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 PAN-AMAZONIAN SPECIES DELIMITATION: HIGH SPECIES DIVERSITY WITHIN THE GENUS AMAZOPHRYNELLA (ANURA: BUFONIDAE)
Review round: 1
Reviewer: 1

Output:
Basic reporting: - The article is clear, and is written in a Clear and unambiguous, professional English used throughout.
R: No comments

- Literature references, sufficient field background/context provided
R: In general, the ms offers a good background on the main subject, the taxonomy and systematics of Amazophrynella. However, the ms failed in provide introduction of one aspect investigated, the relationship between environmental variables and the taxonomy and distribution of putative species proposed.

- Professional article structure, figs, tables. Raw data shared
R: No comments

- Self-contained with relevant results to hypotheses
R: No comments
Experimental design: -Original primary research within Aims and Scope of the journal.
R: Yes,  it agrees with PeerJ scope, which is based on methodological and results soundness, and it is also a original research.

-Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.
R: The research question is well defined, the taxonomy and systematics of Amazophrynella. However, as said above, the htpothesis of relationship among Amazophrynella distribution, taxonomy, and environmental variables is unclear and poorly explored. Additionally, one aspect missing on the discussion (and the intro) is how this paper advances the phylogenetic relationship and taxonomy among Amazophrynella clades. The authors need to be specific in highlight samples from new localities and new clades included only in this ms (and not in previous studies like Fouquet et al 2012, Rojas et al 2016).

-Rigorous investigation performed to a high technical & ethical standard.
R: No comments

-Methods described with sufficient detail & information to replicate
R: The methods fail in provide more details on the parameters used during tree search on Bayesian analysis, and also on dating analysis on BEAST. Please see attached comments on pdf file for more details.
Validity of the findings: -Impact and novelty not assessed. Negative/inconclusive results accepted. Meaningful replication encouraged where rationale & benefit to literature is clearly stated.
R:  The ms deals with a very interesting question, the taxonomy of a cryptic species groups of frogs in one of the most biodiverse ecosystems in the world. There is no replication of methods, however, the authors must be explicit in how many samples are new and not included in previous studies dealing with Amazophrynella systematics and taxonomy.

-Data is robust, statistically sound, & controlled.
R: Yes, however, all the conclusions are based only in mtDNA molecular markers. Although this is not an impediment for the authors conclusions (at least from my point of view), is well know on the literature (see pdf file for references) the limitations of single marker results for taxonomy, species delimitation and phylogenetic relationships conclusions. I suggest to add a paragraph acknowledging the limitations of results.

-Conclusion are well stated, linked to original research question & limited to supporting results.
R: In general it is, although the relationship among taxonomy, distribution and environmental variables was not explored on the discussion. Also, the ms lacks a final session of conclusion, summarizing the advances, limitations and future prospects.

-Speculation is welcome, but should be identified as such.
R: On this, maybe the biogeographic portion of discussion should be indicated as speculation, as no formal test was applied on this (e.g. BioGeoBears, for example).
Additional comments: The ms deals with the biodiversity of a very interesting group, in which was considered, until very recently, as a single, widespread species. By disentangle the diversity and systematics of lineages and species, as well as to provide a reproducible taxonomic framework on Amazophrynella, I considered this ms as very important and relevant. However, I am not satisfied with methodological and results reporting (refers to pdf file for more details) and discussion, specially the environmental variables, which appears pointless to include, and is making the ms more confusing. I detect some possible errors in morphological PCA analysis and in the geological epochs bar on figure 2. Additionally, in the pdf file I highlight several small issues that the authors should deal with. For that reasons, I recommended major revisions. I also put myself available for future revisions.


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 PAN-AMAZONIAN SPECIES DELIMITATION: HIGH SPECIES DIVERSITY WITHIN THE GENUS AMAZOPHRYNELLA (ANURA: BUFONIDAE)
Review round: 1
Reviewer: 2

Output:
Basic reporting: Dear editor,

I have read the manuscript entitled “A Pan-Amazonian species delimitation: high species diversity within the genus Amazophrynella (Anura:Bufonidae)“ submitted to PeerJ for consideration for publication.

The study represents a robust systematics revision of the toads genus Amazophrynella, with taxonomic implications. The results presented on it will eventually be relevant for a wide audience interested on species diversity and biogeographical patterns of Amazonian anurofauna.

The article is well structured, provide sufficient background on its field, abundant analyses and raw data.
Experimental design: The approach used is highly integrative, and the methods well defined in terms of species concept and delimitation, quantitative analysis implemented, and detailed descriptions.
Validity of the findings: Although the authors assumed a conservative criteria for their taxonomic decisions, the advances are inestimable for future studies on the group.
Additional comments: I have some punctual observations for the authors:

Line 131. I suppose that “heap shape” means “head shape”.
Line 159. Please, exchange “GRT” with GTR.
Line 203. The authors stated that the “effects of variables on percent variance explained” was evaluated. But, this may seem confusing because PCA is an exploratory approach, not a statistical test. In fact, it detects the individual contribution of each variable for total variance. It’s better to rewrite this sentence.
Line 204. Please, mention if DFA was also made on the size-free dataset.
Line 208. Please, mention here that univariate test was made for each morphometric variable separately.
Line 240. The PTP model recovered eighteen lineages, not seventeen.
Line 260. It would be interesting to state how many of the lineages are represented on quantitative analysis.
Line 266. A. bokermanni appears on the graphics but are not presented on the morphometric dataset (table S6).
Line 266. Eigenvalues are missing on Appendix S7.
Line 271. I suggest to the authors to take of the grey background of DFA graphics (Fig. 3).
Line 284. Same as line 260.
Line 303. …environmental variables that most contributed…
Line 899. …by Conselho Nacional de Pesquisa…

Figure 1. As node support represents Posterior Probabilities, it should be presented as fractional numbers between 0-1, or it must be clearly stated on captions that it is presented as percentage (pp *100).
Figure 2. On Fig. 2 and Fig. S5, Dendrophryniscus proboscideus is wrongly referred as D. boulengeri.


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 PAN-AMAZONIAN SPECIES DELIMITATION: HIGH SPECIES DIVERSITY WITHIN THE GENUS AMAZOPHRYNELLA (ANURA: BUFONIDAE)
Review round: 1
Reviewer: 3

Output:
Basic reporting: All good. Please refer to my comments to the authors, below.
Experimental design: All good. Please refer to my comments to the authors, below.
Validity of the findings: All good. Please refer to my comments to the authors, below.
Additional comments: This is significant and important contribution to our knowledge of taxonomic diversity in a widespread yet poorly known group of Amazonian toads, the genus Amazophrynella. The scope of the study is impressive, and the data and methods are appropriate for the study's goals.

Overall, my comments refer to minor clarifications and suggestions about grammar and style. However, one issue may deserve further explanation and even reanalysis - the implementation of a species-tree method (based on the multi-species coalescent) on a dataset that effectively corresponds to only one (mitochondrial) locus. Please refer to my comments to the authors below.

1. Line 67. You state that "delimiting species solely based on molecular characters or genetic distances harbors potential pitfalls that have been extensively documented". I think that providing a few examples of these problems may improve the justification of your integrative approach, and hopefully inspire similar comprehensive studies.

2. Line 109. Please replace "corresponds" with "correspond".

3. Line 112. Please replace "was" with "were".

4. Line 114. It is not clear why you cite Sabaj (2016) as a reference for museum acronyms given that all museum acronyms are spelled out in the following paragraph.

5. Line 132. "venter coloration" is listed twice.

6. Line 129. The qualitative and quantitative morphological traits used are described in distinct sections of the text, with the molecular methods in-between, which feels a bit awkward. It may be best to have the morphological traits presented in the same section (or at least consecutively).

7. Line 133. Did you use a ventral incision to perform gonadal analyses? Please clarify.

8. Line 159. Did you use gene partitions? Alternatively, did you implement a single model of evolution across all genes? Please clarify.

9. Line 163. A brief description of the Poisson tree process (PTP) model would be welcome for those not familiar with this method, given it is not necessarily standard in taxonomic studies (as compared, for instance, to the now standard use of phylogenetic trees).

10. Line 171. Please replace "generated" with "generate".

11. Line 171. Please replace "trees" with "tree".

12. Line 171. By "species tree in Beast", do you mean using the Star Beast method based on the multi-species coalescent? If so, did you link all your partitions into a single gene tree? Please note that the mitochondrial genes that you used effectively correspond to a single locus and should be treated as so. Otherwise, Star Beast has treated each gene as an independent locus, which would be a violation of model assumptions.

13. Also, please note that if you only used one (mitochondrial) locus, Star Beast is not the right analysis to do. If you have a single locus, a mitochondrial gene tree (MrBayes) is the best approximation of the species tree that you will get.

14. Line 172. Are you using normal distributions for these calibration priors? Please clarify.

15. Line 180. By "consensus tree", do you mean a maximum-clade credibility tree as summarized in Tree Annotator? Please clarify.

16. Line 197. What kind of "multivariate analyses" were used? What programs were used for that? If this refers to something that is described in detail later in the text, please make this fact clear.

17. Line 201. From this description, is not clear why you separated the eastern and western clades in PCA analyses. Please justify.

18. Line 207. Please replace "incorrectly" with "incorrect".

19. Line 268. It is unclear what is meant by "The PCA of the eastern and western clades revealed a grouping of specimens in the morphometric space".

20. Line 291. As above, it is unclear what is meant by "the PCA of the eastern and western clades revealed a grouping of specimens in the multivariate space".

21. The descriptions (for instance, of the holotypes) are not entirely consistent across the four new species. Different traits are often presented, and overlapping traits are often presented in different orders. Please be consistent.

22. Line 350, 361 and throughout. Please replace "creamy" with "cream", "creamish" or "cream-colored".

23. Line 351. Please include comparisons between A. teko sp. nov. and the other newly described taxa as well (only comparisons with previously described Amazophrynella species are provided).

24. Line 356 and throughout. Some of the trait comparisons between species rely on differences of the order of 0.01 mm, which is hardly useful (and even reliable).

25. Line 356 and throughout. Ratios between measurements expressed in the same unit are unit-less (i.e., TAL/SVL is not expressed in mm).

26. Line 354. Please replace "minor" with "smaller".

27. Line 355. Please replace "minor" with "smaller".

28. Line 402. Coloration in life? Please clarify.

29. Line 408 and elsewhere. Please remove "was".

30. Line 431. Please replace "need" with "needs".

31. Line 488. Please replace "Noviembre" with "November".

32. Line 502 and elsewhere. By "fingers", do you mean "fringes"?

33. Line 503. Here again, some species comparisons are missing.

34. Line 531, 766, and elsewhere. By "vocal", do you mean "vocal sac"?

35. Line 545. I'm not sure referring to a website in this way is appropriate.

36. Line 577. "opening directed" sounds odd. Please verify.

37. Line 580. A dot (".") is missing before "Oral".

38. Line 644. Please replace "largely" with "large".

39. Line 654. Is "black dots on venter (black dots)" correct? So, there is no difference between the two species in this trait?

40. Line 656. Please replace "have" with "having".

41. Line 656, 657. Who is "their" referring to - the new species or the other species? Please clarify.

42. Line 670, 675. State of cloacal opening shows up twice in this paragraph.

43. Line 682. "The abundance of granules on ventral surfaces vary in abundance" - please fix the redundancy statements.

44. Line 685. Please replace "between" with "from".

45. Line 753. Please replace "For" with "From".

46. Line 859. Please replace "marchland" with "marshland".

47. Line 1195, 1196. Please be consistent with legend terminology to avoid confusion - you use "dots" and "circles" to refer to the same thing, then "dotted" to refer to something else, and then "dotted and colored circles".

48. Line 1199. Please replace "calibrate" with "calibrated".

49. Line 1228, 1230. Please replace "variations" with "variation".

50. Figs of specimens: Some figures have values corresponding to the scale bars indicated in the legend, others have it on the image. Moreover, different bars correspond to different scales. Please make scaling scheme (and legend) consistent.

51. Fig. 1. The colors of different clades are too similar of overlap - please consider combining colors with symbols (or implementing some other scheme) to facilitate telling them apart on maps.

52. Fig. 5, 21, and 22. Are you including data of specimens from clades identified by "aff." along with data from closely-related nominal species? For instance, do data for A. vote in this table include also data from A. aff. vote sp 1 and A. aff. vote sp 2?

53. Fig. 6, 7, and 8. Please add to figure legends (within parentheses) the corresponding name/state given to each species' traits (e.g., blotches, dots, small blotches, etc), so that readers can understand your terminology with graphical examples. Same thing for hand tubercles (round, oval, etc) and snout in profile (truncated, rounded, etc), etc.

54. Table 1. In the legend, please correct "Uncorfirmed" (misspelled).

55. Table 1. Add "DCL" to the legend and spell out the acronym.

56. Table 1. Do you expect the uncategorized lineage sp. 1 to correspond to A. teko sp. nov.? They seem to be morphologically uniform... same for A. minuta and A. aff. minuta sp1. I would appreciate some comments about the taxonomic status of those clades indicated with "aff.", which may guide future studies and support biological inventories in the region.

57. Table 1. Why do you present p-distances for only part of the listed clades?

58. Table 1. Some of the traits are very subjective and the terminology is a bit confusing. How do you discriminate between "granular" and "highly granular" skin texture? What is the difference between "small dots" and "tiny dots", or between them and "medium size dots"? How are "blotches" different from "medium blotches"? Perhaps images could help here - see my comment about Fig. 6, 7, and 8, above.

59. Table 1. You present SW, NW, NE and SE clades, but most of the text refers only to east and west clades. Please be consistent.

60. Table 2 and 3. Are you including data of specimens from clades identified by "aff." along with data from closely-related nominal species? For instance, do data for A. vote in this table include also data from A. aff. vote sp 1 and A. aff. vote sp 2?

61. Table 4 and 5. Please include "aff." in the column names of corresponding clades (e.g., replace "A. vote sp. 1" to "A. aff. vote sp 1").

Congratulations for this formidable initiative!


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: XENOPOSEIDON IS THE EARLIEST KNOWN REBBACHISAURID SAUROPOD DINOSAUR
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors made a re-interpretation of a fragmentary sauropod vertebra, previously erected as Xenoposeidon by the author of this manuscript as the leader author.
This taxon was subsequently considered as nomen dubium.
The english is clear, but the manuscript is wrote mainly as an opinion note. I personally think that most of it should be re-writed. I have the feeling that in some parts there is some circularity in the ideas exposed, this is explained below. For example a really important aim of the manuscript, which is defend the validity of the species, is presented in the introduction. This is, probably, one of the most important aims that the author should adress, and is not correct to mention this point in the introduction becouase gives the false impression that no detailed explanations are needed, that sounds some pedant. I personally believe that most of the diagnostic characters falls to be clear and that some of them are product of preservation. This was mentioned by other authors and a proper discussion is deserves.
I made some comments on the manuscript.
Experimental design: In this paper the element, holotype of Xenoposeidon, is re-interpreted and the validity of the taxon is reinforced. In the base of the new laminae interpretation, based on Rebbachisaurus, the authors indicates the rebbachisaurid affinities of Xenoposeidon (I have the impression that some circularity is present in that).
In my opinion the manuscipt, deserves, at least, some extra work.
The M pattern observed in the fragmentary vertebra is also present in some other sauropods (see for example Neuquensaurus), which laminae are different to those of Rebbachisaurus. I see the similarities between Xenoposeidon and Rebbachisaurus, but I also feel that the material is to fragmentary to clearly refer this taxon to this clade. At least some phylogenetic analysis could be made, but again the fragmentary nature of the specimen precludes to unambuguosly reinterpret the laminae.
Validity of the findings: As explained above I am not convinced on the results. Briefly, the weakness points are:

1-The vertebra is too fragmentary, despite the validity of the taxon is defended. Its laminae patter is not as obvious as the author statted.

2-The diagnosis is not very well explained and some characters looks like prodcut of breakage (dorsal neural arch covering the dorsal surface of the centrum, which should be posterior as the anterior one is much damaged) or the possibility of incorrect orientation of the element (the inclination of the anterior edge).

3-The phylogenetic interpretation (as a rebbachisaurid) is made in the base of the laminae interpretation made with a rebbachisaurid.... .

4-The main goal of the manuscript is based on the phylogenetic interpretation (see above) and the age of the specimen. The age informed is also some dubious as not exact position is know, and although the age proposed sounds like the most probable, is not possible to strongly confirm this.
Additional comments: No additional comments


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

Input:
Title: XENOPOSEIDON IS THE EARLIEST KNOWN REBBACHISAURID SAUROPOD DINOSAUR
Review round: 1
Reviewer: 2

Output:
Basic reporting: I have only a positive comment here: the inclusion of 3D data of vertebral specimens in this paper is very helpful and should be supported. It makes the paper more transparent, as characters can be easier checked.
Experimental design: no comment
Validity of the findings: In this manuscript, a dorsal vertebra of a sauropod dinosaur, described in 2007 by Taylor & Naish, is re-interpreted and re-described. The work is based on comparison with dorsal vertebrae of rebbachisaurid sauropods (in particular Rebbachisaurus garasbae), for showing a unique "M" shared arrangement of laminae associated with the parapophysis and the vertebral centrum. The author of the manuscript challenges here some of his earlier interpretations of lamina arrangement (and determination) and position of the parapophysis and thus revises his own work in a positive way.
Given the doubts on the validity of the described vertebra NHMUK R2095 (e.g., D’Emic 2012) and the limited anatomical information available from the fragmentary specimen, this manuscript is very helpful as it resolves the interpretation of the lamina system at the lateral vertebral centrum; helps to understand its morphology better; and gives new insights into the systematic relationships of Xenoposeidon.

The paper discusses four main issues that I want to comment on:
1. I do strongly agree with the new interpretation of the vertebral laminae as discussed here and the interpretation of the specimen to belong to a rebbachisaurid sauropod. This alone would be worth publishing and as the attached figures underline, is very obvious. I would suggest that the description of the lamina system in Rebbachisaurus garasbae could be a bit more detailed, for example, how does the lamina system change throughout the dorsal vertebral column of this taxon, or is there always an “M” shape present?

2. I disagree on the interpretation of the position of the parapophysis to be elevated above the level of the prezygapophysis. In the described specimen, both elements are not preserved (indeed, most of the neural arch is missing) and this means that the position of zygapophyses and parapophyses cannot be reconstructed. I consider it not appropriate to base the interpretation of the specimen's anatomy on an interpretative reconstruction of  in dependence on a complete rebbachisaurid vertebra. Even if the arrangement of laminae is similar in both specimens, this does not mean that the position of the parapophysis is, too. Although it cannot be excluded that the parapophysis was positioned above the level of the prezygapophysis, there is no possibility to positively demonstrate that it was the case, and this condition should simply not be used as a character. Additionally, as Fig. 4 clearly shows, the 2D lateral view seems to indicate an elevated parapophysis, but this can also be just in reference to the perspective of the drawing (by showing the laminae ventrally to the transverse process). Only an anterior or posterior view can show the pristine elevation of the parapophysis. I think that the parts of the discussion basing on the elevation of the parapophysis in the described vertebra should be omitted.

3. With respect to the missing zygapophyses and parapophyses, I suggest to revise the interpretation of the anatomical position of the specimen in the dorsal vertebral column. As the author mentions in the paper, the described vertebra is longer than a rebbachisaurid vertebra in the posterior dorsal region. The determination as a posterior dorsal vertebra is based on the placement of the parapophyses, which are not preserved; however, the elongation of the vertebral centrum (which is preserved) allows an alternative interpretation as mid-dorsal vertebra. I suggest to at least discuss/consider the alternative possibility that this vertebra is a mid-dorsal one instead of a posterior dorsal vertebra. Would this have an effect on the interpretation of the laminae?

4. I find it difficult to understand in which respect the revised diagnosis differs from the original one (both should be compared here, given that not all readers will know the paper of Taylor & Naish 2007) except to the new interpretation of the laminae. The five characters listed for the revised diagnosis of this paper are more or less undiscussed and in this form do not provide definitive evidence for the validity of the taxon Xenoposeidon per se. If the validity of the taxon is to be demonstrated here, there should be a slightly more detailed description and comparison of the listed autapomorphies to at least some other sauropods. This does not say that I doubt the validity of Xenoposeidon, but I consider it helpful to get a somewhat sharpened discussion here. Parts of the introduction, discussing the validity of the taxon with respect to the paper of D’Emic 2012, should be moved into this part of the discussion. It would be great also to have these characters outlined in one of the figures.
Additional comments: No additional comments


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

Input:
Title: XENOPOSEIDON IS THE EARLIEST KNOWN REBBACHISAURID SAUROPOD DINOSAUR
Review round: 1
Reviewer: 3

Output:
Basic reporting: The paper is well-written throughout, although there are a few instances where other references should be cited (see detailed annotations on the MS). My only real criticism of the Basic reporting is that there is little in the way of background/context. In some ways the current Introduction is welcome in that it gets straight to the point, but it feels unusual in that there is so little of the usual kind of background information, e.g. that sauropods were dominant herbivores in the Mesozoic, etc. It would be worth considering adding some kind of introduction that both sets the general scene, but that also places Xenoposeidon in some sort of context: i.e. why is it remotely important/interesting to know what Xenoposeidon is? The earliest Cretaceous is a bit of a blank in most regions for sauropods (and for most groups in general), and so it's at least important for helping us understand more about that time interval. The long rebbachisaurid ghost lineage is also another important and relevant issue.

Also, perhaps consider adding a short Conclusions section.
Experimental design: No issues here, other than by not including some kind of Background/Context (see above), the MS does not really state why this work is relevant and meaningful, or how this fills a research gap. I believe that it is all of these, but currently the MS does not do a good job of conveying that significance.
Validity of the findings: Although I agree with the main conclusion of the MS (i.e. that Xenoposeidon is likely a rebbachisaurid, and thus the earliest known member of this clade), I disagree or have reservations about a number of the other reported findings. All of these are documented in the annotated version of the MS, but I've summarised the main ones below:

(1) I'm unconvinced by all five proposed autapomorphies for Xenoposeidon:

Autapomorphy #1 - It looks like the neural arch continues to the posterior margin of the centrum in Rebbachisaurus too.

Autapomorphy #2 - The strong anterior slant of the neural arch appears to be dependent on how you've chosen to orientate the vertebra, but there doesn't appear to be any need to orientate it in this way (expanded upon in the annotated MS).

Autapomorphy #3 - How does the "broad, flat, featureless bone on the lateral face of neural arch" differ from the condition in Rebbachisaurus or Nigersaurus?

Autapomorphy #4 - The teardrop-shaped centroprezygapophyseal fossa does not appear to be all that different to the one in Rebbachisaurus.

Autapomorphy #5 - The arched laminae that form the boundary of the centroprezygapophyseal fossa (CPRF) are the medial CPRLs in Rebbachisaurus. By definition, the CPRF has to be bounded by centroprezygapophyseal laminae (see Wilson et al. 2011). If we follow Wilson & Allain (2015) for Rebbachisaurus, then their medial CPRLs form the margins of the CPRF, meeting at the CPRF apex and contacting the prezygapophyses (required for them to be interpreted as CPRLs in the first place). In most other sauropods, they couldn't be called CPRLs in this instance, because the prezygapophyses would be interrupted by a TPRL, but the zygapophyses meet at their midline in rebbachisaurids. As such, why can't these arched laminae in Xenoposeidon be medial CPRLs, meeting the (unpreserved) prezygapophyses at their midline? If you maintained the orientation of the unpreserved portion of what you are interpreting as the lateral CPRL such that it follows that of the preserved portion (rather than deflecting it dorsally in your reconstruction), it looks like all of these laminae end up at roughly the same height on the vertebra. A remaining issue though would be that this would mean that you have three CPRLs but, if the lateral CPRL is correctly identified, then the medial CPRL could be interpreted as being excavated/bifurcated, resulting in a medial centroprezygapophyseal lamina fossa (mCPRL-F), following the nomenclature of Wilson et al. (2011). This bifid/excavated mCPRL might then be considered an autapomorphy...

(2) A couple of remaining putative differences between Xenoposeidon and other rebbachisaurids can probably be readily resolved. The elongate centrum doesn't appear to be much different from a posterior dorsal vertebra of Nigersaurus (http://digimorph.org/specimens/Nigersaurus_taqueti/dorsal_vertebra/). I also don't think that Xenoposeidon necessarily lacks a strongly arched ventral margin, once you take into account that the ventral margin of the posterior cotyle is incomplete and the anterior end of the centrum is missing. There's every possibility that it might have looked like a slightly elongate version of the Rebbachisaurus vertebra illustrated in Fig. 4D of Wilson and Allain (2015).

(3) The lateral pneumatic foramen of Xenoposeidon is set within a distinct fossa, similar to that of many somphospondylans, and is very different to the condition in Rebbachisaurus - I don't think that they can or should be described as comparable, and would be better kept as a notable difference (possibly as a local autapomorphy of Xenoposeidon).

(4) It's stated that the internal tissue structure of Xenoposeidon differs from the camellate condition of most rebbachisaurids (lines 318-320); however, this is incorrect: there is no documented evidence for camellae in any rebbachisaurid dorsal vertebra: they all seem to have a camerate internal tissue structure.
Additional comments: This is a welcome reinterpretation of Xenoposeidon, and I am in agreement that a rebbachisaurid identification appears likely. In addition to the above comments, I have made a number of comments/suggestions on an annotated PDF of the MS, as well as spotting a few typos.

I look forward to seeing the final version of this paper.

Best wishes,

Phil Mannion


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: XENOPOSEIDON IS THE EARLIEST KNOWN REBBACHISAURID SAUROPOD DINOSAUR
Review round: 2
Reviewer: 1

Output:
Basic reporting: I'm much happier with this aspect of the revised MS, and have no further comments regarding Basic reporting.
Experimental design: I'm also happy with this
Validity of the findings: I'm still unconvinced by the proposed anterior slant of the vertebra and don't think that there's any evidence for orientating it in this way. I went into the NHM to re-look at this. No aspect of the posterior articular surface of the centrum leads me to orient the vertebra in the same way of shown in your figures. In addition, as currently orientated, the floor of the neural canal is strongly tilted - it seems more conservative to assume that this is horizontal. Similarly, by following that orientation, this would then make the long-axis of the lateral pneumatic opening closer to horizontal. By orientating the vertebra this way, the anterior margin is sub-vertical, with a very gentle anterior deflection (i.e. fairly normal for a sauropod), and the M-lamina is much closer in orientation to that of Rebbachisaurus.

I also remain unconvinced by the interpretation of what's going on with the laminae that frame the CPRF, as well as the reasoning that these can't be bifid medial CPRLs based on the inferred position of the prezygapophyses. Do the prezygapophyses really have to be placed so high? If you continue the chords for the mCPRL and lCPRL in the same orientation as the preserved portions of the laminae, they meet much lower down than currently inferred in Fig. 5. Also, rebbachisaurid zygapophyses are strongly tilted - see your reproduction of a Rebbachisaurus dorsal in anterior view - so where the two prezygapophyses meet (it's unlikely there would have been a TPRL) is much lower than where the lCPRL would contact the prezygapophysis. Also, as previously mentioned, if the CPRF isn't bound by CPRLs, then it technically isn't a CPRF.

My other comments are very minor and are included in an attached annotated version of the MS.
Additional comments: Aside from those contested features, I'm essentially happy with the revised MS, and remain in agreement that Xenoposeidon is probably a rebbachisaurid.

Best wishes,

Phil Mannion


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: XENOPOSEIDON IS THE EARLIEST KNOWN REBBACHISAURID SAUROPOD DINOSAUR
Review round: 2
Reviewer: 2

Output:
Basic reporting: I am not a native English speaker; however, the English appear to be appropriate for a scientific manuscript. The manuscript includes the majority of the articles related to the group; therefore, the literature is well referenced (with few exceptions, see annotated pdf).  Likewise, the rebbachisaurid taxa are all included. The figures described correctly the aim of the manuscript, particularly after the inclusion of the figures suggested by reviewers. In agreement with the author, the 3D model is an important tool, which helps to better understand morphology of the dorsal vertebra (see annotated pdf).
Experimental design: The main aim of the manuscript is to support the inclusion of R2095 within Rebbachisauridae. It is well-supported (throughout the text and figures), however, because the material is fragmentary in many aspects is “controversial” (see annotated pdf).
Validity of the findings: The manuscript is well stated and it is directly linked to the main question about the assignation of the material as a rebbachisaurid sauropod. Additionally, the different points of view regarding this material is mentioned in the manuscript (for example those of Upchurch et al., 2011; D’Emick 2012 and Mannion et al., 2013) leaving this controversy open to the reader (an interesting arguable topic). I think that the author may have to go deeper in some aspects. He supported the inclusion of BMNH R2095 within Rebbachisauridae and mentioned in the title (“the earliest known rebbachisaurid”) and in the introduction (earliest Cretaceous sauropods are important for our understanding of the evolution). Nevertheless, despite some phrases throughout the text, there are not a detailed or more clear explanation about the importance that its assignation has, considering that BMNH R2095 is now the oldest representative of Rebbachisauridae (see pdf). I think that could be interesting to analyze this topic deeply, which may enrich the manuscript and the impact on the group (i.e., within Diplodocoidea in general and Rebbachisauridae in particular). Comments within the pdf (particularly, in Discussion section) may help on this topic.
Additional comments: The fossil record of Rebbachisauridae is scarce compared to other groups of sauropods (inclusive within Diplodocoidea). Therefore, every new record of this clade adds important information increasing our knowledge on the group. The fragmentary nature of BMNH R2095	difficult its assignation (mentioned in the ms in 2007/2011/2012/2013 papers). However, the manuscript added important information to this topic, and leads to continue the discussion about it. The putative assignation of BMNH R2095 within Rebbachisauridae is important because it is (now) the oldest representative of the group. Therefore, it has a direct relation with the evolutionary dynamic of Rebbachisauridae. In sum, the manuscript, after the inclusion of several points raised by the reviewers (particularly the new figure) improved substantially. However, please, see annotations on the pdf.


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

Input:
Title: XENOPOSEIDON IS THE EARLIEST KNOWN REBBACHISAURID SAUROPOD DINOSAUR
Review round: 3
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I'm happy to agree to disagree on what are relatively minor aspects of anatomy that do not impact upon the proposed placement of Xenoposeidon as a rebbachisaurid.

Best wishes,

Phil


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

Input:
Title: EFFECTS OF SIZE AND MICROCLIMATE ON WHOLE-TREE WATER USE AND HYDRAULIC REGULATION IN SCHIMA SUPERBA TREES
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The Schima superba plantation has been widely established in South China, mainly for the purpose of forest restoration. Using the TDP method, the authors aim to investigate seasonal water use patterns and hydraulic characteristics of four diameter size groups of a Schima superba plantation during 2010-2011. A novelty of this study is to improve our understanding for the water consumptions of this important plantation. I believe this paper will be of general interests to the readers of the journal, but can be improved significantly after revision. It would also be better to be edited by a native speaker. Below are comments:
1. Abstract. Line22 and 23, the authors mention ‘rank 3’, but without any information about this term. Add interpretations in Line 10 when the four ranks are first mentioned .
2. Introduction. In the first paragraph, I do not understand why the authors introduce the background of exotic vs native species plantations, because it is not related to the objectives of this study.
3. Line 81, 21 samples are selected for the study. But in Table 1, the total number is 15. I have a little confusion about the Table 1. It is too simple for the reader to obtain more specific information about the materials.
4. Line 84, ‘…..which avoided age effects…’ ? Should there be ‘season’ ?
5. In this study, all the sample trees are classified into four ranks according to their DBH. However, in Figure 1-5 and Figure 8, those tree individuals are classified into four groups as dominant, codominant, middle and depressed. Therefore, it is hard for readers to capture some key results.
6. Discussion. This section should be improved substantially. For example, in the first paragraph, they explain what is sap flux density (this should be put in introduction or method section), list a number of studies that compare inter- and intra-specific difference in Js, but talk less about their own results. Generally, the authors should first focus on the most important findings, followed by a mechanical explanation.


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

Input:
Title: EFFECTS OF SIZE AND MICROCLIMATE ON WHOLE-TREE WATER USE AND HYDRAULIC REGULATION IN SCHIMA SUPERBA TREES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The topic of this paper is of great interest. The measurements seem to be well planed and carried out effectively resulting in a rich and valuable data set. With these data on plant sap flow and microclimate data, potentially interesting patterns can be identified that can be used to answer important scientific questions. A potentially great paper can be resulted from this work. However, I feel the paper need to be substantially improved before publication in the following aspects:
1) More detailed information need to be given in Materials and Methods regarding the number of trees used for each of the measurements. Need to tell how many trees in each of the rank are used for sap flow, water potentials and Kl. In case only a subset of trees were used for a specific measurement, explanations need to be given why not all the trees were measured.

2) The results need to be much better organized. The Table and Figures especially needs more works to be publishable. For example, in the caption/legends more detailed information need to be added to make it more easily understandable to readers. See more details below.

Introduction
Since the study is only about one native species, the mention of studies on exotic trees is not very relevant and confusing. Suggest not saying anything about exotic vs. native species in the Introduction.

The reasons given in line57-65 were not enough to justify the present study. Clear scientific questions or hypotheses need to be stated. For example, if you think the study between different DBH categories is important. You may expect them to be different in sap flow, water potential, KL, etc. You can then develop your hypotheses about the comparisons between DBH ranks.

Materials and Methods

Sap Flow measurements:
It is not totally clear how many trees were used for sap flow measurements. In line 111, it is said “we classified 15 trees into 4 groups” but in line 113-114 it is said 21 trees (instead of 15) were measured? What are the DBH ranges of trees No. 16-21? Why not also classify tree No. 16-21 into the four DBH categories rather than separate these trees from Tree No. 1-15?

Leaf water potential and stomatal conductance measurements (Line 134-144):
According to the description, trees No. 16-21 were measured and these trees were classified into the four DBH classes. How many trees in each of the four classes? If the purpose were to compare between different DBH classes, there would not be enough replicates (trees) for each of the classes.

Results
Overall need to me more concise and better organized to show the overall patterns. It would be better to show some of the major comparisons between Ranks in a table. Some of the important linear regressions are better shown graphically.

The quality of table and figures especially need to be improved:

Tables and figures need to be self-explanatory, e.g. all abbreviations need to be defined.

More detailed information need to be added to Table 1 to allow the readers understand your results, e.g. need to tell the tree identities (No. 1-21) within each of the four ranks. The DBH of the 21 sampled trees were measured and need to be reported in Table 1. Suggest to arrange and number the sample trees according to their DBH and tell in the table what kind of measurements were done for each of the tree.

All the figure legends are too short (only one short sentence) and do not provide sufficient information needed to understand your figures.

Figure 1&2: What do you mean by dominant, codominant, middle and depressed trees? The terms need to be defined in Materials and Methods. Do they correspond to tree Rank 1, 2, 3 and 4, respectively?

Fig. 4: According to M&M, 6 trees were used for water potential measurements. Are there 2 trees for each of the three classes? Two trees would not allow calculating standard errors. What are the error bars for in Fig. 4a?

Fig. 5. With these many data points, it is difficult to see the general patterns. Need some sort of simplification/summary to clearly show the pattern.

Fig. 6,7,8: Why only the specific Rank is shown but not other ranks?

Discussion

If I understand correctly, one of the major aims of the study is to compare plant water use of different DBH ranks. Thus, the discussions need to be more centered on the comparisons between the tree ranks.

Line 334-340: the discussion about Kl need to be expanded a bit. There is actually no real “discussion” about Kl but rather repeating some of the results.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The topic of this paper is of great interest. The measurements seem to be well planed and carried out effectively resulting in a rich and valuable data set. With these data on plant sap flow and microclimate data, potentially interesting patterns can be identified that can be used to answer important scientific questions. A potentially great paper can be resulted from this work. However, I feel the paper need to be substantially improved before publication in the following aspects:
1) More detailed information need to be given in Materials and Methods regarding the number of trees used for each of the measurements. Need to tell how many trees in each of the rank are used for sap flow, water potentials and Kl. In case only a subset of trees were used for a specific measurement, explanations need to be given why not all the trees were measured.

2) The results need to be much better organized. The Table and Figures especially needs more works to be publishable. For example, in the caption/legends more detailed information need to be added to make it more easily understandable to readers. See more details below.

Introduction
Since the study is only about one native species, the mention of studies on exotic trees is not very relevant and confusing. Suggest not saying anything about exotic vs. native species in the Introduction.

The reasons given in line57-65 were not enough to justify the present study. Clear scientific questions or hypotheses need to be stated. For example, if you think the study between different DBH categories is important. You may expect them to be different in sap flow, water potential, KL, etc. You can then develop your hypotheses about the comparisons between DBH ranks.

Materials and Methods

Sap Flow measurements:
It is not totally clear how many trees were used for sap flow measurements. In line 111, it is said “we classified 15 trees into 4 groups” but in line 113-114 it is said 21 trees (instead of 15) were measured? What are the DBH ranges of trees No. 16-21? Why not also classify tree No. 16-21 into the four DBH categories rather than separate these trees from Tree No. 1-15?

Leaf water potential and stomatal conductance measurements (Line 134-144):
According to the description, trees No. 16-21 were measured and these trees were classified into the four DBH classes. How many trees in each of the four classes? If the purpose were to compare between different DBH classes, there would not be enough replicates (trees) for each of the classes.

Results
Overall need to me more concise and better organized to show the overall patterns. It would be better to show some of the major comparisons between Ranks in a table. Some of the important linear regressions are better shown graphically.

The quality of table and figures especially need to be improved:

Tables and figures need to be self-explanatory, e.g. all abbreviations need to be defined.

More detailed information need to be added to Table 1 to allow the readers understand your results, e.g. need to tell the tree identities (No. 1-21) within each of the four ranks. The DBH of the 21 sampled trees were measured and need to be reported in Table 1. Suggest to arrange and number the sample trees according to their DBH and tell in the table what kind of measurements were done for each of the tree.

All the figure legends are too short (only one short sentence) and do not provide sufficient information needed to understand your figures.

Figure 1&2: What do you mean by dominant, codominant, middle and depressed trees? The terms need to be defined in Materials and Methods. Do they correspond to tree Rank 1, 2, 3 and 4, respectively?

Fig. 4: According to M&M, 6 trees were used for water potential measurements. Are there 2 trees for each of the three classes? Two trees would not allow calculating standard errors. What are the error bars for in Fig. 4a?

Fig. 5. With these many data points, it is difficult to see the general patterns. Need some sort of simplification/summary to clearly show the pattern.

Fig. 6,7,8: Why only the specific Rank is shown but not other ranks?

Discussion

If I understand correctly, one of the major aims of the study is to compare plant water use of different DBH ranks. Thus, the discussions need to be more centered on the comparisons between the tree ranks.

Line 334-340: the discussion about Kl need to be expanded a bit. There is actually no real “discussion” about Kl but rather repeating some of the results.


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

Input:
Title: EFFECTS OF SIZE AND MICROCLIMATE ON WHOLE-TREE WATER USE AND HYDRAULIC REGULATION IN SCHIMA SUPERBA TREES
Review round: 1
Reviewer: 3

Output:
Basic reporting: see detailed comments in pdf file.
Experimental design: see detailed comments in word file.
Validity of the findings: see detailed comments in word file.
Additional comments: see detailed comments in word file.


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

Input:
Title: EFFECTS OF SIZE AND MICROCLIMATE ON WHOLE-TREE WATER USE AND HYDRAULIC REGULATION IN SCHIMA SUPERBA TREES
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The manuscript has been improved by the authors and deserves to be published in PeerJ. However, there are still several points that should be considered before publication.
1) This manuscript have many language problems, it would be better if edited by a native speaker who is an expert in water relations.
2) The ABSTRACT should be rewritten, I cannot find any key results of this study here, and the final conclusion makes no sense.
3) The DISCUSSION section, although improved, still needs extensive revisions. The authors should focus on their key results. This paper have six figures and six tables (too many).
4) The legends of the figures are too simple. Generally, we can understand the figure without reading the main text.
In figures 1-2, what is the rank 1-4? And it is not easy to distinguish different ranks by using the four symbols.
In figure 4B, change “maximum” to “minimum” if the water potential indicates the lowest value during a day.
In figure 5, no any explanations for figure 5A, and check the unit of stomatal conductance.
In figure 6, the symbols of the four ranks are different from figure 1-2.


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

Input:
Title: EFFECTS OF SIZE AND MICROCLIMATE ON WHOLE-TREE WATER USE AND HYDRAULIC REGULATION IN SCHIMA SUPERBA TREES
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors did a good job in revising their manuscript according to the comments from the three reviewers. I have no further concerns for the publication of this paper.
Experimental design: The authors did a good job in revising their manuscript according to the comments from the three reviewers. I have no further concerns for the publication of this paper.
Validity of the findings: The authors did a good job in revising their manuscript according to the comments from the three reviewers. I have no further concerns for the publication of this paper.
Additional comments: The authors did a good job in revising their manuscript according to the comments from the three reviewers. I have no further concerns for the publication of this 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: EFFECTS OF SIZE AND MICROCLIMATE ON WHOLE-TREE WATER USE AND HYDRAULIC REGULATION IN SCHIMA SUPERBA TREES
Review round: 2
Reviewer: 3

Output:
Basic reporting: see comments in  word version
Experimental design: see comments in  word version
Validity of the findings: see comments in  word version
Additional comments: The author did lot of work on revising the manuscript which smooth the whole text substantially. However, I still have some concerns before acceptance.


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

Input:
Title: REVISITING HISTORICAL BEECH AND OAK FORESTS IN INDIANA USING A GIS METHOD TO RECOVER INFORMATION FROM BAR CHARTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well written. This article meets the basic reporting criteria. The manuscript use ArcGIS to recover information content of historical ecological data. This method should be inspired for who have historical descriptive data. Increasing the possibility of carrying out spatial analysis of historical forest data.
Experimental design: Experimental design is fine. I have only a suggestion for the author. Author had used the bar graphs from Potzger et al. (1956) as the metadata. I think author should provide the supplemental files to show how the PDF file of the bar graphs is. Even use a sample to describe the bar graphs would be useful to future readers. Based on my understanding, many readers have difficulty to access these historical data. In such way, readers would be better understand this method.
Validity of the findings: All data is robust, and analyses are sound. Conclusions and recommendations are well stated. This paper translates historical data into spatial data by GIS technology, which can better analyze the spatial distribution and temporal changes of the forest.
Additional comments: One of my comments is that the authors should provide a flowchart for the methods. A flowchart would help clarify what technique and criterion should being used at each of the step of analysis. In this way, others can better understand and duplicate this method.


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: REVISITING HISTORICAL BEECH AND OAK FORESTS IN INDIANA USING A GIS METHOD TO RECOVER INFORMATION FROM BAR CHARTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: see general comments
Experimental design: see general comments
Validity of the findings: see general comments
Additional comments: This paper contains much useful material, but it needs to have a clearer focus before it can be published. At present it is impossible to decide what the author really wants to do. Until the end of the Introduction (or in fact middle of Methods), the paper appears to be focusing on method: how to convert pictorial representations of data processed earlier into useful data similar to what the bar charts had been based on. The Results chapter then describes something different: the pre-European settlement vegetation of the region. Results concerning what the paper claims to be its aim (“my objective was to convert the bar chart ...into compositional values joined to a GIS layer of townships”) show up in the Discussion. In general, the Discussion appears to be a long list of results (mostly answering questions that were not asked by the author) rather than a discussion.
That said, there is a lot to be said for the paper as well. It contains huge amounts of material carefully described (if not much analysed). My advice would be to rethink and restructure the paper. It seems that the actual aim of the paper is to describe the past vegetation of Indiana both for itself and in relation to certain environmental factors. To this aim, turning bar charts into percentages is a mere method. In such a paper, aims should be more clearly defined and justified, and results and discussion properly separated. Alternatively, the paper could retain its methodological focus as well (I personally found this bit quite fascinating), but again aims and structures should be clear. In addition, I think the description of methods is in any case rather difficult to follow with too many things unsaid that are known to GLO specialists but certainly not to the general reader. A figure of the original charts would have been most welcome and so has some form of discussion on the potential amount of similar chart data to contextualize the potential value of this new method.
Lastly, all maps included need a scale and at least one an orientation map showing the position of the study area in north America.


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: REVISITING HISTORICAL BEECH AND OAK FORESTS IN INDIANA USING A GIS METHOD TO RECOVER INFORMATION FROM BAR CHARTS
Review round: 1
Reviewer: 3

Output:
Basic reporting: 'no comment'
Experimental design: 1. Methodology
The author should explain better, perhaps showing some framework of used source, how graphs were transformed into numerical values. Images in the contribution version available online (http://www.jstor.org/stable/pdf/41822538.pdf?seq=1#page_scan_tab_contents) are in very poor condition, and if the same source was used, degree of transformation (R2=97%) may be insufficient.

2. Questions
a) Would it be possible to cross the Vettorializati data of this research with the geological ones pertaining to soil (USGS.gov)? This could probably allow to determine further correlations between soil type and vegetation.
b) In the representation of two tree species within the same square section (e.g. a species with 25% and another with 70%) how can the author recognize/mark this difference?
Validity of the findings: 'no comment'
Additional comments: 'no comment'


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

Input:
Title: REVISITING HISTORICAL BEECH AND OAK FORESTS IN INDIANA USING A GIS METHOD TO RECOVER INFORMATION FROM BAR CHARTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: 'no comment'
Experimental design: 'no comment'
Validity of the findings: 'no comment'
Additional comments: I think this article is now very interesting for PeerJ readers.


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: THE CRANIAL ENDOCAST OF THE UPPER DEVONIAN DIPNOAN ‘CHIRODIPTERUS’ AUSTRALIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: •	I was unable to find any information in SI regarding the codings for Chirodipterus used in the current analysis. A full character list or matrix is not necessarily required but at a minimum you should include the codings for C. australis.
•	The raw scan slices are available via figshare, but it might be nice if the authors could include a simple spinning animation or similar of the segmented endocasts
•	I would suggest perhaps moving the tables to SI rather than include then in the main text
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This is a considered and professional contribution to palaeoneurology. The language is (mostly) clear and unambiguous with just a few areas marked on the manuscript requiring further clarification. The introduction and background are thorough and give good context for the article. The figures are high quality and clear, with relevant features clearly labelled and label abbreviations given in the figure captions for ease of interpretation. Some minor grammatical/spelling errors are highlighted in yellow in the attached PDF.

The research question is well defined and fills an obvious gap in our current understanding of lungfish endocasts. The investigation was rigorous and performed to a high technical standard resulting in one of the best quality studies of lungfish endocasts known thus far.

The conclusions are well supported and link clearly to the original research question. This is an important addition to the growing body of work on lungfish cranial endocasts and the early neurobiological evolution of the group.

In addition to those marked on the PDF, some further points for attention:
•	It might be nice on one or more of the figures to include lines showing the approximate boundaries between the major brain regions – or include an additional figure showing this
•	Remember to italicize taxon names in references
•	Supp Info – list Qingmenodus species epithet in tree


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: THE CRANIAL ENDOCAST OF THE UPPER DEVONIAN DIPNOAN ‘CHIRODIPTERUS’ AUSTRALIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: There are no serious problems in this area. A number of minor niggles regarding language and references are flagged up under "general comments for the authors"
Experimental design: No problems.
Validity of the findings: No problems.
Additional comments: This manuscript is a valuable contribution to our understanding of Devonian lungfishes. There's nothing fundamentally wrong with it, but having said that there are quite a lot of minor-ish problems that need to be addressed. I have flagged it for 'major revision' because I think it will need to be re-reviewed after revision.

My comments are listed by line number as given in the manuscript.

Line 46: You should explain that you are talking about brain histology here. There's lots of histological data from fossils, but almost all of it is hard-tissue histology.

Lines 47-50: The parentheses around the sentence beginning "Stensiö's inferences..." are really awkward and also unnecessary.

Lines 69-73: You say that Campbell and Barwick 2000 argued that pedunculate olfactory bulbs (and a range of other characters) are primitive for lungfishes, and then say that Clement et al. (2016) have "for the best part" validated this hypothesis, but Clement et al. actually showed that Dipnorhynchus has sessile olfactory bulbs, which, if anything, contradicts the hypothesis rather than validating it.

Lines 73-77: Careful! These are characters of the primitive lungfish Dipnorhynchus, but that does not necessarily equate to the actual characters being primitive for lungfishes.

Line 82: You introduce Rhinodipterus without a citation, making it look like it is described along with Dipterus in Challands 2015.

Lines 84-85: Are these characters also present in modern lungfishes? You imply that they are, but I'm not so sure.

Line 88: There's a space missing between "the" and "posterior".

Line 89: There's a space missing between "ampullae" and "(inflated". The entire sentence spanning lines 88-90 is awkward and clumsy.

Line 169: It is not clear whether "fig. 2" here refers to Fig 2 in Challands 2015 or in the present paper. Also, a guide figure for the measurements would be useful.

Lines 203-204: Two "using" in one sentence is definitely overkill.

Line 237: Here and in many other places we hit a problem that you need to take a strategic grip on. It is perfectly clear from your data that "Chirodipterus" australis cannot possibly belong to the same genus as Chirodipterus wildungensis. Your Figure 9 shows this very clearly: the two endocasts are not merely distinguishable but completely different from each other. It puzzles me why you haven't taken this opportunity to erect a new genus for "C." australis, but in any case you really need to indicate in the text that these two lungfishes don't belong together. How about writing "Chirodipterus" australis throughout?

Lines 242-245: You are missing something important here: Devonian lungfishes as a group are renowned for their high levels of asymmetry, as shown in the dermal bone pattern of the skull. It may be that you are picking up the same signal in the cranial cavities. I suggest you read up on this topic and include a brief discussion here.

Line 247: Strictly speaking, what you are describing is not the nasal capsule (which is a cartilage, eventually fused and co-ossified with the rest of the snout) but the space within the nasal capsule that housed the nasal sac.

Line 261: "carries" should be "continues", I think.

Lines 277-281: The anterior cerebral vein canals you describe from the two specimens are remarkably different; I feel you brush this off rather too lightly. In fact, there's a thematic issue here, where I feel you have made less of your data than you could have done. Almost everything we know about sarcopterygian endocranial cavities comes from single specimens: we have ONE Eusthenopteron, ONE Tungsenia and so forth. This means that it is impossible to determine the degree of individual variation within taxa. Given our human propensity for trying to find patterns, I suspect there's a real danger that we both underestimate the degree of within-taxon variation and over-interpret minor differences between the exemplars we have as phylogenetically important signals. It was thus a very good idea on your part to scan two skulls of "C." australis - but the way you handle the comparison between the two is rather disappointing. I would like to see a systematic overview of similarities and differences between the two specimens, where you discuss in each instance whether the difference is definitely real (as it clearly is in the case of the anterior cerebral vein) or could be due to preservation problems (which should be described: just saying "as being one of preservation", as you do on line 287, doesn't really cut it). This would really advance our understanding of this important topic.

Line 307: I can't see the bifurcation or trace the paths of the internal carotid and pseudobranchial arteries in the figures.

Line 387: Surely the canal is wider than the notochord, not narrower, as this sentence implies?

Lines 387-390: This sentence is difficult to understand.

Lines 433-434: It is difficult to see the hypophyseal recess in the figures because it is partly covered by the jugular vein canal. Why not include an inset figure of this bit of the cranial cavity without the jugular vein?

Line 437: How could a digital endocast possibly have higher resolution than a physical endocast, when it is an image (slightly degraded, like all images) OF a physical endocast??

Lines 447-450: The sentence beginning "While similarly---" is incomprehensible.

Line 461: "to" should be "from".

Lines 464-469: I'm not so sure about this character polarity. Read Ahlberg 1991 (A re-examination of sarcopterygian interrelationships, with special reference to the Porolepiformes. Zool. J.Linn. Soc. 103, 241-287.) and Clement & Ahlberg 2010 (The endocranial anatomy of the early sarcopterygian Powichthys from Spitsbergen, based on CT scanning. In Elliott, D. K., Maisey, J. G., Yu, X. Miao, D. (eds.) Morphology, Phylogeny and Paleobiogeography of Fossil Fishes, 363-377. Verlag Dr Friedrich Pfeil, München.)

Line 478: Porolepiforms and Powichthys, which are probably also members of the lungfish stem group, show a different character state. See references above.

Line 516: For goodness' sake look carefully! Chang's Youngolepis shows a beautiful bifurcation in the right olfactory tract, carefully drawn in her figs 17 and 18.

Lines 534-539: Surely the ventral deflection of the olfactory tracts is simply a reflection of the skull shape - not only short-snouted but with an unusually deep snout? It is not a case of a 'solution' to anything, just overall morphing of the whole cranial package.

Lines 540-548: The argument presented here ignores the fact that a ventral expansion of the telencephalon is present in Dipnorhynchus.

Line 554: In the juvenile Neoceratodus scanned by Clement et al the olfactory bulbs are not obviously pedunculate.

Line 575: What do you mean by the statement that the endocast of Chirodipterus wildungensis is "inaccurate"?

Line 591: "hypophyseal" should be "recess".

Lines 590-606: You should cite Clement & Ahlberg on Powichthys in this section. Also, you are missing the real point here: Youngolepis and less crownward forms have a buccohypophysial foramen; higher lungfishes do not. If you don't retain the foramen there's no point in having a hypophysial recess that reaches down towards the palate.

Lines 609-610: This sentence contradicts itself.

Line 648: whiteii should be in italics.

Lines 660-664: Why do you discuss the endolymphatic ducts here, rather than in connection with the labyrinth?

Lines 716-729: Why do you not discus the size of the utriculus here?

Lines 732-733: "Chirodipterus" australis does not resolve as the "more basal sister taxon" to C. wildungensis! Two taxa are only sister taxa if they form a clade together. "C" australis and C. wildungensis are separate plesions on the dipnoan stem. This is an important piece of terminology that must be used with precision.

Line 741: A closing parenthesis is missing after "V".

Line 763: Why "reduced"? This suggests that a small utriculus is a derived state, which seems very unlikely.

Lines 774-778: I don't believe lungfishes are using any "method" at all to reduce the length of the endocranial cavity. The shortening of the region between nerve VII and the hypophysis is a passive consequence of the loss of the intracranial joint. The downward flexion of the forebrain in "C." australis is a passive consequence of evolving a deep snout.

Lines 779-780: Why does the relatively short notochordal tunnel indicate shortening of the endocranial cavity? It is a complete non sequitur, these are separate structures.

Line 785: Is it OK to cite a paper in review?

Lines 790-792: Couldn't you have carried out a taxonomic revision of Chirodipterus in this paper? Why wait?

REFERENCES: Why are Latin names in the references all given in plain script, not italics?

Challands & Den Blaauwen 2016, Clement et al. 2016b, and Goloboff 2008 are cited in the text but not listed in the references.

Jarvik 1972, Säve-Söderbergh 1952, Stensiö 1927 and 1963, and Thomson & Campbell 1971 are all cite incorrectly. These are all Journal articles and should be cited with volume and page numbers in the usual way. All are cited correctly in Jarvik's (1980) magnum opus Basic Structure and Evolution of Vertebrates if you want to look them up.

FIGURES: You inconsistently use "NHM" and "NHMUK" in the figures and figure legends.

The cranial cavity models would look much better in colour. This would allow you to distinguish veins (which could be shown in blue) and arteries (red) from the cranial cavity and nerve canals. Why not use Romundina (Dupret et al. 2017. The internal cranial anatomy of Romundina stellina Ørvig, 1975 (Vertebrata, Placodermi, Acanthothoraci) and the origin of jawed vertebrates —Anatomical atlas of a primitive gnathostome. PLoS ONE 12(2), e0171241) as a model?


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: THE CRANIAL ENDOCAST OF THE UPPER DEVONIAN DIPNOAN ‘CHIRODIPTERUS’ AUSTRALIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: On the whole, the manuscript is fine now, and the coloured figures are a major improvement. However, there are still quite a few minor editorial problems that need to be sorted out:

Line 31-34: This is confusing! It is true that the endocast of Chirodipterus wildungensis was the first to be realised (by Säve-Söderbergh in 1952), but the description you give ("not based on a natural cast or 'steinkern'") does not fit: the broken C. wildungensis braincase does contain a steinkern. Furthermore, it is not immediately obvious how you can test the validity of this cranial cavity reconstruction by presenting the cranial cavity of 'Chirodipterus' australis. Why should that be informative about C. wildungensis, especially when you have already put scare quotes around the generic name of 'C' australis to hint that it isn't a true Chirodipterus? The answer is of course that this entire text segment actually refers to Miles's 1977 description of the cranial cavity of 'C' australis! Then the decription makes sense, because the acid-prepared 'C.' australis specimens do not contain steinkerns, and it also makes sense that you can test Miles's reconstruction by presenting a CT-based reconstruction of the same taxon. In other words, by 'correcting' australis to wildungensis in line 32 without changing anything else you have short-cirquited the entire argumentation. Please sort this out.

Line 36-37: You don't describe a description.

Line 48: A monophyletic clade is like a round circle: there's no other kind.

Line 49: The earliest known lungfish, Diabolepis speratus, comes from the Xitun Formation of Yunnan, China, which is late Lochkovian and thus about 410-415 million years old.

Line 96: There should be an "as" before "opposed".

Line 147: There's no such thing as the "crown of Devonian lungfish". The term "crown" has a very specific meaning in phylogenetics: it is a monophyletic group defined by the existence of living members. The lungfish crown group is the clade containing Neoceratodus, Protopterus and Lepidosiren and their last common ancestor.

Line 161-162: On line 154 you have deleted a claim that C. wildungensis and Rhinodipterus kimberleyensis (NOT "kimberlyensis"! This needs to be corrected throughout) have similar cranial cavities, but here the claim persists. Make up your minds!

Line 263: "has been reached" should be "has reached".

Line 703: The hyophyseal what? You can't use "hypophyseal" as a stand-alone noun.

Line 893: "not bifurcation is seen" should be "bifurcation is not seen".

Line 927: "notochords" should be "notochord's"

Figure legends: Figures 1-8 consistently use Chirodipterus australis, not 'Chirodipterus' australis. Figure 9 correctly uses 'C.' australis, but in Figure 10 we have 'Chirodipterus australis'. Sort this out!


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: FOSSIL EGGSHELL CUTICLE ELUCIDATES DINOSAUR NESTING ECOLOGY
Review round: 1
Reviewer: 1

Output:
Basic reporting: Although authors intend to highlight a possible boundary between the sediment and an enigmatic layer in fig.3A, significant peaks of P in fig. 3D, E, F and fig.4E, the white dashed line and yellow bars totally cover the elements they want to show. I suggest they use arrows instead.
Experimental design: No comment
Validity of the findings: Authors argued that "the P concentration increases from the mammillary layer to the prismatic layer but decreases from the prismatic layer to the external layer" in line 262-263, but said "the P concentration is homogeneous throughout the mammillary and prismatic layers, but decreases in the external layer"in the note of fig.4E.
Additional comments: This article is really interesting for authors have found a chemical method to detect the existence of cuticle layer in fossil eggs. I am looking forward to seeing more chemical methods which can solve the issues in dinosaur nesting ecology.


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: FOSSIL EGGSHELL CUTICLE ELUCIDATES DINOSAUR NESTING ECOLOGY
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The manuscript entitled “Fossil eggshell cuticle elucidates dinosaur nesting ecology” by Yang et al. presents chemical analyses suggesting the preservation of eggshell cuticle in non-avian dinosaur eggs from China and North America. I find that this research is deserving of publication and requires only minor revisions before final acceptance by the journal.

While I find the experimental design to be appropriate, I would suggest the inclusion of a negative control. Chemical analysis of a modern reptilian eggshell will provide an appropriate comparison for fossil specimens and will support the conclusions found in the study. Specific questions that I have include, is a phosphorus peak present on modern eggshells that do not contain a cuticle layer and if so, what does this imply for fossil specimens?

I also believe that the main conclusions of this research are appropriate. However, I do not agree with the conclusion that the “tube-like” structure found at the inner eggshell surface of one of the fossil specimens is a capillary vessel associated with the chorioallantoic membrane. Similar structures have been mentioned previously in the literature and tentatively identified as fibers of the outer eggshell layer but never as a capillary vessel. Additionally, Figure 4 does not demonstrate that this structure is hollow and therefore, not “tube-like”. This is in contrast to preserved capillary structures found in non-avian dinosaurs by Schweitzer’s lab, in which vessels are preserved in three-dimensions and are hollow. I would suggest listing all possible structures that this item could be identified as or provide more evidence as to why it is or isn’t a capillary vessel.

Finally, while the manuscript is generally well written, I have made some minor suggestions that should improve the grammar and legibility of the paper. See attached pdf for suggested edits.


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: FOSSIL EGGSHELL CUTICLE ELUCIDATES DINOSAUR NESTING ECOLOGY
Review round: 1
Reviewer: 3

Output:
Basic reporting: See general comments
Experimental design: no comments
Validity of the findings: See general comments
Additional comments: Comments on manuscript #19998
Yang et al.: Fossil eggshell cuticle elucidates dinosaur nesting ecology

In this study, the authors used for the first time a combination of microscopic and chemical techniques (SEM, EPMA, Raman Spectroscopy) to test for the presence of a cuticle layer in the eggshells of 4 non-avian dinosaurs eggs.
This is a very interesting study and the manuscript is well written. They present several evidences for the preservation of a cuticle layer in these non-avian dinosaur eggs.
However, as mentioned in the comments below, some of their statements are vague or inexact. Their discussion regarding the dinosaur nesting ecology should be further developed. The authors should nuance some of their interpretations on the nesting ecology of non-avian dinosaurs.

In summary, there are some points in the introduction and the discussion that should be clarified/ developed before acceptance of the manuscript.

Comments

Introduction, L 56: “In addition to lipids, the avian cuticle contains proteins, polysaccharides, calcium carbonate (vaterite), calcium phosphates (hydroxyapatite, HAp)…(…)…. Among these components, the vaterite and HAp in avian cuticle are stored in the form of nanospheres”.
To my understanding, avian cuticle always contains lipids, proteins, and polysaccharids. However, the nano-spheres of vaterite and hydroxyapatite are not always present (e.g., D’Alba et al., 2016). You should thus be more precise in your statement here.

Introduction, L 64: “Basically, the cuticle is divided into two distinct layers, including an amorphous HAp inner layer and a proteinaceous outer layer (Simons, 1971; Dennis et al., 1996; Fraser, Bain & Solomon, 1999)”. Is that always the case? Some bird cuticles do not comprise Hap nano-spheres (e.g., D’Alba et al., 2016).

Introduction, L 83: “Conversely, avian eggshells have HAp granules along the inner periphery on calcareous eggshells, which are absent in reptilian eggshells”. Again, you should be more precise with your statements. The structure and chemical compositions of cuticles greatly vary between bird species. Only some avian species present Hap granules in their cuticle. Some species present vaterite granules instead. Some species do not show these mineral nano-spheres at all (e.g., D’Alba et al., 2016).

Introduction, L86: “to map the P and calcium distribution”. Precise at least once that “P” refers to phosphorus.

Introduction, L86: “Kusada et al. (2011) applied electron microscopy to map the P and calcium distribution in several extant avian eggshells and discovered that P is confined to the cuticle layer. Hence, P is a distinct marker for identifying the cuticle layer in case of P depletion in sediment.” You should precise that the phosphorus concentration in the cuticle varies greatly between bird species and that phosphorus can potentially be absent (cf. Pelican specimen in the study of Kusada et al., 2011).

Introduction, L89: “Although it is still not clear how P functions during the eggshell formation, a study suggested that P terminates eggshell growth since it competes with calcium during the eggshell crystallization”. You could maybe be more precise and say something like “the inclusion of P stops the eggshell growth”…

Introduction, L 117: “Wiemann et al. 2017”. For consistency, there is a comma missing after “et al.” Please check and modify, if necessary, all other citations.

Introduction, L 122: “Among all dinosaurs, the nesting type of titanosaur, troodontid, and oviraptorid dinosaurs were comparatively well documented”. Provide some citations here.

Introduction, “Dinosaur nesting ecology”: In this section I would expect to learn more about the difference in cuticle structure between the megapodes and other birds and see if there is a direct relationship between the cuticle structure or the presence/absence of cuticle and the type of nest (open vs. buried) and the environment (dry vs. humid). This is not detailed enough. You should further present the studies of d’Alba et al. (2016, 2017) that have shown that the presence of vaterite or hydroxyapatite nano-spheres in the cuticle of some bird species is likely related to the environment (warm and/or humid) and the nest type (on the ground or mount).

Introduction, L 134: “has been remained uncertain". This is not correct English. You could rather say “has remained uncertain”.

Introduction, L144: “The goal of this study is to present further evidence of the cuticle preservation on dinosaur eggshells by means of the elemental analysis and Raman microscopy”. You should also mention the use of SEM imaging.

Introduction, L148: “Besides, nesting on the ground or in mounds increase the risk of microbial invasions, a cuticle layer should hence be prevalent on eggshells of semi-open nesting theropods”. Provide citations here.

Material and Methods, L 157: “We sampled three oviraptorid eggshells that were collected from three localities in China (Henan Province, Jiangxi Province, and Guangdong Province)”. You should precise here that the three localities are all part of the Nanxiong Group.

Material and Methods, L 158: “were housed at the NMNS and STIPB". To which museums do these abbreviations correspond? Give the full museums’ names or refer to the supplementary information file.

Discussion, L 267: “While previous studies have reported possible preservation of cuticle and membrane testacea”. The membrane testacea studies were not mentioned in the introduction. Provide a brief description of this structure.

Discussion, L270: “In this study, elemental analysis suggested the preservation of the inner hydroxyapatitic cuticle layer based on the high concentration of P at the boundary between eggshell and sediment.” You should also discuss the “negative” results that you obtained. You mentioned in the results section that “Of in total 30 line-mappings on the three Macroolithus yaotunensis eggshell, only two of them, which were from the Jiangxi and Guangdong specimens, show a significant peak for rich phosphorus on the boundary between the eggshell and surrounding sediment”. How do you explain that only 2 out of 30 line-mappings done on the Macroolithus yaotunensis specimens show a significant peak for phosphorus at the boundary between the eggshell and the sediment? You should discuss that.

Discussion, L281: “(Maiber et al., 2015)”. This reference is listed as Maiber et al., 2016 in the references list.

Discussion, L283: “However, no features of chorioallantoic membrane was observed. The preservation of the vessel in the chorioallantoic membrane is hence pending for more supporting evidence”. Specify what would be features of the chorioallantoic membrane. Also, how could you test for the presence of vessels of the chorioallantoic membrane?

Discussion, L288: “The elemental analyses show that P concentration increases from the mammillary layer to the prismatic layer of both Macroolithus yaotunensis and Triprismatoolithus stephensi eggshells (Figs. 3D-F & 4E)”. This statement is not observable on Fig. 3D-F, because the mammillary layer is not represented on these spectra. This is not clear either on Fig. 4E. You should maybe refer to the raw data.

Discussion, L296: “Moreover, their study also revealed that the P concentration increases more sharply in the eggshell of younger birds than in older birds.” Increase in P concentration between the mammillary layer and the prismatic layer?? Precise.

Discussion, L302: “Furthermore, the difference in P distribution between young and older birds can probably help paleontologists decipher if an oviraptorid clutch was laid by a single female or several females”. Why? Because females would be expected to have different ages? You should elaborate on that.

Discussion, L312: “Three hypotheses can be formulated to explain the different spectral patterns from 960 cm-1 to 980 cm-1 in extant cuticle vs. the fossil eggshells”. Where do you get these values from? Explain and cite Supplementary Information if needed.

Discussion, L345: “Thomas et al. (2016)” is listed as Thomas et al. (2015) in the references list.

Discussion, L351: You should develop much more the discussion on the nesting ecology of the sampled dinosaurs. I would suggest, for example, to explain in a few sentences, how eggshell porosity and eggshell color relate to the nest type.

Discussion, L355: “However, an intermediate mode — semi-open nests in oviraptorid dinosaurs was proposed based on detection of pigments and porosity evaluation (Yang et al., 2015; Wiemann et al., 2017).” Develop a bit on that. Why does egg pigmentation suggests an open nest in oviraptorid dinosaurs?

Discussion, L360: “Our detection of a cuticle in these eggs also supports this nesting ecology since the cuticle layer hinders microbial invasions (D'Alba et al., 2016)”. Develop on that. D’Alba et al., 2016, 2017 papers have shown that this is more specifically the mineral nano-spheres present in the cuticle of some bird species that help reduce microbial invasion in humid/warm environments. The cuticle itself is of course an important component of the antimicrobial defense, but its presence is not necessarily indicative of a humid/warm environment. A cuticle can be present in bird species nesting in very different environments.

Discussion, L362: “However, it was suggested that Mongolian oviraptorid clutches were discovered in the sand dune deposits (eolian) such as Baruungoyot Formation or Djadokhta Formation (Norell et al., 1995). Given the arid sand deposits, the cuticle layer was hence unlikely present on Mongolia oviraptorid eggshells, superficially contradicting to the inferences of this study.” Not necessarily. It has been shown that some bird species living in very arid environments present a relatively thick cuticle. This is for example the case of the Adelie penguin living in the very arid Antarctic environment. These birds present a very thick cuticle that helps reducing the rate of water loss of the egg (Thompson & Goldie, 1990).

Discussion, L363: Norell et al., 1995 is missing in the references list.

Conclusions, L376: “Our study suggests preservation of the inner cuticle layer in eggs of the oviraptorid Macroolithus yaotunensis”. You should rather say “in Macroolithus yaotunensis eggs” or “in eggs assigned to the oviraptorid Heyuannia huangi”.

Conclusion, L378: “The potential co-evolution of a cuticle layer and semi-open nesting in humid environments may have allowed theropod dinosaurs to nest in fluvial environments, as does the cuticle layer of extant birds nesting in humid environment”. Again, the presence of a cuticle is not necessarily indicative of a humid environment in modern birds (see D’Alba et al., 2016, 2017).

Figure caption 1F: “Two significant peaks at 967 cm-1 and 1087 cm-1 are indicated by yellow bars, representing HAp and calcite, respectively”. The yellow bars are actually not visible on the spectrum.

Figure caption 2A: “Raman spectra derived from chicken, fossil eggshells, and surrounding sediments. The peaks around 972-986 cm-1 and 1063-1097 cm-1 are marked by yellow bars, indicating the calcite and phosphate bonds”. You could actually indicate directly on the spectrum that the first peak represents the phosphate bounds and that the second peak represents the calcite bounds.

Figure caption 3: “Microscopic images of Heyuannia huangi eggshells”. To avoid confusion, and be consistent with the rest of the figures/text, you should rather say “Microscopic images of Macroolithus yaotunensis eggshells”.

Figure 3A: “EPMA Line-Scan (B)” is indicated on the image. Shouldn’t it be “EPMA Line-Scan (D)”?

Figure 4A: you should orientate the cross-section. Which side corresponds to the surface of the eggshell (with the cuticle layer)?

Table 1: “Oospecies” is misspelled.

Literature cited:
D'Alba, L., Maia, R., Hauber, M. E., & Shawkey, M. D. 2016. The evolution of eggshell cuticle in relation to nesting ecology. Proc. R. Soc. B, 283(1836), 20160687.
D’Alba, L., Torres, R., Waterhouse, G. I., Eliason, C., Hauber, M. E., & Shawkey, M. D. 2017. What Does the Eggshell Cuticle Do? A Functional Comparison of Avian Eggshell Cuticles. Physiological and Biochemical Zoology, 90(5), 588-599.
Thompson MB, Goldie KN. 1990 Conductance and structure of eggs of Adelie penguins Pygoscelis adeliae and its implications for incubation. Condor 92, 304–312.