the study design or implementation. The writing is clear and professional.
The references are adequate. All required components -tables, data, etcetera -have been shared.
Experimental design: The design has now been clarified in the areas identified in the review where there was unclear rationale or insufficient details about what was done.
Validity of the findings: The findings are now situated within a number of limitations that were previously not included. This helps with interpretation of the study results and the implications (as a pilot study) for next steps.
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: NEW RECORDS OF THE ARCHAIC DOLPHIN AGOROPHIUS (MAMMALIA: CETACEA) FROM THE UPPER OLIGOCENE CHANDLER BRIDGE FORMATION OF SOUTH CAROLINA, USA
Review round: 1
Reviewer: 1

Output:
Basic reporting: This article meets the PeerJ standards.
Experimental design: PeerJ standards met.
Validity of the findings: Findings valid and well-substantiated.
Additional comments: Nice tight article. Conclusions justified based on the limited data...we always wish for fossil skulls to be better preserved.
My only concern/caution to the authors is the significantly different slope to the occipital shield preserved in CCNHM 1921. It seems really different from all other agorophiid specimens...
Minor editorial corrections/suggestions are to be found within the body of the ms.
Best,
Stephen Godfrey


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: NEW RECORDS OF THE ARCHAIC DOLPHIN AGOROPHIUS (MAMMALIA: CETACEA) FROM THE UPPER OLIGOCENE CHANDLER BRIDGE FORMATION OF SOUTH CAROLINA, USA
Review round: 1
Reviewer: 2

Output:
Basic reporting: English language is used effectively throughout nearly all of the paper. The Introduction and Discussion are particularly clear and provide ample background information. Figures need clarification, particularly Figs. 2 and 4.

I would suggest labeling the supraorbital process, sutural surface between the maxilla and the posterolateral plate of premaxilla, premaxillary cleft, and frontal groove. These are mentioned in the text, but are not labeled on any figures.

I would suggest giving the Ethmoid its own subheading, separate from the Frontal.

Line 187: If the cribriform plate is not preserved in CCNHM 1921, why is it labeled in Fig. 2F?

Your statement in Lines 191-192 that “The ethmoturbinal recess and olfactory nerve canal are confluent via a pair of crescentic foramina” confuses me. I am not convinced of where the ethmoturbinal recess may be in CCNHM 1921 and 1922, especially since you have not labeled any ethmoturbinates. The ethmoturbinal recess and crescentic foramina are continuous in Godfrey, 2013, so I would expect for you to find something similar. The olfactory nerve canal should essentially not be continuous with the ethmoturbinal recess or crescentic foramina. The cribriform plate should block them from being continuous, except for the foramina within the cribriform plate which I would not expect to be patent in a fossil anyway. Additionally, there are two ethmoturbinal recesses (Godfrey, 2013). Your language should reflect that. You describe the cribriform plate as being lenticular. I don’t think of any part of the cribriform plate as being lenticular, except for possibly the crista galli. I’m doubtful that what you have identified as the cribriform plate is actually the cribriform plate.
In general, I am not convinced of some of your findings regarding the olfactory anatomy. Your identification of the proximal olfactory nerve tract makes sense to me, although the presence of “longitudinal sulci” (Line 196) surprise me. I would like to see an indication of where the olfactory bulbs would sit, largely because your identification of the cribriform plate seems faulty. In CCNHM 1922 and 1921, it seems the partial cribriform plate consists of a septum-like projection that closely straddles the midline. There seem to be no fossae or flat areas on it where olfactory bulbs would contact it, allowing olfactory sensory neurons to go towards areas where olfactory epithelium is located.
It appears that the olfactory nerve canal bifurcates distally. Is this true? If so, then the crescentic foramina (Fig. 4), could be were a left and right olfactory bulb would sit. Then the cribriform plate (Fig. 4) would actually be a bony septum separating the distal olfactory nerve tracts, like in Godfrey et al, 2013.

Line 228: Do you mean to switch those specimen numbers around? The nuchal crest of CCNHM 1922 seems to come to a sharper point anteriorly than in CCNHM 1921.

Line 253: I would be surprised if the “incipient” cribriform plate were to change much morphologically during life unless the individual were very young or very old. You tentatively claim CCNHM 1922 is subadult (and not juvenile) and that CCNHM 1921 is an adult (Lines 282-284). Therefore I doubt that what you have identified as a cribriform plate is an incipient cribriform plate.
Experimental design: Yes, this research clearly fills a gap in our knowledge.
Validity of the findings: Assertions made regarding olfaction are not well supported; more anatomical evidence must be clearly presented in order to convince the reader that these specimens contain as much olfactory anatomy, particularly the cribriform plate and ethmoturbinates, as claimed here.
Additional comments: Some minor errors include
Line 88: the degree sign
Line 104: misspelling
Line 136: insert the word “and”
The captions for Fig. 1 are not identical. Boessenecker et al. (2017a) isn’t cited in both.
Insert “(F)” into the caption for Fig. 2
In Fig. 4, “parietal” needs a leader line