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: INTERACTION EFFECTS OF AGING, WORD FREQUENCY, AND PREDICTABILITY ON SACCADE LENGTH IN CHINESE READING
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors report an interesting study investigating age effects in Chinese reading.  The paper is well structured and the discussion of the existing literature looks appropriate to me.  Some comments regarding the presentation:

1. The patters in the data are reported verbally and in terms of numerical statistical inferences.  Given the complexity of the findings (e.g., three-way interactions), readers would greatly benefit from a graphical representations of the results, both for descriptive stats and inferential stats.

2. The paper does not follow APA guidelines, e.g. with respect to the document structure.  Not sure, thought, whether APA is relevant for PeerJ.

3. There is no information about the nature of the comprehension questions and their frequency.  This should be added.

4. Fillers were apparently not used.  That’s okay in this particular case, but since it is unusual it is worth mentioning.

5. The reporting with regard to the statistical analysis was incomplete and I was unable to reconstruct the precise analysis that the authors conducted:

   - In the LMM analysis, what was the contrast coding for age group?

   - From the data, I can infer that log10 was used to transform the reading time measures, but this is not mentioned in the paper.  This information is needed to make sense of the parameter estimates and should be added.

   - It is not clear whether saccade length measures were only for first-pass saccades or also for later saccades.  Please clarify.

6. I suggest that the authors have a look at the paper below on the effect of age on German reading behavior.  It reports relevant findings on many of the issues discussed in the present manuscript.

   - von der Malsburg, T., Kliegl, R., & Vasishth,
     A. (2015). Determinants of scanpath regularity in reading. Cognitive
     Science, 39(7), 1675–1703. http://dx.doi.org/10.1111/cogs.12208

7. The paper is understandable but there are some problems with English grammar and some typos that should be fixed.  This may require input from an English native speaker.
Experimental design: I don’t speak Chinese but the design looks largely appropriate to me.  There is one potential issue though with the design of the sentences: The HF-P and the LF-U conditions have a different sentence prefix than the LF-P and HF-U conditions (see Table 2).  I think this could give rise to differential spill-over effects which could introduce spurious interaction effects or mask true interaction effects.  It would be good to discuss this issue briefly in the manuscript and to qualify conclusions accordingly.
Validity of the findings: The statistical analysis look largely appropriate and I could replicate most findings in my own analysis of the data.  My code is attached to this review; please share with the authors.  The biggest  issue is multiple comparisons.  The author’s hypotheses are relatively vague and each hypothesis is tested multiple times (details below).  The best way to address this is using Bonferroni corrections.  I examined the impact of Bonferroni corrections in my own analysis and luckily most (but not all) of the findings hold up.  For details on the issue of multiple comparisons in the context of eye-tracking studies I recommend that the authors read this paper:

- von der Malsburg, T., & Angele, B. (2016). False positives and other statistical errors in standard analyses of eye movements in reading. Journal of Memory and Language, 94(), 119–133. http://dx.doi.org/10.1016/j.jml.2016.10.003

Detailed comments:

- In the discussion, the authors make claims about parafoveal processing.  I think any such claims would need support from boundary-paradigm experiments.  The present experiment provides only indirect and therefore weak information about parafoveal processing.

- I could not reproduce the descriptive stats in table 3.  My own values for first pass reading time and gaze duration are very close but my values for total viewing time are considerably lower than the author’s.

- There were no predictions for duration measures (as far as I can see), but I imagine that the authors were primarily interested in the interactions of predictability and frequency with age.  There were three such interactions per each of the three measures, so 9 tests of the general hypothesis (age has an impact in frequency and predictability effects).  The freq × group interaction is just borderline significant and does not survive a correction for multiple comparisons.  None of the other interactions were significant by conventional standards.  So, no age interactions in duration measures.  However, most main effects (frequency, predictability, age) do survive a Bonferroni correction.

- It appears that the authors analyzed raw saccade length.  Since this variable is strictly positive, some kind of transform is needed.  My own investigation of the data shows that a log-transform yields close to normally distributed residuals.  My evaluation of saccade length effects in the comments below is based on my own log-transformed analysis which yields considerably more robust results than the analysis of raw saccade length conducted by the authors.  Note, though, that due to time limitations I ran intercept-only models which tend to be anticonservative.  (I calculated p-values using the lmerTest package.)  The authors should redo the analysis with log-transformed saccade length and report only results from those analyses.

- The prediction for incoming saccade length (ISL) was that age may somehow interact with frequency and predictability.  There are three concrete ways in which this could pan happen: 1. effect in frequency × age interaction, 2. predictability × age, 3. frequency × predictability × age.  A Bonferroni correction is therefore appropriate (new α = 0.05 / 3 ≈ 0.017).  The three-way interaction survives this correction but the frequency × group interaction does not.

- The prediction for outgoing saccade length (OSL) was again that age may somehow interact with frequency and predictability.  The same interactions are relevant as for ISL.  Unfortunately, the observed interaction effects do not survive the Bonferroni correction.

- In OSL, I found a highly reliable predictability effect that the authors didn’t find.  When predictability was low, the outgoing saccade was shorter, consistent with the author’s earlier findings (Liu, Guo, Yu, Reichle, 2018).  Nice!

- I can’t get the glmer models for skipping and refixation to converge even with intercept-only random effects.  How did the authors deal with that?  More generally: If a maximal model fails to converge, the authors should specify which simplified model they’re reporting and by which procedure they arrived at this model.

- In the discussion, the authors interpret various null results.  However, it is unclear whether these were due to the true absence of an effect or due to a lack of power.  While useful, I would tone this discussion down.
Additional comments: Overall a worthwhile contribution that provides some interesting new insights along with replications of effects reported earlier.  The statistical analysis needs some (easy) fixes and as a result some results will change and the discussion will have to be adjusted accordingly.  However, the key findings will likely hold up and some effects will actually become stronger and clearer.  I would happily recommend publication once the statistical issues are addressed.

Comments regarding the supplementary information:  I applaud the authors for publishing their data.  Having the data really helped me to better understand the results.  Some possible improvements: 1. The read-me file describing the variables in the two CSV files is not entirely accurate.  Please fix.  It’s also not clear why there are two files.  Isn’t most of the information redundant?  My impression is that one table should be sufficient.  If not, please explain why.  2. Comprehension performance not included in the data and should be added.  3. The analysis code is not part of the supplementary information.  From the description in the manuscript alone I was not able to fully reconstruct the analysis.  Please add the R code in the supplementary section.


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

Input:
Title: PALUSTRINE FORESTED WETLAND VEGETATION COMMUNITIES CHANGE ACROSS AN ELEVATION GRADIENT, WASHINGTON STATE, USA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The author has used professional English throughout the paper. It is well written and easy to read. The author is well versed with the topic.

In the Results section of the Abstract (line 41 – 47) “This study quantifies…” is more like the aims and objectives of the study and should be stated there. It could be replaced by the research questions in the Background section of the Abstract.

Generally the introduction and background lacked structure in the sense it does not give a broad scope of the study and its relevance. For example, what are some of the “ecosystem functions and services” provided by these wetland vegetation? The last paragraph of the introduction and background (lines 84 – 90) could be expanded a bit more where the points 1 and 2 currently stated as a question are structured as the objectives of the study clearly stating the purpose and techniques used to address the aim of the study in lines 84 – 85.

Figures are relevant but bot great in quality. I suggest the following changes;
-	Figure 1 – useful to include the names of some of the major streams within the catchment. Contour lines may also be useful to show elevation.
-	Figure 2 – graphs need to be made clearer. Could DistWater be changed to different symbols rather than a colour gradient? Increase font size of the axis labels
-	Figure 3 – the bar graph does not need a colour gradient, the bars itself indicate the values. What are the codes on the bars and on the x-axis? It may be helpful to include the scientific names of the trees on the bars rather than the codes which have not been defined anywhere in the paper.
-	Graphs in Figures 4 should have individual labels, for example could be labelled as Figure 4a and Figure 4b and referred to accordingly in the paper. Same goes for the graphs in Figure 5.
-	Figure 5 graphs – ensure that the labels are not overlapping so that they can be read clearly

Appendix 1 and 2 referred to in the context of the paper were not included in the paper though mentioned several times throughout the document
Experimental design: The title indicates that the paper is about flooding stress on freshwater wetland vegetation however this message did not come out prominently in the findings of this study. While it is addressed throughout the paper, the findings should be emphasised in greater detail. The author has stated that this study “will improve regional understanding of forested wetland vegetation and inform restoration and forest practice policies” but does not provide clear signposts of the in the article. Also, this is not later addressed in the conclusions. I therefore recommend that before the paper is published, the overall significance of the findings needs to be elaborated and emphasised more clearly in the discussion and conclusions of this article.

I suggestion the following changes to the discussion section to focus on the findings;
-	First paragraph of discussion is background information. The author should start their discussion with a sentence like that in line 270. Lines 313 – 325 is also background information and should not be in the discussion. These could be moved to the introduction section
-	Line 271 and 272 is missing how many “meters above the OHWM relative to deciduous species… “
-	Line 282 “Because I did not measure tree age…” is not a good way to start a paragraph. Also check this paragraph – the two points made, are they related to flooding?
-	Discussion could be divided into sub-headings addressing the different objectives of this study. Section 1 – “overstory and understory forest composition change across an elevation gradient”, discuss how similar or different it is from other sites. Section 2 – “what elevations relative to the ordinary high-water mark are different plant species found within forested wetlands” and discuss which vegetation has a higher capacity to tolerate flooding. The final 2 paragraphs of the discussion should be a separate section called “limitations and recommendations”

In the Methods section, the author could expand on the threshold of the statistical analysis performed; “All statistical tests were performed with an alpha of P < 0.05” which means that the relationship was deemed statistically significant between the measured variables.
Validity of the findings: In my opinion all underlying data have been provided; they are robust, statistically sound, & controlled but a few points could be made clearer. For example;

-	What percentage of “species lacked sufficient replicates”
-	Sentence in lines 206 – 207 and 224 – 226 should be in your methods as it was the techniques used for the different scenarios.

The conclusion of this article is a bit weak and could be improved by incorporating the suggestions I made earlier. The author could include names of plants that most prominently showed resilience to flooding to those that did not. Sentences, such as that in lines 354 – 356 should not be in your conclusion.
Additional comments: I recommend stylistic changes to the paper, for example;
-	The overuse of personal pronouns gives the article an informal tone and makes it too subjective. I would suggest making changes where “I” could be replaced by statements like - “This study aims to investigate…” and “The overstory tree and understory vascular plant composition and structure of the three zones was measured using…” and “This study was done by collecting…”
-	Paragraphs or sentences should not begin with the conjunction “because”
-	Very long sentence for example, lines 54 – 59 that should be separated.
-	Check sentences in lines 72, 97, 100 – 102, 113, 149, 211, 307 – 310.
-	Explain/define “exploratory analysis”
-	Subheadings in line 123, 137, 145 should be secondary to Methods sub-heading
-	FACU not defined in the article
-	Species names of the different vegetation tend to be long and sometimes difficult to include in graphs, they therefore should be properly abbreviated and used consistently throughout the paper.


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: PALUSTRINE FORESTED WETLAND VEGETATION COMMUNITIES CHANGE ACROSS AN ELEVATION GRADIENT, WASHINGTON STATE, USA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The present manuscript investigates species composition of overstory and understory plants along an elevational gradient in a forested wetland in the U.S. NW Pacific. Overall, I judge the manuscript design, style, and presentation as suitable, however, I think that the methodology presents some aspects/uncertainities which should be improved before acceptance (details below). In addition, I have suggestions for some minor issues which also could be improved (details below).
Experimental design: The entire study design, main results, and discussion is dependent on the exact location of plant species relative to the ordinary high water mark (OHWM) and the delineation of the three elevational units (lower and upper wetland, wetland buffer). Therefore, I think that the definition of the OHWM and the three zones should receive more attention, also concerning potential bias. The OHWM is variable in time and scale, even in such a small forest swamp. Therefore, mean days of inundation per time unit would provide the best scale for vegetation inventories along the elevational gradient. In my point of view, it is not sufficient to describe the different soil types for each zone for exact delineation, rather, exact measurements (i.e., by using a theodolite or any other kind of measuring device) relative to the water level should be provided. If soil types were the unique fator evaluated leading to the definition of the three elevational units, please indicate how many soil samples, profile descriptions etc. were performed.

In L125ff you state a 10m grid of your wetland for the selection of vegetation plots - but this is not shown in Fig.1. I suggest to present the GIS-based map in this figure, which also could show the three elevational units that were mapped out.

Starting in L128 you mention the 10x10m plots for vegetation sampling, but it is unclear how many plots were established in total, and in each unit WB, LW, and LW. As I understood, you did 12 x 10x10 m plots = 1200 m2 in each unit (0,36 ha in total). Correct? Please clarify and state like this.

I  L133, you state that understory species cover was measured. How? Did you count the abundance and/or estimated the coverage? Especially for herbaceous species this would be an important information. How many individuals in both the understory and overstory were sampled in total?

In the statistical analyses, I missed a species rarefaction and/or species-area curve to test for representativity of your vegetation/species samples. Given the sampled area, is your inventory representative for the different vegetation types in both the understory and overstory?
Validity of the findings: L196: If species are not abundant enough to show the relationship between tree size and elevation, why they are presented in Fig.2? On the other hand: if this relationship was not aim of your study, why did you mention it for some species, and not for others?

L201-207: This entire paragraph is methods, and not results.

L281: You repeatedly mention that some of the results you describe and discuss here were not measured and/or aim of the study. I would avoid this because it makes the entire manuscript and findings a bit weak. If not aim of your study and/or not measured, simply excluding it from the text would be better.
Additional comments: In L79 you state that few studies exist in the Pacific NW. Which ones? Their main findings should be briefly described and adequately cited.

Again Fig.2: You state that tree dbh-elevation was not aim of your study. If so, you should delete Fig.2. If not, please justify the presentation of OHWM-dbh/basal area relationships through the entire text (starting in the last paragraphs of the Introduction).

All Figures should be self-explaining, without the need to read the text. Figures 2 and 3 use a lot of abbreviations for the single species which are not explained. Please explain all abbreviations in the legends.

Table 1: Avoid wording such as "generally perched" and "generally inundated". This makes the entire reasoning weak. It seems that youself are not convinced of the methodology and the delineation of the OHWM.


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: PALUSTRINE FORESTED WETLAND VEGETATION COMMUNITIES CHANGE ACROSS AN ELEVATION GRADIENT, WASHINGTON STATE, USA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The author has improved the latest version of the paper. Well done! However the Discussion and Conclusion sections of the new version still lacks structure.
I had suggested before that the Discussion could be sub-divided to address each of the objectives. It will be helpful for the reader to understand the major findings of the paper if the author considered addressing his two objectives clearly. The author choose to not incorporate this in the revision by saying "This is a stylistic change, and while I appreciate the suggestion, the discussion is relatively short and transitions abound between sections."
I do not think that the Discussion is relatively short, there is still substantial information there but if the author wishes to follow his format then I'd suggest the following changes;
-	re-write the first paragraph to clearly discuss that species assemblages represent elevation gradient across the wetland surface. You do not need to stress again what you did, “Here I quantified…” you have already covered this in your methods.
-	Line 289 “high to low” what “within a wetland”?
-	“This study” has been used repeatedly in the paragraph in line 358.
-	Check sentence in lines 382-384. Define "designed hydrology" if you want to use the term here?
Experimental design: Methods described with sufficient detail
Validity of the findings: -	Conclusion – sentence in lines 390-392 arbitrary and not necessary here. Expand the sentence in lines 392-394 to elaborate your findings which will address both your objectives
Additional comments: -	Figure 1 –
(i). useful to include the names of some of the major streams within the catchment. Contour lines may also be useful to show elevation.
response from author - Within this figure there are no named streams
(ii). I still do not like how Figure 1 looks. Suggestion to make it a bit aesthetic – add in an insert map of the country showing Washington State then a box around Ash Wetland. Grids would be helpful too. That grey bit of the State in the legend does not look nice. Also you could make the bigger map satellite and insert map of the wetland topographic. Also Ash Wetland must have some kind of landmark – label that on the map.
-	Figure 2 –
(i). graphs need to be made clearer. Could DistWater be changed to different symbols rather than a colour gradient? Increase font size of the axis labels
response from author - The colour gradient has been removed.
(ii). DistWater colour gradient still there. Increase the font size. Figure caption is self-explanatory now – well done
-	Swap figures 2 and 3 as you mention figure 3 first in your results, might as well call it Figure 2 (line 213)
-	Figure 3 box plot reads much better but I wonder if instead of having the species on the x-axis in alphabetical order they could be based on average elevation? so you can see a pattern from lowest to highest elevation.
-	Figure 6 – plants species in photographs not labelled. Arrow on the side not useful
-	Break the sentence in lines 113 – 115 in to two.
-	Line 116 “Wetland has an average elevation of 281-meters” above what?
-	Line 117/118 “The water table rises with fall and winter rain and falls throughout the growing season into late summer” – check this line. Also fall could just be called autumn like all the other seasons to avoid confusion with falls which I presume means ‘rainfall’
-	Line 133/134 “These zones were based on within wetland elevation” – check sentence tense
-	Careful with presentation of "P" – value, either have it italised throughout the document or not, e.g. 206, 229. Technically I think it should be lower case and not in italics (p = 0.0001)


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

Input:
Title: A NEW PLESIOSAURIAN FROM THE JURASSIC–CRETACEOUS TRANSITIONAL INTERVAL OF THE SLOTTSMØYA MEMBER (VOLGIAN), WITH INSIGHTS INTO THE CRANIAL ANATOMY OF CRYPTOCLIDIDS USING COMPUTED TOMOGRAPHY
Review round: 1
Reviewer: 1

Output:
Basic reporting: Dear editor, dear authors,

This is a great paper, describing a peculiar and very interesting new taxon. The paper meets the highest standards in all categories here.
Experimental design: I see only a couple of suggestions here:

-The comparative description is thorough and detailed but is very focussed on a a couple of well-known cryptoclidids from southern UK and Spitsbergen; while the cryptoclidid record is indeed strongly biased, I would just suggest to add some additional taxa to the comparisons, notably taxa from elsewhere as well as microcleidids and Plesiopterys, to have a sense of how derived or plesiomorphic some regions of the skeleton are in Ophthamothule. The number of comparisons also strongly diminishes when the girdles and fins are discussed.

-I have indicated in a .pdf copy of the paper instances where the wording is unclear/incorrect as well as minor questions and suggestions. I have also indicated other papers that could help with the discussion of visual acuity.
Validity of the findings: -gastroliths (p. 31). "Pebbles" are sediment grains above 20mm; under that size, you have to talk about "gravel", which is what you seemingly have here. Since it is a gravel, I think it does not works efficiently as gastroliths. The non-deliberate ingestion of sediments (diamectites?) when feeding on the sea floor appears more likely.

-This one is a rather general question/point: existence of (another) Slottmoya-only clade of marine animals. I find it puzzling that many of the distinct genera and species described by the same team cluster together very often in phylogenetic analyses. It is the case for ophthalmosaurid ichthyosaurs and is now the case for cryptoclidids as well. Don't get me wrong, it is fully possible that these environments forced a combination of (very) high cladogenesis rates and low dispersal rates. But I can't help but wondering whether this is *unconsciously* biased or a true effect. A recent reinterpretation for ichthyosaurs by Zverkov & Prilepskaya 2019 PeerJ concluded that was an effect of taxonomic oversplitting. While the distinctness of Ophthalmothule as a generic taxon appears clear, I wonder what is your take, many years afterwards and with all this new information provided by the holotype of Ophthalmothule, at the possible taxonomic status of the other cryptoclidids from Spitsbergen.
Additional comments: All the best,

Valentin Fischer


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

Input:
Title: A NEW PLESIOSAURIAN FROM THE JURASSIC–CRETACEOUS TRANSITIONAL INTERVAL OF THE SLOTTSMØYA MEMBER (VOLGIAN), WITH INSIGHTS INTO THE CRANIAL ANATOMY OF CRYPTOCLIDIDS USING COMPUTED TOMOGRAPHY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors present a detailed description of a new cryptoclidid plesiosaur from the Late Jurassic (or earliest Cretaceous?) of Svalbard; the implication of µCT allows to highlight some details of otherwise hidden cranial morphology.

The manuscript is well structured and the level of English is high, however, unlike the authors, I’m not a native speaker, thus I hardly can assess this aspect of the work appropriately.

Literature is reasonably referenced. In the specific comments below, I added several additional references, some of which, in my opinion, could be beneficial for the MS.

Figures are relevant and their quality is good; they are well labeled and described. I indicated some artifacts on fig. 15 that should be cleaned. Additionally, I recommend indicating the catalogue numbers of specimens on the stratigraphic column of fig. 1; and, where possible, to be consistent with the length of scale bars - from the reader's perspective, it is hard to have scale bars of different length in every figure. It hampers an easy perception of the material.

Raw data supplied for the µCT. However, I encourage the authors to supply 3d models of processed µCT in any of the 3d formats - it will be more useful than video and screenshots provided in the current version. Additionally, I would recommend the authors to supply the dataset for their phylogenetic analysis in the nexus file format or another appropriate format for easier and faster replication of the results. Currently, there are many supplemental small word documents and jpg images. I would rather recommend making a single pdf with all these data included.
Experimental design: No comment. It is original research within scope of the journal.
Validity of the findings: I agree with the authors that the specimen represents a new species of a cryptoclidid plesiosaur. The material is good and the description is extensive and thorough. There are some minor points indicated in the marked-up pdf related to ambiguous interpretations of some observed morphologies and structures (e.g. parasphenoid, enamel ornamentation, dorsal ramus of the scapula, preaxial accessory elements) these should be clearly indicated as interpretations or illustrated more carefully so that questions regarding the validity of authors observations do not arise.

In my opinion, the most problematic issue in the current version of the MS is the speculation on the stratigraphic position of the specimen and consequently on the impact of the new specimen on the understanding of the Jurassic-Cretaceous transition in plesiosaurs. After reading the MS, I do not see how the specimen shed light on the supposed turnover. There is no discussion on the transition in plesiosaurs and other fossil groups and the research of this issue is not discussed and cited appropriately. In current form, it is not appropriate: either the expanded discussion should be added, or phrasings regarding the impact of this research for the understanding of the Jurassic–Cretaceous faunal turnover should be reduced if not completely omitted in the MS (see my comments to lines 37-40).
The stratigraphic position of the specimen is ambiguous. As with other specimens from Slottsmøya, authors use the relative position (in meters) to a “marker bed” as a definer of a stratigraphic level. However, considering the large area of excavations and that the thickness and composition of the member vary significantly even in the studied area (for details see my comments for lines 73–77), such an approach is not effective and results in a dubious stratigraphic position of all Svalbard marine reptile materials. As the authors correctly noted, in the Boreal Realm there is Volgian stage, which poorly correlates with the Tithonian international unit, except for its base. Actually, it is hardly possible to say to which part of the Tithonian the Slottsmøya Member corresponds, even having precise biostratigraphic data (authors have no biostratigraphic data at all). Authors declare that there are some data for Early Cretaceous age of seeps, located stratigraphically above the level with the specimen (with reference to another research, but no details) – this phrasing is too general and imprecise and such a data has no significant impact for understanding the age of underlying sediments. Actually, there is no robust evidence that the specimen was located on to the Jurassic–Cretaceous boundary or in the Cretaceous part of the outcrop. What can be said, is only that the specimen is closer to the J/K boundary than most other plesiosaur specimens from the locality. In this regard, the conclusion (lines 1141-1143) that “the phylogenetic results of this study indicate that two separate clades of cryptoclidids crossed the Jurassic – Cretaceous boundary in the Boreal region of Spitsbergen and the sub-Boreal region of Russia” is not well stated.
Additional comments: It is nice to see the study of this astonishing specimen on its final way to publication. My congratulations to the authors! I enjoyed the extensive and detailed description and good figures. In my opinion, this work should be accepted for publication in PeerJ after minor revision. I hope my remarks and advice will be of some help in improving the accuracy of the paper. Looking forward to seeing it published!

Below is a list of all my specific comments (for making authors work on the revision of the MS easier these could also be found in the attached marked-up pdf):

Line 1. “boundary”
I suggest replacing with “transitional interval”
J/K boundary is a problematic case and your specimen is clearly not from a boundary, but from an interval, where the boundary is presumed to be.

Lines 18-19
Not clear. How you count this? 'Taxon' is a broad term implying a taxonomic group of any rank. In such a phasing it appears that you consider a taxon of specific rank, presumably genera. When considering not only species but also supraspecific taxa - there will be more than 13... Another problem is that it is not clear that you consider valid taxa, because there are much more than 13 "known cryptoclidid taxa", but not all of them are recognized as valid currently.
Please, list the ‘taxa” in parentheses. I wonder what these five are. Even for genera, there are more than five: Cryptoclidus (good stuff), Tricleidus (good stuff), Picrocleidus, Muraenosaurus (great stuff), Tatenectes, Vinialesaurus, Kimmerosaurus (good stuff), Spitrasaurus, Djupedalia, Abyssosaurus - 10

Rephrase, please. You can use e.g. "genera" in both sentences to avoid confusions.
Also not really clear what is 'complete' for you (what percentage of completeness would be enough to be 'complete'? 100-90? >80?). For many genera of OCF cryptoclidids there are very good cranial materials (Muraenosaurus, Tricleidus, Cryptoclidus).  So which cryptoclidid, in your opinion, is the only that "has a complete, but compressed cranium".  Please add its name in parentheses. Your new specimen has incomplete skull as well... as some parts (postorbitals, jugals, medial squamosals) are either missing or too poorly preserved.

L 23 add “gen. et sp. nov.” after the taxon name

L 31-32
Not demonstrated in the MS. You have no robust evidence that the new plesiosaur is Early Cretaceous, but not latest Jurassic, thus still the only robust evidence for boundary crossing is Hauterivian Abyssosaurus. I would suggest deleting this highlighted part.

L 37-40
I do not think that this is an appropriate formulation. Patterns of faunal turnover during the Jurassic–Cretaceous boundary interval are contentious, and potentially varied among different groups and environments. In fact, the lack of consensus over the importance and severity of faunal turnover during this interval suggests that it does not represent a discrete mass extinction and may not have differed from background patterns of turnover.
"As with most other marine reptile groups, plesiosaur taxonomic diversity was heavily affected by eustatic sea-level changes during the Jurassic – Cretaceous transition" . You know that it is not the case for ichthyosaurs (Fischer et al., 2012; Zverkov & Prilepskaya, 2019). Recently we also discussed the turnover in pliosaurids (Zverkov et al., 2018) and demonstrated that it is complex and there was no decrease in disparity during this transition... So not really clear for me which "most other marine reptile groups" you imply here...

L 46
It seems that something is missing here... Furthermore you are citing a paper on ichthyosaurs - inappropriate citation, please replace. You can cite your previous paper (Roberts et al., 2017) and numerous papers of Espen Knutsen et al (2012)...

L 47
why brackets? I would suggest neither parentheses no brackets, but "Colymbosaurinae Benson et Bowdler, 2014" as a first mention of the taxon name with reference to authors and year as it should be when mentioning the taxon for the first time in the MS. Please also check other taxa for this.

L 55
Incorrect phrasing. 1 - you are writing "representing a new genus" but then giving a species name - so either give only a generic name or write "representing a new genus and species" 2 - optional and my subjective opinion - from the sentence it appears like the specimen is significant because it is a new taxon, but it is an outcome of its uniqueness, not a reason. It is unique because it has a number of unique features that allow you to propose a new genus and species.

L 58
Cryptoclidid genus?
Yet again a confusion with counting
You have three cryptoclidid genera and four species already in the Slottsmøya Member. And much more described specimens. So here you describe representative of the fourth genus and fifth species and ??? specimen of cryptoclidid from the member.

L 61-62
After reading the MS I don't see how the specimen shed light on the supposed turnover. As there is no discussion on the transition in plesiosaurs, it should be either added, or such phrasings should be omitted in the MS.

L 73-74
12 Myr is obviously a mistake. On what data this estimation is based? Even in the cited work  (Hammer et al. 2012, fig. 7), the Slottsmøya Member spans less than 6 Myr. Actually, the whole Tithonian was 7 Myr by the results of recent research (Lena et al. 2019). Here you are speaking about "upper Tithonian" to lower Berriassian time interval - in no way it can be 12 Myr. Another problem is that, as you correctly noted, you have Volgian, which poorly correlates with the Tithonian, except for its base. Actually, you cannot say to which part of the Tithonian the Slottsmøya Member in your section corresponds, as you have no biostratigraphic data. You can say that the Slottsmøya Member corresponds to middle to upper Volgian (for the biostratigraphic correlation of the base of the member see Rogov, 2010), which, in its turn, could be approximately correlated with the interval from the middle of the lower Tithonian to the lowermost Berriassian (see e.g. Rogov 2014).

L 75. Add “On Janusfjellet (central Spitsbergen), the member is divided...”
This 'division' in Collignon & Hammer (2012: 92) is for Janusfjellet. In Wimanfjellet, from which PMO 224.248 derives, there is different section already (see Dypvik et al., 1991, fig. 5) - from that the scheme it appears that there is no such units in Wimanfjellet, or the thickness of these units is significantly different as the whole thickness of Slottsmøya on Wimanfjellet exceeds that of Janusfjellet 1,4 times! (Dypvik et al., 1991, fig. 5). This should be kept in mind (the best way, probably, is to omit the sentence). The thickness of the Slottsmøya Member varies, generally from 70 to 100 m, and is 84 m in the stratotype at Slottsmøya, western Sabine Land (Dallmann (Ed.), 1999, p. 190), thus the division on three units by meters for 52 m thick Slottsmøya Member of Janusfjellet is actually inapplicable for other outcrops of the member on the archipelago.

L77 “The specimen (PMO 224.248) described here derives from the upper unit (at 38.5 m)”
As I wrote above, that unit is found on Janusfjellet. You have no robust data for the presence of the same units and their volume on Wimanfjellet, thus the only thing you can say is that "In case if found on the Janusfjellet, PMO 24.248 would have been within the upper unit..."

L 164 “narrow sagittal crest”
mediolaterally
Here and throughout the MS, please indicate the directions and orientations when needed in order to avoid confusions.

L 167 – same as for L164

L 181 “faint longitudinal ridged teeth, distinct on labial side”
longitudinally ridged teeth, or longitudinal ridges on teeth?
not clear from your figures. It would be great to have magnified regions of the enamel on the labial and lingual surfaces to make this clear. In fact, it sounds really strange to have ridges on the labial surface but not on the lingual. To my knowledge, it is more common in plesiosaurs when the labial surface is smooth and the lingual is ridged.

L 184 “hypophyseal eminence” vs “ventral keel”
It is a terminological issue and should be made clearer. Benson & Bowdler (2014) call morphologies with the keel "hypophyseal eminence" as well, so not really clear what you mean in this context as it seems like 'ventral keel' and 'hypophyseal eminence' are different morphologies for you, but boundaries between the two states are not defined, e.g. "However, the hypophyseal eminence of Kimmerosaurus is a narrow ridge, and extends along the entire ventral length of the atlas-axis complex. This is unlike the anteriorly located, mammilate hypophyseal eminence of Colymbosaurus" (Benson, Bowdler, 2014, p. 1066)

L 196 mid-posterior cervicals are not known for Kimmerosaurus, at least in published works

L 199 “short and reduced”
I would not be so sure. It seems more like broken and lost than reduced.

L 200 Add Spitrasaurus, Djupedalia, 'Plesiosaurus' manselii,
How do you choosing which taxa to list? Throughout the diagnosis you listing 2-3 taxa with different morphologies even when there are much more of them bearing a certain trait… Please reread your diagnosis and try to consider all the know taxa when certain trait could be compared.

L 201 As you have only fragments of the femur preserved, this assumption is speculative – thus not for the diagnosis. Even considering your statement in the description that the diaphyseal cross-section of the femur is not as large as in the humerus... From my knowledge, in plesiosauroids femora commonly have more slender diaphyseal part than the humeri, so this suggestion regarding the size based on such assumption means nothing and should not be in the diagnosis. Even though it is very likely, considering other cryptoclidids, that your suggestion that the femora were smaller is correct.

L 202 “sigmoid humerus in dorsal view*”
Considered autapomorphic. However, this is too general formulation. The curvature is too slight if present (I do not see this curvature compared to that pronounced in xenopsarians). Such an outline is not unique among Cryptoclidids. Similar outline e.g. in Picrocleidus beloclis holotype
“forelimbs” - humeri - there are many distal facets in forelimbs

L205 - This section is better fitting for Materials. Not for Systematic Palaeontology

L 206 “near-complete” - I would not say that the near lack of pelvic girdle, hindlimbs, and a tail is insufficient loss and that with such a lack the skeleton is still near-complete. You can only suggest that it was near complete before being eroded...

L234 “Fig. 3.3” – correct this

L238 “rugose” - same, but even rougher in Tricleidus...

L 263 – five pmx teeth not only in Muraenosaurus, but also in Vinialesaurus caroli and Tricleidus seeleyi

L 280 “heterodonty” - anisodonty. Although these terms are commonly mixed up, it is better to use isodonty/anisodonty when speaking of size of the dentition and homodonty/heterodonty when assessing its morphology.

L 348 “tall and sharp crest” also in Tricleidus seeleyi and Muraenosaurus leedsii

L 365 “anterior” – are you sure?

L 398 “posterolateral”  - maybe anterolateral?

L 426
I would not be so sure regarding the presence of additional anterior articulation having CT results of such poor quality. In your models, I do not see the morphology - only irregular fragments that are asymmetrical in addition.

L 437 “the parabasisphenoid is very thin and somewhat damaged” - Indeed. I would rather suggest that parasphenoid is detached and lost in your specimen so that the element you describe as parabasisphenoid is a body of the basisphenoid solely.

L 440 “lacks a projecting cultiform process”
Please consider the case that the parasphenoid can be too poorly preserved for correct processing or even lost (considering the irregular surface with cracks and breakages in this region) and you interpret and describe an incomplete palate as complete...

L 467
I doubt this is due to crushing - it is normal for plesiosaurs to have a common jugular canal (i.e., canal for X and XI nerves, and for the jugular vein)
From L486- (Vomer, Palatine, Pterygoid, )
add references to figures somewhere in the sections

L 492 “Iturralde-Vincent» - check the spelling – Vinent

L 561-562
“possibly due to taphonomy” - you can say the same regarding PMO 224.248. Based on my observations on this nicely preserved specimen it is more likely a natural condition than a taphonomic distortion.
“it appears absent on the holotype” - the mandible of the holotype is disarticulated. The dentaries are nearly completely preserved and fused. their posterior ends are mediolaterally wide. It is possible that this could be due to taphonomy, but I would rather suggest that this is a natural condition further supporting your observation of this morphology in the referred specimen.
Photograph of dentaries of the holotype - https://www.dropbox.com/s/g40mop6l28nuyka/IMG_5879.JPG?dl=0

L585 what about Kimmerosaurus?

L 593 anisodinty

L 603 “ridging is most prominent on the labial side”
Could you provide close-up photographs of the enamel ornamentation as supplemental files, please? This interpretation sounds confusing to me and it would be nice to have pictures for agreeing that your description is correct.

L 609-612
Incorrect interpretation of Kimmerosaurus dentition. In this taxon, the crown cross-section is markedly D-shaped and strongly labiolingually compressed. Please check the holotype, or you can cite this as my personal communication. In OCF cryptoclidids circular in cross-section indeed.
By the link are my photographs of Kimmerosaurus langhami holotype teeth:
https://www.dropbox.com/s/qdq4sut9zmg6esp/IMG_5894.JPG?dl=0
https://www.dropbox.com/s/h2yklqpxjvx0as8/IMG_5896.JPG?dl=0

L 697 This is quite a speculative suggestion. The morphology of zygapophyses in sauropod cervical vertebra and in plesiosaurs are significantly different. The morphology you describe for PMO 224.248 would be a significant constraint for flexibility.

L 715 and other mentions of this taxon – Picrocleidus in quotation marks
Although synonymized with Muraenosaurus by Brown, its validity is supported in recent studies - I see no reason to keep this generic name in quotation marks.

L 729 “Cryptoclididae indet” why in italic?

L 784 In my opinion, this section adds nothing to the description and is too superficial. It could be moved to Materials section along with Taphonomy.

L 791 see O'Keefe et al., 2009 A plesiosaur, containing...

L 816 Are you sure in this interpretation? From your figure, it seems more likely that the dorsal rami of scapulae are broken and lost, rather than reduced

L 853 “resulting in a sigmoidal shape” add somewhat... slightly... the thing is that it is not as marked as in xenopsarians.

L 873 From your figure, it seems that there is many bones around the limb so why you are so sure that this is a preaxial accessory element, but not e.g. displaced postaxial accessory element. Don't you think that it is strange that the whole distal forelimb is disarticulated and displaced, but a small ossicle with loose contact is still in situ?

L 878  -Four distal facets in Tricleidus with corresponding two postaxial accessory elements! See Andrews, 1910, fig. 77

L879 “‘Plesiosaurus’ mansellii” – manselii check spelling here and throughout the MS

L883-885 see comment for L 873 above. This is not really robust evidence for pae

L914-915
Please delete the sentence as it is speculation
(i) - there are two elements in 'P.' manselii, and one preserved in PMO 214.248 - doesn't mean there was no second or even third pae.
(ii) - the posterodistal edge of the humerus in 'P.' manselii is broken and lost, thus its morphology is unknown

L 953 – “S.11” – 10

L 945 “tibiale” and “astragalus”
if you have astragalus, you can’t have the tibiale the same time. either interpret it as a centrale, or apply a traditional interpretation with the intermedium (not astragalus) and tibiale.
I had no time for publishing this, but discussed at SATLW-2017 - https://www.researchgate.net/publication/319454783_MESOPODIAL_ELEMENTS_IN_HINDLIMBS_OF_ICHTHYOSAURS_AND_PLESIOSAURS_CONTROVERSIAL_INTERPRETATIONS_AND_POSSIBLE_SOLUTION

L 1009 – “Abyssosaurus laramiensis” - check taxon name

L 1022 - nice statement, especially after the paragraph listing 7 postcranial synapomorphies of cryptoclidids and no cranial. Everything could be supposed and called problematic when some parts are missing. Still you have no sufficient reasons for this suggestion.

L 1034 “in light of the new taxon (PMO 224.248)”
If you write 'new taxon', you should give its name in the parentheses, but not the specimen number.

L 1035 Please, mark which of the synapomorphies are non-unique

L 1047 “were present in the Boreal region during the Late Jurassic – Early Cretaceous.”
Only "during the Late Jurassic". You have no robust evidence for the presence of the second lineage in the Early Cretaceous

L 1071-1074
If you intended to mention aristonectines, please cite also the recent papers with relevant discussions of this issue O'Keefe et al., 2017; Otero et al., 2018

L 1079 mention for the clarity that the mandible is incomplete and this estimation is approximate

L 1104
It could be nice if you tried to add your new taxon to the dataset of Foffa et al., 2018 and see if it occupy the close dental morphospace to e.g. Kimmerosaurus...

L 1112
Although the subject of this section is important and extremely interesting, in its current form... this is a very short and superficial part that adds nothing to the paper. I would rather suggest to remove it, or expand so that it will be more sound. Maybe by adding some sort of analysis? Have you seen a paper by Soul & Benson (2017)?

L 1139 “and likely Berriasian in age” no idea why do you think so. It is not impossible, but you have no evidence

L 1257 not cited in the text

Comments to supplemental information

I like the new characters you added to the dataset.
In the section “The impact of the new characters” there is nothing regarding the IMPACT of character 272: Dentary, mediolateral expansion of the dorsal surface.

“Table S1.1: Table over the first and last occurrences of taxa.”
“Data from PBDB with some geological age mistakes corrected.”
Please explain, what exactly and why was corrected.

Literature cited in the review:
Benson R.B. J., Bowdler T. 2014. Anatomy of Colymbosaurus megadeirus (Reptilia, Plesiosauria) from the Kimmeridge Clay Formation of the U.K., and high diversity among Late Jurassic plesiosauroids. Journal of Vertebrate Paleontology, 34:5, 1053-1071
Dypvik, H., Nagy, J., Eikeland, T.A., Backer-Owe, K., Andresen, A., Haremo, P., Bjærke, T. & Johansen, H. 1991. The Janusfjellet Subgroup (Bathonian to Hauterivian) on central Spitsbergen: a revised lithostratigraphy. Polar Research, 9 (1): 21-44.
Dallmann W.K. (Ed.) 1999. Lithostratigraphic Lexicon of Svalbard. Upper Palaeozoic to Quaternary Bedrock. Review and Recommendations for Nomenclature Use, Committee on the Stratigraphy of Svalbard/Norsk Polarinstitutt, 320 pp.
Fischer V, Maisch MW, Naish D, Kosma R, Liston J, Joger U, Krüger FJ, Pardo Pérez J, Tainsh J, Appleby RM. 2012. New ophthalmosaurid ichthyosaurs from the European Lower Cretaceous demonstrate extensive ichthyosaur survival across the Jurassic–Cretaceous boundary. PLOS ONE 7(1):e29234
Foffa D, Young MT, Stubbs TL, Dexter KG, Brusatte SL. 2018. The long-term ecology and evolution of marine reptiles in a Jurassic seaway. Nature Ecology & Evolution 2: 1548–1555.
Hammer Ø, Collignon M, Nakrem HA. 2012. Organic carbon isotope chemostratigraphy and cyclostratigraphy in the Volgian of Svalbard. Norwegian Journal of Geology 92:103–112
Knutsen, E. M., P. S. Druckenmiller, and J. H. Hurum. 2012a. Redescription and taxonomic clarification of ‘Tricleidus’ svalbardensis based on new material from the Agardhfjellet Formation (middle Volgian). Norwegian Journal of Geology 92:175–186.
Knutsen, E. M., P. S. Druckenmiller, and J. H. Hurum. 2012b. Two new species of long-necked plesiosaurians (Reptilia: Sauropterygia) from the Upper Jurassic (middle Volgian) Agardhfjellet Formation of central Spitsbergen. Norwegian Journal of Geology 92:187–212.
Knutsen, E. M., P. S. Druckenmiller, and J. H. Hurum. 2012c. A new plesiosauroid (Reptilia: Sauropterygia from the Agardhfjellet Formation (middle Volgian) of central Spitsbergen, Norway. Norwegian Journal of Geology 92:213–234.
Lena L. et al. 2019. High-precision U–Pb ages in the early Tithonian to early Berriasian and implications for the numerical age of the Jurassic–Cretaceous boundary. Solid Earth, 10, 1-14, https://doi.org/10.5194/se-10-1-2019
O'Keefe F. R., Street H.P., Cavigelli J.P., Socha J.J., O'Keefe R. D. 2009. A Plesiosaur Containing an Ichthyosaur Embryo as Stomach Contents from the Sundance Formation of the Bighorn Basin, Wyoming. Journal of Vertebrate Paleontology. 29(4) 1306-1310
O’Keefe, F. R., Otero R. A., Soto-Acuna S., O’Gorman J. P., Godfrey S. J., Chatterjee S. 2017. Cranial anatomy of Morturneria seymourensis from Antarctica, and the evolution of filter feeding in plesiosaurs of the austral Late Cretaceous. Journal of Vertebrate Paleontology. 37:4, doi: 10.1080/02724634.2017.1347570.
Otero R.A., Soto-Acuña S., O'Keefe F.R. 2018. Osteology of Aristonectes quiriquinensis (Elasmosauridae, Aristonectinae) from the upper Maastrichtian of central Chile. Journal of Vertebrate Paleontology, 38:1, doi: 10.1080/02724634.2017.1408638
Rogov, M. A. 2010. New data on ammonites and stratigraphy of the Volgian stage in Spitzbergen. Stratigraphy and Geological Correlation, 18, 505–531.
Rogov MA. 2014. Infrazonal subdivision of the Volgian Stage in its type area using ammonites and correlation of the Volgian and Tithonian Stages. STRATI 2013. First International Congress on Stratigraphy. At the Cutting Edge of Stratigraphy. Cham: Springer Geology, 577–580.
Soul L., Benson R.B.J. 2017. Developmental mechanisms of macroevolutionary change in the tetrapod axis: A case study of Sauropterygia. Evolution, 71(5), 1164–1177.
Zverkov NG, Fischer V, Madzia D, Benson RBJ. 2018. Increased pliosaurid dental disparity across the Jurassic–Cretaceous transition. Palaeontology 61(6): 825–846
Zverkov NG, Prilepskaya NE. 2019. A prevalence of Arthropterygius (Ichthyosauria: Ophthalmosauridae) in the Late Jurassic—earliest Cretaceous of the Boreal Realm. PeerJ 7:e6799

The following papers not cited in the current version could also be helpful as are related to the topic of the research:

Evans M. 1999. A new reconstruction of the skull of the Callovian elasmosaurid plesiosaur Muraenosaurus leedsii Seeley. Mercian Geologist 14:191–196.

Maisch M.W. 1998. Notes on the cranial osteology of Muraenosaurus Seeley, 1874 (Sauropterygia, Jurassic), with special reference to the neurocranium and its implications for sauropterygian phylogeny. Neues Jahrbuch für Geologie und Paläontologie Abhandlungen. 207: 207–253.


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

Input:
Title: A NEW PLESIOSAURIAN FROM THE JURASSIC–CRETACEOUS TRANSITIONAL INTERVAL OF THE SLOTTSMØYA MEMBER (VOLGIAN), WITH INSIGHTS INTO THE CRANIAL ANATOMY OF CRYPTOCLIDIDS USING COMPUTED TOMOGRAPHY
Review round: 2
Reviewer: 1

Output:
Basic reporting: Dear editor, dear authors,

The only point I would like to bring here is the following one, related to the sharing of data, as requested by the journal:

As my colleague reviewing the paper, I also strongly encourage the authors to find a way to provide .stl or .ply (or else) files of the volumetric renderings of the elements that have been CT-scanned. This participates to the initiative of making scientific data open and widely distributed.
Experimental design: I would like to bring two points here: one related to the topic of the paper (J/K boundary) and one related to the phylogenetic methods:

A. J/K boundary turnover:
The added caveats of the stratigraphic position of the specimen make its weird to maintain an emphasis on the J/K turnover in the paper. Now, the end of the abstract mentions that a *possibility* is *raised* that two lineages *may* have crossed the boundary. Such level of uncertainty renders this part of the MS dispensable at the new specimen is not shedding a new light on the very topic of the Jurassic/Cretaceous boundary turnover.

B. Phylogenetic methods:
The way phylogenetic methods are described (L987-1109) is still ambiguous. Here is a suggestion (please make sure it perfectly matches with what you have done):

Ophthalmothule cryostea (PMO 224.248) was scored into the data matrix of Roberts et al., (2017), which stems from the matrix from Benson and Druckenmiller (2014). Based on the results of the present study, three new characters (Characters 271-273) were created, relying on features relevant for cryptoclidids and include two cranial and one post-cranial features (See Data S1 for further discussion and description). Alternative scores and additional information on how to discern character states of individual cryptoclidid taxa are available in the supplementary information. The first new cranial character relates to the presence of an interfrontal vacuity and the second relates to the dorsal surface of the dentary. We edited a previously used postcranial character related to the fibular morphology and included in the matrix. The resulting matrix totals 273 unordered morphological characters and 76 OTUs.
The analysis was performed in TNT (V.1.5) (Goloboff and Catalano, 2016) using the  parsimony ratchet, followed by a heuristic search using Tree bisection reconnection (TBR) that used the trees recovered from the parsimony rachet analysis. The parsimony ratchet analysis used 1000 ratchet iterations, with 10 random addition sequences
###
Please indicate here if you used drift and how many cycles (most of the times, people use the default value of 10)
###
Please indicate here how many trees were allowed in the memory. By default, TNT proposes of a value 100 which is may too low for any serious analysis. Many analyses nowadays go for 200.000 (the command is “hold 200000;”).
###

. All trees were kept and auto constrain turned off and all characters were equally weighted. Yunguisaurus was defined as the outgroup taxon (Cheng et al., 2006). The bremer function in TNT (V 1.5) was used to calculate Bremer support (decay index). Bootstrap resampling (1000 replications), was also performed (Fig. S.5). The scripts stats.run was used to calculate CI and RI. The strict consensus tree for Plesiosauroidea is available in supplementary information (Fig. S.14).
A posteriori time scaling of the strict consensus tree was computed in the R statistical environment and used data collected from the PBDB (Paleobiology Database, paleobiodb.org), and was completed by the literature
###
please indicate the references used, if any
###
. The Datephylo function from the R package strap (Bell and Lloyd, 2014), was utilised to form the time scaled tree (See supplementary information for data).

###
	Please indicate the way the tree was timescaled (i.e. how the length of internal branches was computed): equal? Mbl? Modified Hedman?
###
Validity of the findings: A comment on evolutionary drivers:

The section (L1108 to 1130) appears unclear and I find it difficult to follow your thinking process. Here are some points/thoughts that I hope will help you regarding your interpretation of the cranial shape of Ophthalmothule :

In said section, you seem to oppose the ‘mean’ of evolving larger eyes (through the evolutionary process of paedomorphy) versus the possible driver (increase visual acuity) and versus the possible relative changes due to allometry and the integration of the skull (the reduction in relative size of other cranial parts). All of these can actually be combined to explain a phenotype.

In lines 1123 to 1125, you seem to suggest that the skull is fixed in total length and that any change in one part (e.g. larger eyes) necessarily result in shortening of the others. However, skulls are never 100% integrated and it is well known in plesiosaurians and marine reptiles in general that some parts can be extended without necessarily reducing the others (e.g. the longer snouts and larger eyes in ichthyosaurs).

An important point to add here is that mechanical advantages are computed as ratios and are thus dimensionless while visual acuity is based on the *absolute* size of the eye (notably the diameter of the dilatated pupil). Hence, an animal with a shorter rostrum and similarly sized eyes than its ancestor would have a different mechanical advantage and relatively larger eyes, but no change in actual visual acuity at all. Comparing the ancestral condition to that of Ophthalmothule might be the key to highlight the changes going in that particular lineage.
Additional comments: Line-by-line minor comments:

L25: Could you please add “ and species” after “genus”.

L26: double space before “The holotype”

L28: double space before “observed”

L28: “incorporating” instead of “incorporting”

L40 and throughout. “Plesiosaurian” and “plesiosaur” are used interchangeably throughout the text. Could you make it more consistent?

L893: “Andrews” instead of “Andres”

L1014: could state whether these are ambiguous (i.e. ‘local’, homoplasic) or non-ambiguous (i.e. ‘global’, non-homoplasic) synapomorphies?

L1134, L1136: It is best not to not start a sentence with an abbreviated term (here “O.”)

Best wishes,

Valentin Fischer


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

Input:
Title: A NEW PLESIOSAURIAN FROM THE JURASSIC–CRETACEOUS TRANSITIONAL INTERVAL OF THE SLOTTSMØYA MEMBER (VOLGIAN), WITH INSIGHTS INTO THE CRANIAL ANATOMY OF CRYPTOCLIDIDS USING COMPUTED TOMOGRAPHY
Review round: 2
Reviewer: 2

Output:
Basic reporting: As I reviewed the MS before and suggested minor revisions, I will not follow the recommended scheme of review this time. All my comments are in "comments for the author" section.

I'm happy with the changes the Authors did.

There are several typos I found (listed in comments for the author section).

My recommendation would be rather to accept the paper as is. However, as I added some additional comments, I put a tick near "minor revision" again so that authors have time to correct typos and, if they consider it necessary (hopefully not), to respond to my comments.
Experimental design: no comments
Validity of the findings: no comments
Additional comments: I feel the need to comment on some of the Authors' rebuttals. These comments are given below along with other line-by-line corrections.

Line 25
“representing a new genus Ophthalmothule cryostea gen et sp. nov.,”

Either write “taxon” or “genus and species” as in the current form you wrote genus but then give a name of the new species.

Line 31
“incorporting”

incorporAting?

Line 169
“basioccipital tubera broad and flattened”

As I asked in the previous round, please add how these are broad mediolaterally or anteroposteriorly?
Surprisingly in your rebuttal, you wrote that corrected this, but actually not.

Line 199
“Kimmerosaurus langhami”

As I noted in the previous round, mid-posterior cervicals are not known for this taxon, at least in published works, so please either add “pers. obs.” and reference to the undescribed specimen in which you observed this trait (with the number), or delete the mention of this taxon. This is not critical at all. As I spent a couple of weeks studying the collections of the NHMUK, I can say that, as far as I know, there is only one specimen of Kimmerosaurus with cervical vertebra preserved – NHMUK R 10042, described by Brown, Milner & Taylor (1986). This specimen has 5! postaxial cervical centra preserved. You are welcome to share your observations on the undescribed specimens from the Etches collection, but please make this clear to readers. Still, I do not understand why to write: “Response: There are anterior-mid cervical available for Kimmerosaurus at the NHM in London. There are also more posterior vertebrae present in the Etches collection.”
Do you mean any specimen from the NHMUK that has more than 5 postaxial vertebrae preserved? So please give a reference as this is not formally described to my knowledge, or you imply that Kimmerosaurus had 15-20 cervical vertebrae (so that 7th vertebra could be considered "anterior-mid cervical")?

Line 201-202

"L 199 “short and reduced”
I would not be so sure. It seems more like broken and lost than reduced.
“Response: As I (A Roberts) personally excavated and prepared the specimen, I can personally stand for that the dorsal process of the scapula is indeed low and not broken. On the right side, there is some damage due to the overlying vertebrae and ribs. However, the left side is complete, although cracked due to congelifraction.”

Please remember that as a reviewer I’m trying to help you not to make a mistake and/or misinterpretation. Personal excavation of the specimen does not guarantee the original completeness of the specimen and that the broken part was not displaced during taphonomy. I cannot insist on the suggestion but hope that your further research of plesiosaurian materials will help your better understanding of the morphology of their pectoral girdle. As I (N Zverkov) personally re-examined the plesiosaur and ichthyosaur materials from Svalbard that you and your colleagues have previously described, I know well the problems with preservation and taphonomic tricks in this stuff – e.g. the case with the right scapula of the holotype of plesiosaur Djupedalia engeri that was excavated as three disarticulated and scattered fragments and subsequently described as clavicles and interclavicle and even added to the diagnosis of the new taxon (Knutsen et al., 2012). Their broken edges were identified as facets, but when all three parts are putten together they form a complete right scapula instead:
https://www.dropbox.com/sh/gnjbafrwmcgvdli/AAArYyNwYK5n6_XgkJ0tlwi5a?dl=0
As far as I know, you were informed about this my "discovery" by J Hurum right during my visit. I haven't checked your coding for this particular case, but hope that you considered this in the current contribution.
This is just one example of how taphonomy can bias interpretations and further work. With your specific Svalbard material, such things should be always kept in mind.
Please beware the misinterpretations and better examine the morphology of scapulae in other cryptoclidids including Muraenosaurus, Tricleidus and Cryptoclidus (e.g. Andrews, 1910).

Line 210
“The preserved skeleton of PMO 224.248 is well-preserved and fully articulated”

Consider rewording, e.g. deleting the first “preserved”.

“ L 561-562
“possibly due to taphonomy” - you can say the same regarding PMO 224.248. Based on my observations on this nicely preserved specimen it is more likely a natural condition than a taphonomic distortion.
“it appears absent on the holotype” - the mandible of the holotype is disarticulated. The dentaries are nearly completely preserved and fused. their posterior ends are mediolaterally wide. It is possible that this could be due to taphonomy, but I would rather suggest that this is a natural condition further supporting your observation of this morphology in the referred specimen.
Photograph of dentaries of the holotype - https://www.dropbox.com/s/g40mop6l28nuyka/IMG_5879.JPG?dl=0
Response: Corrected and edited to support this”

I see no correction that agrees with the observations. The feature is present in the holotype specimen. I have no idea why you are still insisting on your interpretation even after getting photographs of the specimen – leaving this at your conscience.

“L 603 “ridging is most prominent on the labial side”
Could you provide close-up photographs of the enamel ornamentation as supplemental files, please? This interpretation sounds confusing to me and it would be nice to have pictures for agreeing that your description is correct.
Response: Unfortunately, I do not have access to the specimen currently and cannot get more detailed photos of the dentition. Although we do believe the current images suffice as supplement to the description. Regarding the D-shaped cross-section in Kimmerosaurus, this was an error on our part and has now been fixed in text. ”

That’s unfortunate, that from the five authors of the paper only the lading author is capable of taking additional pictures, but cannot get them as well… Hopefully, you will be able to provide these in your further works.

Line 893
“Andres”
Andrews

Line 930
“mansellii”
manselii

“L914-915
Please delete the sentence as it is speculation
(i) - there are two elements in 'P.' manselii, and one preserved in PMO 214.248 - doesn't mean there was no second or even third pae.
(ii) - the posterodistal edge of the humerus in 'P.' manselii is broken and lost, thus its morphology is unknown
Response: Regarding this sentence “This is somewhat different from “Plesiosaurus” manselii, where the postaxial elements occupy the entire distal postaxial margin (Hulke, 1870).” We have edited it to make it clear that this evidence is suggested from the publication and not from the specimen itself.”

In case you want to support your statement by the reference only, please see the original publication carefully and pay attention that the posterodistal portion of the humerus was missing during the original description (Hulke, 1870: pl XLI, fig 3). To leave this citation you should write something like: "according to the reconstruction of Hulke (1870)".

“L 945 “tibiale” and “astragalus”
if you have astragalus, you can’t have the tibiale the same time. either interpret it as a centrale, or apply a traditional interpretation with the intermedium (not astragalus) and tibiale.
I had no time for publishing this, but discussed at SATLW-2017 - https://www.researchgate.net/publication/319454783_MESOPODIAL_ELEMENTS_IN_HINDLIMBS_OF_ICHTHYOSAURS_AND_PLESIOSAURS_CONTROVERSIAL_INTERPRETATIONS_AND_POSSIBLE_SOLUTION
Response: As far as I am aware it is correct terminology to use astragalus in the hind limb and intermedium in the fore limb. As such, I have let this stand.”

This is not critical and you can interpret the element in any way you want to. Just for accuracy of your further work I recommend to read something about limb evolution and development in tetrapods – this is not only interesting but also very useful. Regarding the interpretations in limbs of sauropterygians you can read e.g. Caldwell, 1997 (Limb osteology and ossification patterns in Cryptoclidus….)

Best wishes

Nikolay


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: OVEREXPRESSION OF PHENAC3 FROM MOSO BAMBOO PROMOTES LEAF SENESCENCE AND ENHANCES ABIOTIC STRESS TOLERANCE IN ARABIDOPSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this manuscript, the authors have studied the effect PheNAC3 over expression in Arabidopsis. Overall, the manuscript is nicely written and provides all the necessary details to understand or to reproduce the work.
Experimental design: However, there are few questions that need to be addressed before the manuscript can be considered for the publication. These questions are related to the figures and their analyses and include:

Figure 1B: Why different domains are in different color? What does a particular color signify? And what do the integers in each domain represent?

Figure 2A: As per the text (line 197), GFP control is localized throughout the cell. However, the GFP (control experiment) signal in Figure 2A is localized to the periphery.  Please comment on this. Moreover, I see a co-localized signal of GFP and DAPI in the lower panel suggesting that the GFP control is also localized to the nuclei. Please comment on this.

Figure 2B: Please add a figure-panel showing the plasmid map details of GAL4-PheNAC3

Figure 3 Dto I: Please specify the conc. of different chemicals (ABA, MeJA, NaCl etc) in the graphs.

Figure 4A: Briefly describe the phenotypic differences (if any) between Col and OE-PheNAC3 plants

Figure 4B: What do G1, G2, G3 stand for?
Validity of the findings: no comments
Additional comments: The manuscript should be revised for the english. Few examples of sentences that need to be revised:

"Normally, bamboo plants expend so much energy during flowering and fruiting that will senescence and die shortly thereafter."
"… very high sequence similarity…"

Minor comments:
1.	Describe the full form of acronyms at their first occurrences. Such as NAC, WRKY, bZIP, MYB, and AP2/EREBP
2.	Briefly describe the terminology at their first occurrence. Such as: precocious senescence, ONAC011, heading time etc.
3.	“PheNAC3, which has high 93 similarity to ONAC011”
4.	Line 84: “PeNAC1” Is it PheNAC1 or PeNAC1?
5.	Line 59: “The transactivation activity of the PheNAC3 protein was evaluated according to Chen et al. (2011).” Describe the method in brief.
6.	Line 163: “Arabidopsis” should be italic
7.	Line 179: Do not use words like “great similarity”. Instead specify the value or write  > XX%
8.	Line 185: “very high sequence similarity” specify the value.
Please mention the sequence similarity value? Please specify if mentioned similarity is amino acid- based or the DNA-sequence based?


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: OVEREXPRESSION OF PHENAC3 FROM MOSO BAMBOO PROMOTES LEAF SENESCENCE AND ENHANCES ABIOTIC STRESS TOLERANCE IN ARABIDOPSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: No Comment
Experimental design: No comment
Validity of the findings: No comments
Additional comments: Major comments:
1.	All the experiments are done by ectopically overexpressing PheNAC3 in Arabidopsis but what would happen if these experiments (at least overexpression or downregulation) are performed in moso bamboo transgenics? I know it is not easy to modify the genomes of many plants but can authors try? I would suggest to do at least one experiment in mono bamboo to confirm their finding.  The reason to ask this question is because sequence homolog protein can have different roles in their native organisms and by studying in lab models, authors might miss some new information about that given protein. This will also increase the impact of the work.
2.	Abstract is the first attraction of any article. Current abstract is not very clearly written specially use of tenses, for eg: “PheNAC3 belonged to the NAC1 subgroup and had a conserved NAC domain on the N-terminus”: should be “PheNAC3 belong to the NAC1 subgroup...” . Please format the abstract with proper use of tense. Sentences flow better in active voice, so try to use some active voice in abstract.
3.	Introduction should be more fluid. It misses the connection between paragraphs. In the last para of the introduction it is not clear why authors studied PheNAC3. Even-though the reasoning is given in method section line 116-119 but motivation in introduction is missing.

Minor Comments:
4.	Line 43: “that will senescence” change to “that they will senescence”
5.	Line 176: change “great” to “high”
6.	In fig 2A, I see a localized signal in GFP only.  Can authors explain why there is a localization signal in GFP only? Is the PheNAC3-GFP fusion is functional?
7.	In fig 2B, the blue colour is not very prominent. Authors should provide better images.
8.	 Why there is higher expression of PheNAC3 gene in mature than old leaves while old leaves should have more senescence and thus higher expression in Fig 3B?
9.	Fig 3 contains too many panels.  Authors do not need to show all the panels in main figure. I would suggest to divide the results (Expression profile of PheNAC3 during senescence of moso bamboo leaves and shoots) between natural and induced senescence or move some results to supplementary information.
10.	 In some panels of fig3, Y-axis contains too many ticks. Please make them less.
11.	What was the criteria behind dividing detached leaves in three categories G1-G3 and why G2 was used to do the experiments? Doesn’t this bias the finding? I would suggest to move RT-PCR (Fig 4C) to supplemental information.
12.	I could not understand the use of qRT-PCR data for AtABF4, AtNCED3, AtRD29A and At RD29B (Fig 4E) in the same panel. Authors need to discuss a bit more in the main text (Line 251-256).
13.	Panels in Fig 5B are not clear. Please level properly.
14.	Line 266-267: Growth and root length (Fig 6) information is only given in images. Can authors provide more information about root length in a quantitative way?
15.	Line 269-271: Authors should provide quantitative information before saying significant different in number of lateral roots.


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: OVEREXPRESSION OF PHENAC3 FROM MOSO BAMBOO PROMOTES LEAF SENESCENCE AND ENHANCES ABIOTIC STRESS TOLERANCE IN ARABIDOPSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Overall manuscript has been improved with writing and clarity.
Experimental design: Everything is clear and methods are well described.
Validity of the findings: Finding are well explained.
Additional comments: Great work and interesting finding.


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: FOOD ADDITIVE “LAURIC ACID” POSSESS NON-TOXIC PROFILE ON BIOCHEMICAL, HAEMATOLOGICAL AND HISTOPATHOLOGICAL STUDIES IN FEMALE SPRAGUE DAWLEY (SD) RATS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This study contains the acute toxicological evaluation of lauric acid, a commom food additive. The authors performed the experiments following the recommendations of OECD (423 - acute oral toxicity) but underestimated the possibilities of investigation. A few parameters were assessed and they are not enough to affirm the absence of toxicity.

The authors affirmed that no data concerning the potential toxicological properties of LA are available; however, I found the following studies about this substance: “Final Report on the Safety Assessment of Oleic Acid, Laurie Acid, Palmitic Acid, Myristic Acid, and Stearic Acid” and Safety assessment of widely used fermented virgin coconut oil (Cocos nucifera) in Malaysia: Chronic toxicity studies and SAR analysis of the active components” (DOI:10.1016/j.yrtph.2016.10.004).

Avoid using the word “sacrifice” (line 163) because it is not correct. This term is not technical. Replace it by euthanasia.

The whole manuscript lacks a high standard quality of the English language. The text contains several no-technical terms and sentences as well as syntaxis errors. Thus, I am strongly recommending a detailed revision of English grammar.
Experimental design: The authors carried out the experiments in accordance with the OECD to acute oral toxicity. However, I identified some important issues that must be taken into account:

It is not correct to affirm that no toxicological effects were caused by the administration of LA based on relative organs weigh, some plasma biochemical markers of function and histological evaluations. The oxidative status of the tissues, mainly liver and kidney, could be assessed in order to discard any impairment due to metabolization and elimination of LA. Thus, it would be interesting recognize such limitations.

The reagents used to the histological staining should be informed in the correct section (drugs and reagents) instead of the histopathological analysis. Please, correct it and provide additional information about the dyes used.

The age of the animals should be mentioned.

How the authors selected the doses used in the study? What were the scientific criteria followed?

Locomotor and coordination behaviors would provide reliable evidence concerning the occurrence of toxic effects caused by substances administration.  Did the authors perform any behavioral evaluation with the animals?

In the section 2.7 – the authors should mention the biochemical parameters that were determined. Such information was provided in the result section. Please, modify it to make easier to the reader.

In the section 3.2, the following sentence “…on the day fourteenth of LA administration,…” is giving an incorrect idea of repeated administration. Please, revise it.

In the section 3.5, the authors did not adequately describe the results of histological evaluation. In the current form, the morphological characteristics of the tissues were barely mentioned. Instead of describing the tissue features in the discussion (line 309 to 343), the authors must add those data herein, in the correct section.
Validity of the findings: Concerning the validity of the findings, in the discussion, the real scientific contribution and impact of the data are not clear. The authors failed in demonstrating the importance of their study to the field of toxicology. This section is a more extensive format of the results. The authors poorly linked their results with scientific literature, which must be improved using additional studies to support the conclusions. Additionally, a paragraph of potential limitations would fit well due to the lack of more accurate techniques.
Additional comments: The current study contemplates the investigation of acute oral toxicity of lauric acid (LA), a commom food additive. Despite the adequate guideline (OECD 423), the authors collected a small piece of evidence regarding the possible toxic effects caused by LA. The manuscript needs to be doubly-checked to improve the English language and the discussion as well. I suggest the authors a detailed revision of the document taking into consideration the comments made by me.


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

Input:
Title: FOOD ADDITIVE “LAURIC ACID” POSSESS NON-TOXIC PROFILE ON BIOCHEMICAL, HAEMATOLOGICAL AND HISTOPATHOLOGICAL STUDIES IN FEMALE SPRAGUE DAWLEY (SD) RATS
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In their manuscript, Khan and colleagues report the toxic effects lauric acid, a common constituent of coconut oil and it is used as food additives. Identifying toxic effects of lauric acid is important, because it is a product used in the food and has various potential pharmacological properties. The experiments seem to be well performed and the results are sound, but some points need to be addressed by the authors, main the histological analyses.

Abstract
The sentence repeat twice: “(SD) rats”;
The authors need taking care the abbreviations, for example: B.W.;
Keywords:
Please remove OECD 423 of keywords section;
Introduction
The introduction section is very long, I suggest the authors reduce.
Some points the English need be revised.
Methods
Why the authors chose the doses of 300 and 2000 mg/kg?
What the reason to use female?
In the in vivo experiments the correct is using “dose” not “concentration”.
I think that 15 days after the treatment can occurs restoration of hematological and biochemistry parameters. What the authors think about this?
Please explain the use four different histological techniques.
The figures need show the same things in the control group and treated groups.
Results
Please correct this “…as shown in (table xx)”
The authors need include the F values in the results section.
What is gm?
The first sentence of “Effects of LA on Histopathology of internal organs” is about material and methods.
The authors need correct all the images, sometimes the arrow is not in the correct place. This observation is the main point that authors need to correct.

Discussion
A discussion about toxic natural products could be interesting;

Figures
Please check all figures, mainly the arrows.
Please provide the same points of the organs in all groups;


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: FOOD ADDITIVE “LAURIC ACID” POSSESS NON-TOXIC PROFILE ON BIOCHEMICAL, HAEMATOLOGICAL AND HISTOPATHOLOGICAL STUDIES IN FEMALE SPRAGUE DAWLEY (SD) RATS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript of Khan et al. is well written, however some questions need to be clarified.
Why did the authors decide to conduct toxicology testing only on females?
What is the impact of using only females for this research? Is it that many studies today show how males and females respond differently to pharmacological and toxicological treatments?
Experimental design: What werelauric acid concentrations based on?
To Daily observations, how the authors evaluated clinical signs of toxicity?based on what?
Validity of the findings: Are very well described, with no suggestions to expose.
Additional comments: The manuscript is very clear and with consistent results, after some changes I recommend this article 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: FOOD ADDITIVE “LAURIC ACID” POSSESS NON-TOXIC PROFILE ON BIOCHEMICAL, HAEMATOLOGICAL AND HISTOPATHOLOGICAL STUDIES IN FEMALE SPRAGUE DAWLEY (SD) RATS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors took into consideration all the suggestions and queries raised by me to perform the document revision. The current version of the manuscript is now suitable for publication in the journal.
Experimental design: Overall, all my concerns were solved and properly answered. I have no additional comments.
Validity of the findings: The authors attended to my suggestion. The discussion section is now clearer and more informative in the current version of the document.
Additional comments: Dear authors,
The revision made in your manuscript considerably improved its quality and readability. Thus, I am suggesting the acceptance of the document for publication in the PeerJ.


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: PATTERNS OF GENE EVOLUTION FOLLOWING DUPLICATIONS AND SPECIATIONS IN VERTEBRATES
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: Review of David, Oaks, and Halanych: “Patterns of gene evolution following duplications and speciations in vertebrates.”

Overview:
In this manuscript, the authors describe having inferred a large set of gene trees that include branchings due both to speciation and duplication events. They divide the branches in this fashion and estimate branch-specific values of the selective constraint (Ka/Ks) for all branches. They then explore the pattern of shifts in Ka/Ks after speciation and duplication events.  They argue that the pattern of increases in Ka/Ks after duplication events is consistent with the orthology conjecture: that orthologs maintain more similar functions over time than do gene duplicates.

Major comments:
The authors have done a commendable job of assembling a valuable and interesting set of genes for analysis. At the same time, I do not find that authors’ interpretation of their results at all convincing and think that both the methodology and that interpretation need additional analyses and background reading.

My primary concern is that I do not understand at all why the authors dismiss perhaps the most obvious explanation of their results. We expect a relaxation of selective constraint immediately after gene duplication, as is discussed in several of the papers cited here. In many cases, that relaxation will be followed by nonfunctionalization. However, even in surviving duplicates, the relaxation should leave at least some signature on the branch-wise Ka/Ks, even if the genes in question later come under a stronger selective regime (because you cannot “unfix” those neutral amino acid-changing substitutions from the early history of the duplicate.)  To my mind, all of the authors’ results are consistent with this null model, without any need to involve the orthology conjecture, neofunctionalization or any other models of duplicate evolution.  Now, I do not mean by this that no other forces are at work or that the orthology conjecture is wrong.  I just do not find the data here as speaking to these questions.

I also think that the methods used would need some refinement to even support the conclusion of relaxed selection after duplication.  The Ka/Ks ratio can have odd time-dependent behavior that make comparing old and young gene duplications difficult even aside from the complexity of understanding gene duplication (1).  Likewise, although EggNog is a viable orthology inference method, I would like to see at least one more orthology approach (EnsemblCompara?) used in the analysis to be sure that the inference of orthology/paralogy nodes is not biasing any results.

Minor points:

It has been some time since I read Ohno’s book, but I do not recall him introducing the concept of subfunctionalization.  Similarly, I think it is a mistake to claim that other mechanisms of duplicate preservation fall under the sub/neo umbrella: see especially (2-5).

Lines 112-113: I think it is clearer to describe this model as allowing different Ka/Ks ratios on each branch rather than each lineage.

Line 194-196: It is not correct to interpret either elevated Ka/Ks <1.0 or asymmetry in Ka/Ks as evidence of neofunctionalization: many of the works cited here make this point quite clear.

References:

1.	Stoletzki N & Eyre-Walker A (2011) The positive correlation between dN/dS and dS in mammals is due to runs of adjacent substitutions. Molecular Biology and Evolution 28(4):1371-1380.
2.	Kondrashov FA & Kondrashov AS (2006) Role of selection in fixation of gene duplications. Journal of Theoretical Biology 239(2):141-151.
3.	Birchler JA & Veitia RA (2012) Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. Proc Natl Acad Sci U S A 109(37):14746-14753.
4.	Freeling M (2009) Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annual Review of Plant Biology 60:433-453.
5.	Makino T & McLysaght A (2010) Ohnologs in the human genome are dosage balanced and frequently associated with disease. Proceedings of the National Academy of Sciences, U.S.A. 107(20):9270-9274.
Validity of the findings: See #2
Additional comments: See above.


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

Input:
Title: PATTERNS OF GENE EVOLUTION FOLLOWING DUPLICATIONS AND SPECIATIONS IN VERTEBRATES
Review round: 1
Reviewer: 2

Output:
Basic reporting: David et al investigate the differential functional divergence between ortholog and paralog gene lineages, as assumed by the Ortholog Conjecture (i.e. pairs of orthologous gene lineages are assumed to be less divergent than pairs of paralogous gene lineages, since they presumably preserve the same functionality).

They estimate differential functional divergence by first evaluating the ratio of non-synonymous to synonymous substitutions (dN/dS) in independent gene lineages deriving from either speciation events (orthologous lineages) or duplication events (paralogous lineages). Then, they evaluate the difference in dN/dS ratio between pairs of orthologous lineages and paralogous lineages, trying to test if/when there is a significant statistical difference between the two groups (orthologs vs paralogs).

Overall, we found the study to be clear and interesting, and a potentially useful resource as well. Therefore, we would recommend publication after minor changes.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Suggestions/comments:

* Introduction:

The use of the English language is quite clear, the text flows well and is easy to follow. Statements are in general well referenced, but they are perhaps missing the original reference for the “Ortholog Conjecture” (lines 51-53).

* Methods:

Line 92: Since calibration dates seem to be key, we suggest spending some more words on the global clock model with which they are determined (it is well referenced, though).

Line 109: Selection pressure == selective pressure?

* Results:

- Line 156: The authors test if there are significant differences between two categories of duplication events (paralogs): within-species and between-species. We wonder, are there differences between other categories of paralogs, e.g. 1:2, 1:3, etc? Or, perhaps more interesting, when there is a single duplication (1:2) vs. when there are more lineage amplifications (1:many).

- Line 158: “significant (p<0.001, Hedges’ g=0.18) differences in Δω were also recovered between different categories of duplication events”. Even if the difference is significant, it might be useful to stress that the effect size (as estimated by the Hedges’s g) is quite limited. It might also be good to have a figure to illustrate this result.

- Line 161: We wonder whether it would be possible to have a figure for this result as well, since this is one of the most important results.

- Lines 165 –175: These results seem to be consistent with those obtained for differently specialized families after the vertebrate whole genome duplications (Marletaz et al, Nature 2018).

- Will the raw values per gene and species be available as a Supplementary (text) Table? This would be a nice resource for the community.

* Discussion:

- Line 201: this paragraph should be more appropriately explained in the Results section (with relative description of Fig3 there as. well). Also, the sentence could be clearer, e.g.:  “When Δω is estimated over time, two unexpected patterns emerge (Fig. 3). First, there is an apparent spike in Δω between paralogous lineages that diverged ~25 mya, with an average Δω of0.73 ± 0.83 for duplication events from between 10mya and 40mya”.

* Figures:

- Fig1. We have struggled a bit to understand this figure. Therefore, we recommend to modify it a bit to make it easier to follow. Perhaps relatedly, we found the caption incomplete: since the possible fates of paralogs are illustrated, it might be good to mention/comment them in the caption?

- Fig2. It might be better if it was divided in A and B and referenced as such.

- Fig3. The connection between upper and lower panel should be better explained in the caption.


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: PATTERNS OF GENE EVOLUTION FOLLOWING DUPLICATIONS AND SPECIATIONS IN VERTEBRATES
Review round: 1
Reviewer: 3

Output:
Basic reporting: First, I have now understood why some values of Δω are always positive, and others are not. On Fig 1, it is indeed noted that Δω between daughter branches is calculated as an absolute value, whereas Δωp is not, and this is consistent with the R code. Except that in the R code, Δωp is used to call the function run(), which uses abs().
The authors need to (i) clarify whether Δωp is tested with absolute values, and (ii) make it clear in the text which Δω values can or cannot be negative, and why.

The authors continue to ignore previous work in their discussion, even though they are cited in passing. I repeat the references I provided last time, which performed very similar analyses and must be truly discussed:
Brunet et al 2006 https://academic.oup.com/mbe/article/23/9/1808/1014301
Studer et al 2008 https://genome.cshlp.org/content/18/9/1393.abstract
Han et al 2009 https://genome.cshlp.org/content/19/5/859.short

Line 189-191: I repeat a comment from the previous version exactly: why would a speciation event change the evolution of a paralog? A gene copy is in given individuals within a given population, and is not affected by the fact that another population is or is not becoming a new species.

There is no evidence for adaptation in the ms, remove the term from the abstract.

Neofunctionalisation is not presented in Ohno 1970, it was introduced by Force et al 1999 (Genetics April 1, 1999 vol. 151 no. 4 1531-1545).
Experimental design: The authors continue to use a simple in-house algorithm to label tree nodes as duplication or speciation, whereas this is an active domain of research with many elaborate methods and known issues. I repeat my suggestion of using labels from Ensembl Compara. Other methods can provide such labels, see https://questfororthologs.org/orthology_databases

The Figure S2 is extremely important. dS is clearly saturating, and older dN/dS values are thus unreliable. This must be addressed at the very begining of the discussion, and all results must be interpreted in light of this observation.
Notably:
the difference between within-species (on average younger) and between-species (on average older, thus dS saturated) paralogs
Validity of the findings: The authors continue to write that asymmetry implies neo-functionalisation, but this is not true. There is nothing in sub-functionalisation which implies symmetry.
Additional comments: This manuscript by David et al presents an interesting test of the ortholog conjecture using dN/dS (ω) value changes in gene trees. I have previously reviewed this manuscript for another journal, and it has been improved in several ways. Yet I still have some comments.

Improvements include taking into account the bias in which gene trees have more duplications, by removing speciation-only tree and by randomising inside trees, and clarifying terminology in several places.