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: OSTEOLOGY OF BATRACHUPERUS LONDONGENSIS (URODELA, HYNOBIIDAE): STUDY OF BONY ANATOMY OF A FACULTATIVELY NEOTENIC SALAMANDER FROM MOUNT EMEI, SICHUAN PROVINCE, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The text is fairly clear and generally well-written. On the annotated pdf file (attached to this report), I have suggested several minor stylistic improvements, clarifications, and grammatical or typographic corrections.

The description is competent. On this front, I only regret that the authors did not provide more illustrations, especially that on-line journals like PeerJ have less stringent space limitations than their paper-based forebears. In this respect, I would very much like to see an occipital view of the skull, and if possible, a lateral view with the quadrate and squamosal in place. The ypsiloid cartilage, the zeugopod elements (radius, ulna, tibia, fibula) should be illustrated too.

I find the discussion of the paper weaker, and will concentrate the review on this aspect.
The authors do not provide a thorough overview of the evolutionary implications of the anatomical data that they provide. For instance, the seldom-reported ligament connecting the stapes to the quadrate is intriguing. Do taxa that have lost the tympanum (several squamates, some frogs) have this? If not, it would constitute some support for the lepospondyl hypothesis of lissamphibian origins (Laurin, 1998; Marjanovic & Laurin, 2013), because the temnospondyl hypothesis suggests that some distant urodele ancestors had a tympanum (Lombard & Bolt, 1979).
Similarly, the claim that the authors make that the absence of the septomaxilla is not paedomorphic is rather weak, to the extent that this bone is one of the last to ossify, and this appears to have been ancestrally present in urodeles (Germain & Laurin, 2009). Not all paedomorphic characters need to be present in all taxa; indeed, theirs lacks external gills…
The authors have some evidence about carpus and tarsus development, which bears on the pre- or post-axial dominance being ancestral to urodeles (Fröbisch & Shubin, 2011), but they do not discuss this issue; they should. Also, they apparently present only part of the evidence that they have, judging from line 1101, in the discussion. This is too bad; they should present it all and discuss this point more thoroughly.
In the introduction, the authors discuss the fossil record and molecular dates for various cryptobranchoid taxa, but they confuse two (divergence hynobiids/cryptobranchids, and evolutionary radiation of crown-hynobiids), so that the discrepancy between various estimates is even greater than they suggest. This needs to be clarified. Also, I noticed some discrepancies with the latest paleontological timetree for urodeles (Marjanovic & Laurin, 2014); it would be good to know why. Perhaps some more recent research refuted some of the taxonomic positions or stratigraphic age assignments suggested by Marjanovic & Laurin (2014)? The authors, who know these taxa well, could take this opportunity to provide an update.
The nomenclatural review (lines 235-249) leaves some issues dangling because it focuses on homonymy, but it looks like there are also synonymy issues, which are currently not discussed, but should be.
In the discussion, the presence of a contact between radius and centrale is mentioned in some temnospondyls, but the authors are apparently unaware that this also occurs in at least some lepospondyls, such as Pantylus (Carroll, 1968: fig. 2; Carroll & Gaskill, 1978: fig. 125). There is already an extraordinary bias towards the temnospondyl hypothesis in the literature; no need to enhance this by reporting only part of the evidence.

References
Carroll, R. L. (1968). The postcranial skeleton of the Permian microsaur Pantylus. Canadian Journal of Zoology 46, 1175-1192.
Carroll, R. L., and Gaskill, P. (1978) The order Microsauria. Philadelphia: American Philosophical Society. Fröbisch, N. B., and Shubin, N. H. (2011). Salamander limb development: integrating genes, morphology, and fossils. Developmental dynamics 240, 1087–1099.
Germain, D., and Laurin, M. (2009). Evolution of ossification sequences in salamanders and urodele origins assessed through event-pairing and new methods. Evolution & Development 11, 170–190.
Laurin, M. (1998). The importance of global parsimony and historical bias in understanding tetrapod evolution.  Part I.  Systematics, middle ear evolution, and jaw suspension. Annales des Sciences Naturelles, Zoologie, Paris, 13e Série 19, 1-42.
Lombard, R. E., and Bolt, J. R. (1979). Evolution of the tetrapod ear: an analysis and reinterpretation. Biological Journal of the Linnean Society 11, 19-76.
Marjanović, D., and Laurin, M. (2013). The origin(s) of extant amphibians: a review with emphasis on the “lepospondyl hypothesis”. Geodiversitas 35, 207–272.
Experimental design: Paleontology is not an experimental science, like the rest of morphology and systematics. It is a historical and descriptive science. Thus, most of the points mentioned in the form do not apply.
Validity of the findings: Findings seem valid. My only comment is that broader relevance the findings needs to be highlighted better by more thorough discussions of the most interesting findings. The current version is clearly under-developed, on this front. I made various comments in the section “Basic reporting” about this. I think that if the authors follow these suggestions, the paper will be very interesting.
Additional comments: Good work. I hope that you will find my comments useful to make it even better, and more importantly, to better highlight its relevance to a much broader community. Do not hesitate to contact me if you have questions.
Michel Laurin
michel.laurin@mnhn.fr


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: OSTEOLOGY OF BATRACHUPERUS LONDONGENSIS (URODELA, HYNOBIIDAE): STUDY OF BONY ANATOMY OF A FACULTATIVELY NEOTENIC SALAMANDER FROM MOUNT EMEI, SICHUAN PROVINCE, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Overall the manuscript is well written, however many minor changes are required as listed below. The Results are Results  +Discussion and the Discussion is actually a summary. All figures are relevant but not sufficiently cited in the Results part.
Experimental design: The research / manuscript is relevant, and the authors considered all relevant literature. A list with all investigated specimens including also non- B. londongensis specimens would be helpful (supplementary table?).
Validity of the findings: The data can be replicated, and all data seem valid. Conclusions are clearly stated.
Additional comments: Basic reporting
Overall the manuscript is well written, however many minor changes are required as listed below. The Results are Results + Discussion and the Discussion is actually a Summary. All figures are relevant but not sufficiently cited in the Results part.

Experimental design
The research / manuscript is relevant, and the authors considered all relevant literature. A list with all investigated specimens including also non- B. londongensis specimens would be helpful (supplementary table?).

Validity of the findings
The data can be replicated, and all data seem valid. Conclusions are clearly stated.

List of suggested changes: GENERALL
-	get rid of double-spaces between sentences
-	Results: The paper has great figures, but the description (results) fails to refer to them  add Figures throughout Results where appropriate.
o	It would be also easier to read/understand when you make a general anatomical description and then finish the results with a neotenic description where you only highlight what is different between postmetamorphic and neotenic specimens
o	your results are mix of results and discussion and your discussion is a summary – consider changing the headings accordingly
o	you have female and male specimens – are there gender differences? You only cleared and stained two females.
-	Material & Methods:
o	Add a supplementary table where you list the specimens you compared with your CIB samples
o	line 135-136 add numbers for the specimens: e.g., juvenile (1?), adults (11?), postmetamorphic (4), neotenic (8)
o	Introduce abbreviation FMNH as you did with CIB (line 141)
-	change Batrachuperus londongensis to B. londongensis in following lines: 23, 41, 103, 123, 124, 128, 153, 217, 246, 247, 264, 355, 678, 729, 976, 1013, 1136
-	refer to abbreviation list at and of your figure legends Fig. 2 to Fig. 11
-	add spaces after CIB: line 1476, Table 1
-	check if you mean protractor pectoralis in lines 32, 227, 782
-	throughout text change phrasings like “structure FOR attachment (origin, insertion) of muscle xy” to “structure, onto which muscle xy attaches/inserts” or to “structure, from which muscle xy originates”: e.g., lines 32, 441, 616 (ascending process (coronoid process) that serves as insertion …), 707 (projects dorsomedially where the suparcualis rectus II attaches …); 776 (… end expanded where the pectoral muscles attach.); 790; 805, 806; 825; 827; 869; 902, 904, 906; 914, 916; 918
-	throughout text capitalize Fig., e.g., lines 662, 720, 1017, 1047, 1048 (and add space between E, and H), 1055, 1056, 1065, 1066

Changes by line: SPECIFIC
-	line 55: The family Hynobiidae includes 66-67 species …
-	lines 66-81: This paragraph can be shortened as information are repeated.
-	lines 96-97: How does the description of the osteology contribute to the protection of the species? Please, explain.
-	lines 107-113: Delete the sentence (starts with “Two”) – this information is not relevant for this paper.
-	line 151: Reilly & Lauder
-	line 152: Shubin & Wake
-	line 156: add space between number and ‘in’; introduce abbreviation CIB after Chengdu Institute of Biology  use CIB in lines 162, 165
-	line 161: add comma after 2014
-	line 245: “… londongensis”
-	line 259: move ‘characters’ to end of the sentence.
-	line 288: refer to one of your figures here
-	line 307: CN V1?
-	line 328: of the skull roof (not in …)
-	line 364: add space after posteromedially
-	line 369: … the lacrimal extends anteriorly over the border of …  change wording accordingly throughout text
o	978, 979
-	lines 384-385: … through which the superior alveolar branch of the trigeminal nerve (CN V2) and its associated blood vessels pass as in other salamanders (Francis, 1934).
-	lines 404-405: delete both commas in this sentence
-	line 412: The quadrate, as a principal element of the supsensorium, extends …
-	line 427: add comma after ‘(Lebedkina, 1964)’
-	line 448: Can you find a different term for ‘propping’? I am not sure what you want to say by this.
-	lines 461-2: However, B. karlschmidti …
-	line 467: homologous origin or a derived state …
-	474: Those fenestra …
-	478: this should be 14482 instead of 14382? and 14509 has no gills – is it neotenic?
-	516-7: ramus ventralis of trigeminal nerve (CN V1, 2, or 3?)
-	520: The parasphenoid is a dermal bone which forms …
-	529: sort the numbers of the CIB specimens (14482 shouldn’t be the last one)
-	532: … but has an articulation with …
-	559: … stapedial foramen in specimens observed by him.
-	567-570: move paragraph to line 547
-	582-3: … bears the occipital condyle posteriorly which articulates with the cotyle of the atlas.
-	591-2: rephrase this sentence: a bone is not supplying things (arteries do supply): e.g. “The ventral border of the foramen magnum is largely formed by the posteromedian process of the parasphenoid.”
-	596: add comma after ‘angular’
-	599: bone of the mandible
-	603: innervating both the skin and the muscle (arteries supply, nerves innervate)
-	606: add comma after ‘ventral’
-	625-6: In dorsal view, the anterior process of the articular extends between …
-	641: ossified during metamorphosis
-	644: add comma after ‘maxilla’ and delete ‘and’
-	645: … vomer, and dentary.
-	655: There are 20-25 teeth on the dentary.
-	665: add ‘our’ before CT-scanned images  it is actually possible to see cartilages in CT scans if the scanning parameters can be adjusted (also depends on size of specimens), see for example:
o	Figure 3. Anatomic section (A) and CT image (B) of the canine larynx at the section level 10 of the figure 1. :  http://mingaonline.uach.cl/scielo.php?pid=S0301-732X2010000100013&script=sci_arttext
-	680: delete ‘(see discussion below)’ as your results are mixed with discussion – if you want to add something you can say ‘(see below)’
-	692: add comma after ‘(Fei et al., 2006)’
-	708: Ceratobranchials III and IV
-	726: … from all B. londongensis specimens studied here, …
-	728: … caudal (tail) vertebrae
-	733: … widened anteriorly, where it bears a pair of …
-	735: … articulates with the exopccipitals at …
-	737: … pair of foramina through which the first pair of spinal nerves pass. The atlas has no …
-	745: … All presacral vertebrae except the atlas articulate with free ribs. (Ribs are not part of vertebrae)
-	747-8: refer to a figure or add one; also are the ribs bifurcated or do they appear bifurcated because of the uncinate process?
-	758: elongated
-	761: CIB 14485 is the only …
-	765-6: In fully grown adults, 28-30 vertebrae follow the caudosacral series.
-	768-9: All caudal vertebrae, except the posterior-most two or three, ventrally bear a haemal arch, through which the haemal vessels pass.
-	779: cite Table 1 instead of listing CIB specimens
-	785: What do you man with ‘received’? Articulates?
-	792: delete ‘coracoid’ ? Does it really articulate with the humerus?
-	794: … deeply notched where the crista ventralis of the humerus fits …
-	799-804: but you can relate it to size?
-	813: refer to figure? move specimens to end of the sentence (814)
-	820: … two faces for articulation with …
-	830: … radius and ulna are also ossified, …
-	844: add comma after ‘distally’
-	845: delete comma after ‘proximally’
-	860: delete comma after ‘acetabulum’
-	861-2: … vertical position, while the iliac blade is posteriorly slightly inclined.
-	873: delete ‘several’
-	877: refer to Fig. 10
-	883-4: To our knowledge, there are no publications which figured or …
-	887: delete ‘ypsiloid’ (you already have ‘y-shaped’)
-	899: femur (not humerus)
-	909: delete ‘obviously’
-	910: … larger than the fibula condyle.
-	920: … to articulate with the tibia.
-	927: add comma after ‘proximally’
-	928: Distal tarsals 3 and 4 are similar size and both are …
-	929: delete ‘obviously’; Distal tarsal 5 is missing, what is likely related to the loss of digit 5.
-	931-2: delete sentence as paragraph below (935-42) states the same.
-	957: The fibulare is enlarged and roughly …
-	961: Change heading to Summary as you discuss throughout your results
-	980: ‘absent owing to intervention by the lacrimal’ – Please rephrase.
-	991: … four to eight vomerine teeth, …
-	991: add comma after ‘orientated’
-	996: … 18 presacral vertebrae; … (same for line 1139)
-	997: … short with a prominent …
-	1004-6: delete sentence; you already stated that in Materials & Methods
-	1019 & 1036 & 1146 & 1467: ceratobranchials III and IV
-	1019: With regard to …
-	1020: delete ‘so-called’
-	1028: With respect to …
-	1033: Evidently, ossification …
-	1038: … retains a remnant …
-	1050: … ossified in both species.
-	1055: …; however, Xiong et al., 2013b: Fig. 1G shows …
-	1063: … has yet to be recorded.
-	1081-3:  delete ‘in the literature’ and add citation at the end of this sentence
-	1099: … have a large radiale, …
-	1108: … Batrachuperus, several other …
-	1111: Shubin & Wake
-	1117-8: … plesiomorphic feature because it is widely distributed in the family Hynobiidae. However, how many taxa …
-	1125-31: rephrase
-	1158-63: add locations: City, USA / CAN / China …
-	1166-74: that might be journal requirement, but the information is repeated
-	1150: delete ‘(B)’: (B) CIB 14481; (C) CIB 14482, with an incomplete resorption …
-	1453: (A) holotype CIB 65I0013/…
-	1458-9: (A) holotype CIB 65I0013/…
-	1458-61: Figure 4 & 1481-3 Figure 9: add the ‘notes’ where they belong and delete ‘note’ see example above (line 1150)


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: OSTEOLOGY OF BATRACHUPERUS LONDONGENSIS (URODELA, HYNOBIIDAE): STUDY OF BONY ANATOMY OF A FACULTATIVELY NEOTENIC SALAMANDER FROM MOUNT EMEI, SICHUAN PROVINCE, CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have now responded to most of my comments. In my opinion, the minor, stylistic revisions are fine, but the reasons they provide not to develop their embryonic discussion further, or not implement other more substantial changes, are not convincing.

To take only one example, in their rebuttal letter, the authors state “We did not cited Marjanovic & Laurin (2014) because their updated paleontological timetree of lissamphibians provided no specific estimations of Hynobiidae-Cryptobranchidae splitting time.” This is wrong and surprising, and even though the authors revised their sentence regarding the divergence date between hynobiids and cryptobranchids, it is still incompatible with the timetree of Marjanovic & Laurin (2014) because the authors now state: “Recent analyses of the nuclear exon and mitochondrial genome estimate the Cryptobranchidae-Hynobiidae split as ~150 Ma and the origin of crown-group hynobiids as ~125 Ma (Zheng et al., 2011: fig. 3).” According to Marjanovic & Laurin’s (2014) timetree, there are pan-hynoobiids and pan-cryptobranchids from the Bathonian (166-168 Ma). There is a clear incompatibility between these estimates (for once, the molecular estimates look too young), and I am extremely surprised that they authors don’t see this and don’t wish to comment on this. If new dating of the formations of the relevant fossils falsify the timetree proposed by Marjanovic & Laurin (2014), or if the ideas about the affinities of these fossils have changed, it would be a service to the community to indicate this. The timetree indicates that the divergence dates at least from the Bathovian (Middle Jurassic).

The authors should at least rework this point, I think. For the rest, given that I view my role as providing advice, not forcing anybody to do something against their will, so I will not insist further. Some authors are keen on extracting as much impact out of their results as possible, whereas others shy away from drawing inferences based on their findings, and thus, let others exploit their results. The authors appear to fall into this second category ; so be it. They are the ones who will suffer from their academic shyness, and others may reap the rewards of making interesting inferences from these findings, if they happen to notice them (of course, this is far from certain).
Experimental design: Paleontology is not an experimental science, like the rest of morphology and systematics. It is a historical and descriptive science. Thus, most of the points mentioned in the form do not apply.
Validity of the findings: Findings seem valid. My only comment is still that broader relevance the findings needs to be highlighted better by more thorough discussions of the most interesting findings. The current version is clearly under-developed, on this front, but given that the authors are uninterested in improving this aspect of the paper, I have nothing to add.
Additional comments: I have nothing to add. See above.


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

Input:
Title: OSTEOLOGY OF BATRACHUPERUS LONDONGENSIS (URODELA, HYNOBIIDAE): STUDY OF BONY ANATOMY OF A FACULTATIVELY NEOTENIC SALAMANDER FROM MOUNT EMEI, SICHUAN PROVINCE, CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The MS has improved and while I recognize that many suggestions from both reviewers were included, others were not. Most of the not-included ones are well justified in the ‘Rebuttal-letter’. However, one particular suggested change was statet as done but turned out to be not done.
In my first review, I wrote: “throughout text change phrasings like “structure FOR attachment (origin, insertion) of muscle xy” to “structure, onto which muscle xy attaches/inserts” or to “structure, from which muscle xy originates”: e.g., lines 32, 441, 616 (ascending process (coronoid process) that serves as insertion …), 707 (projects dorsomedially where the suparcualis[subarcualis] rectus II attaches …); 776 (… end expanded where the pectoral muscles attach.); 790; 805, 806; 825; 827; 869; 902, 904, 906; 914, 916; 918”
The authors replied: “—Suggested changes have been made throughout our manuscript text.”
But now in the V1 the authors still write: “Proximally on its extensor aspect, the crista dorsalis (dorsal crest) bears a prominent triangular or even knob-like projection, for insertion of the M. subscapularis (Francis, 1934). Proximally on the flexor aspect, the crista ventralis (ventral crest) is a large triangular process, projecting anteroventrally for attachment of the M. pectoralis and M. supra-coracoideus (Francis, 1934) and merging with the head of the humerus (or a facet in some specimens; see below).”

The phrases “For attachment” or “for insertion” can still be found numerous times in the text, but in general this is a form of description that should be avoided – e.g., facets are not developed for the attachment of condyles – both develop & evolve together, processes are not developed for muscles, …. Simply, search the document for those phrases and you will see where it should be corrected. However, if the Editor is fine with the phrase/non-correction, I won’t object.


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: GENETIC DIVERSITY AND MOLECULAR EVOLUTION OF ORNITHOGALUM MOSAIC VIRUS BASED ON THE COAT PROTEIN GENE SEQUENCE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors provide the first molecular evolution analysis for Ornithogalum mosaic virus (OrMV) using currently available sequences for the CP gene. For this, they perform phylogenetic, population structure and selection analyses.
I am not a native English speaker, but I think that language should be checked to correct several typos and/or sentences which are not clear to me. The structure of the manuscript is correct, although the introduction could be more informative; OrMV host range and geographic locations are provided, but information about other biological properties of the virus is not given, if known. This is particularly important, since the discussion also misses this information. The authors do not mention if raw data, i.e., sequence alignment, will be available in an open database or provided upon request.
Experimental design: The authors describe the methods employed in detail, and these are standard tools commonly used for molecular evolution analyses of plant viruses. The goals are clearly defined and analyses are refined and well conceived.
Validity of the findings: I have some main concerns regarding the validity of the results and the conclusions stated by the authors. Since the number of currently available sequences for this virus if still low, results and conclusions obtained with this dataset must be taken cautiously. For instance, the absence of sites under selection is considered a proof of strong purifying selection. Although this could be expected, available data are really scarce and authors should acknowledge. Also, the authors perform recombination analyses but, in my opinion, they should be more conservative when choosing non recombinant sequences. The fact that a short alignment is used in combination with a small number of sequences strongly recommends to remove all potential recombinants, i.e., those detected by at least three methods in RDP, from subsequent selection analyses. Finally, phylogenetics analyses do not provide a strong evidence of two different clusters; this grouping is not based on any biological property and thus phylogenetic classification should be taken cautiously again, since no other genomic regions are available to corroborate these preliminary results.
In conclusion, give the small sample size, most of the conclusions should be toned down.
Additional comments: Lines 103-105: I do not understand why the authors claim that the relaxed uncorrelated lognormal model is a better fit to the data than the strict clock model, but they still choose it to estimate the molecular clock.
Figure 1: Differences between figure 1A and 1B are not provided in the legend, neither in the main text. The same applies to Figure 2.
Table 1: Almost all data provided in this table is already provided in the main text, and then it is not necessary. It could be considered as supplementary table.
Figure 3: Sites under dN/dS=1 are indicated in orange, not “red”. This figure is not particularly informative and it would fit better as supplementary.
Table 3: A column indicating the sample size for each host/country is necessary. In fact, I guess that sample sizes will be particularly low in most of the cases, which would explain the lack of significance usually observed in MC cases. In this sense, for geographic analysis, and given the low number of samples, maybe it would be more reasonable to classify locations in areas wider than countries.


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: GENETIC DIVERSITY AND MOLECULAR EVOLUTION OF ORNITHOGALUM MOSAIC VIRUS BASED ON THE COAT PROTEIN GENE SEQUENCE
Review round: 1
Reviewer: 2

Output:
Basic reporting: It meets standards of English, article structure, but the background needs some work.
Experimental design: The research is original. It appears to be rigorous, but more details are required in the description of the methods. It is also unclear what the is knowledge gap, but this can be amended by improving the text.
Validity of the findings: Some statistical tests are not described in sufficient detail to assess the robustness of some of the results. Again, this can be improved with a better description of the methods.
Additional comments: In this study, Gao et al. conduct a range of population genetics and phylogenetic analyses to investigate the evolutionary dynamics of Ornithogalum mosaic virus. I value the effort that the authors have put into this study, but I think that it needs substantial additional work before it is published. I have suggested a range of statistical checks and analyses that the authors might have already done, but did not explain in the manuscript. Please see my specific points in the following sections.

Major points
- What criterium was used to choose the substitution model?

- What method for molecular clock model selection was used. Ideally, this would be marginal likelihoods via path sampling/stepping stone.

- The authors mention a 'lack of time stamp'. Does this refer to a lack of temporal structure? I assume that this was assessed via a root-to-tip regression or a date-randomisation test, but these are not shown. On that note, the authors calibrated the molecular clock using a prior distribution for the rate. To do this, it is important that the previous rate estimates corresponds to a very closely related virus and that it has strong temporal structure (i.e that it can be considered reasonably accurate) (see Rieux and Balloux 2016; Murray et al. 2016).

- An other important consideration of Bayesian phylogenetic analyses is that the influence of the prior should be assessed. This can be done by rerunning the analysis without data. If estimates of parameters of interest, such as the time to the most recent common ancestor, are reliable then their prior and posterior should differ substantially, such that the prior is not driving the inferences (Bromham et al. 2018; Ho and Duchene 2014).

- In the conclusion the authors acknowledge that their study has limited sampling of geography and host diversity. This can clearly bias inferences of trait evolution, such as geography or host range. This limitation needs to be discussed further.

Abstract
I think some of the language here needs to be explained better. For example, the authors mention BaTs analyses and estimates of \omega. These are measures phylogenetic signal and selective constraints, I suggest using these terms as opposed to just stating the program that was used.

Introduction
This section requires some more background information, such as why it is important to study the evolutionary dynamics of this virus, what is known so far, and what is the gap of knowledge that this study will address.

Minor comments
Line 36. Please not that not all viruses consist of measurably evolving populations. For example, many dsDNA viruses (including HPV, HBV, and Herpes) evolve too slowly to use sampling times of a few years as molecular clock calibrations.

Line 108. This part describes the selection of the tree prior. It is important to be consistent here are refer to the tree prior as a 'prior' rather than a model. More importantly, it states that the constant coalescent tree prior was chosen over the exponential growth, but there is no justification for this choice. This could be done via formal model testing, or by inspecting the posterior distribution of the growth rate. If this parameter includes zero, then one may resort to the constant size coalescent.

References

Rieux, A., & Balloux, F. (2016). Inferences from tip‐calibrated phylogenies: a review and a practical guide. Molecular ecology, 25(9), 1911-1924.

Murray, G. G., Wang, F., Harrison, E. M., Paterson, G. K., Mather, A. E., Harris, S. R., ... & Welch, J. J. (2016). The effect of genetic structure on molecular dating and tests for temporal signal. Methods in ecology and evolution, 7(1), 80-89.

Bromham, L., Duchêne, S., Hua, X., Ritchie, A. M., Duchêne, D. A., & Ho, S. Y. (2018). Bayesian molecular dating: opening up the black box. Biological Reviews.

Ho, S. Y., & Duchêne, S. (2014). Molecular‐clock methods for estimating evolutionary rates and timescales. Molecular ecology, 23(24), 5947-5965.


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: GENETIC DIVERSITY AND MOLECULAR EVOLUTION OF ORNITHOGALUM MOSAIC VIRUS BASED ON THE COAT PROTEIN GENE SEQUENCE
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I appreciate the modifications made by the authors to amend the minor and major weaknesses stressed in my previous review.


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: GENETIC DIVERSITY AND MOLECULAR EVOLUTION OF ORNITHOGALUM MOSAIC VIRUS BASED ON THE COAT PROTEIN GENE SEQUENCE
Review round: 2
Reviewer: 2

Output:
Basic reporting: OK
Experimental design: OK
Validity of the findings: OK
Additional comments: The authors have addressed my comments about Bayesian phylogenetics and other points that I raised.


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 MODERN SPECTRUM OF BIOPSY-PROVEN RENAL DISEASE IN CHINESE DIABETIC PATIENTS—A RETROSPECTIVE DESCRIPTIVE STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: Thanks for asking me to review this manuscript.
In this manuscript, Dr Liu et al has performed a retrospective study to assess common histopathological findings in Chinese diabetic patients with kidney disease who underwent renal biopsy. Isolated diabetic nephropathy was only seen in 44.7% of the patients, while over 50% patients in this cohort were diagnosed as non-diabetic renal disease. This is an interesting study, which has a potential impact on further management of diabetic patients with kidney disease.
I have following comments for the authors to take into consideration.
1.	It would be interesting to know any correlations between histopathological diagnosis based on renal biopsy and clinical parameters. For example, did more patients with NDRD have nephrotic range proteinuria than those with isolated diabetic nephropathy in this cohort? The authors briefly stated this in the discussion section. Can this issue be assessed in more details and presented in a separate paragraph in the result section? Then those results should be interpreted and discussed in the discussion section as well.
2.	In the line 136, should be in the current study.
3.	Please add P values in the first paragraph of the result section.
4.	In the line 225, it seems that the sentence was not complete.
…..should be performed in diabetic patients with kidney disease?
Experimental design: no comment
Validity of the findings: no comments
Additional comments: Thanks for asking me to review this manuscript.
In this manuscript, Dr Liu et al has performed a retrospective study to assess common histopathological findings in Chinese diabetic patients with kidney disease who underwent renal biopsy. Isolated diabetic nephropathy was only seen in 44.7% of the patients, while over 50% patients in this cohort were diagnosed as non-diabetic renal disease. This is an interesting study, which has a potential impact on further management of diabetic patients with kidney disease.
I have following comments for the authors to take into consideration.
1.	It would be interesting to know any correlations between histopathological diagnosis based on renal biopsy and clinical parameters. For example, did more patients with NDRD have nephrotic range proteinuria than those with isolated diabetic nephropathy in this cohort? The authors briefly stated this in the discussion section. Can this issue be assessed in more details and presented in a separate paragraph in the result section? Then those results should be interpreted and discussed in the discussion section as well.
2.	In the line 136, should be in the current study.
3.	Please add P values in the first paragraph of the result section.
4.	In the line 225, it seems that the sentence was not complete.
…..should be performed in diabetic patients with kidney disease?


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 MODERN SPECTRUM OF BIOPSY-PROVEN RENAL DISEASE IN CHINESE DIABETIC PATIENTS—A RETROSPECTIVE DESCRIPTIVE STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is written in clear English maintaining the scientific and professional standards. A few typographical errors in tense and sentence structure were noted.
Line 101; coexisted – coexisting?
Line 150; base – based
Line 197; presented – presenting
Line 255; ends in mid sentence and needs to be completed

In two areas, the meaning of the sentence was unclear and need to be rephrased.
Lines 143 -145; NS was the most common clinical indication for renal biopsy in all the three groups and there was no significant difference between them – please indicate what differences the authors are referring to.
Lines 187,188; The spectrum of NDRD in diabetic patients is consistent with the spectrum of glomerulonephritis in the same area – please specify what is meant by the ‘same area’

Since there are a several abbreviations used, although they are described within the text, tabulating these abbreviations with their meanings at the end of the article will make it easier for the reader.

There is a reasonably good review of background literature and the data is compared with some of the previous findings.

The general structure of the articles and the format of the tables conform to the journal requirements.

The raw data is available as an excel file with comprehensive analysis of all the 71152 cases. It would be useful to include a legend that provides descriptions of the different column headers as many of them are in abbreviated form. Similarly, the label keys for numerical data entry (E.g 1 = yes; 2 = no) will make the raw data independently analyzable for future readers.
Experimental design: The study is essentially a descriptive study, although in lines 85 to 87, three aims have been mentioned; two of which allude to correlative analysis. The results and discussion do not contain much comparative analysis especially on the clinicopathological correlations and determining the usefulness of renal biopsy.

The research question for this study has not been clearly defined in this article. The study has predominantly followed a descriptive pattern and has identified differences in the patterns of nephropathy among the population studied.

The article introduces three aims in lines 85 to 87
1.	Assess the modern spectrum of biopsy proven renal disease in diabetic patients
2.	Analyse the clinical-pathological correlations
3.	Determine the usefulness of renal biopsy in patients with DM

The first aim has been achieved as a descriptive analysis of the histopathological findings of the renal biopsies. The results mainly show that out of the 1604 diabetic patients, NDRD was identified in 887; including 99 in combination with NDRD and DN. These results are not very different to the results found in other studies as tabulated in Table 3.
The authors mention in lines 172-173, that this study provides an important supplement and an extension to previous single centered studies which is agreeable. However, in line 174 they mention that the study ‘better elucidates the characteristics of NDRD among diabetic patients in China’ which has not been adequately described in this article.

The second aim has been addressed to some extent in the results in reference to the SCr levels, presence of proteinuria plus haematuria and CKD. However, given the extensive availability of data, I feel a much deeper analysis and discussion should have been made on this aspect than what is currently available in the article.

It is not clear how the authors have attempted to address the third aim through this study as neither the raw data nor the analysis provides and insight into the usefulness of renal biopsy. This I feel has to be assessed in comparison to the clinical progression of patients or as a case control with biopsied vs non-biopsied DM patients and requires a different methodological approach than what could be achieved through this study. Therefore, this aim should either be removed from the article or better justified by the authors.

Although its not clearly mentioned in the article, the study appears to be of a retrospective nature. The sample population has been categorized into different groups based on previously made diagnoses and not on a strict case definition identified by the authors.  The histopathological data have also been obtained through previous histopathological reporting. It does not appear that all the cases have undergone the same gamut of staining methods and microscopic analysis. These should also be included in the limitations mentioned in the last paragraph under discussion (lines 240-248)

The selection of cases and the protocols used for histopathological grading have been clearly mentioned. However, certain aspects in the study should be made clearer such as; were all cases subjected to LM. EM and IF?. What percentage of cases had special stains?
Validity of the findings: The study has provided some valuable information in terms of renal histopathological findings in diabetes patients which would have some clinical relevance in treatment. However as mentioned above, the results do not provide any major difference to what has been already described and how this study contributes to new knowledge should be better elaborated. The large number of cases covered through this study seems to be its only strength.

The conclusion section is relatively under-written. In line 253 and 254, the sentence ‘renal biopsy is the most accurate method compared with other clinical predictors to distinguish DN from NDRD’ is an unjustified statement since the study results or discussion do not provide any comparison of renal biopsy vs other clinical predictors. Therefore, this statement needs to be removed or clearly justified. The last sentence ends in mid sentence and presumably the section is incomplete
Additional comments: As mentioned above, the study predominantly forms a descriptive analysis of the renal histopathological reports made on renal biopsies collected through a previous survey. A large number of cases from a multicentered selection have been analysed.

The title should be refined to clearly indicate that the study is based on a retrospective analysis of histopathological reports as it does not appear that the slides have been directly assessed by the authors themselves.

Similarly, it should be clearly stated whether all tissue samples have undergone light microscopy, electron microscopy and immunofluorescence. If not, since the study involves a large sample, the authors could reselect the cases which have undergone all three modalities and reanalyze the data.

I feel these factors introduce significant reporting bias to the results which is a limitation that needs to be adequately addressed in the article.

Although the authors have stated three aims in the introduction of the article, all of these aims have not been adequately addressed in the subsequent analysis. The first aim has been addressed reasonably, the second aim to a lesser degree but given the extensive data available I feel this should have been discussed more elaborately. The third aim does not fall within the scope of this study and should be removed.

The conclusion section is weak and needs to be better written to clearly correlate with the outputs of this study and also to give a strong message on the clinical relevance of the findings.

In my opinion this study has excellent potential for a good scientific publication. However, major revisions are needed to enhance its scientific quality and academic integrity prior to publication.


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

Input:
Title: THE MODERN SPECTRUM OF BIOPSY-PROVEN RENAL DISEASE IN CHINESE DIABETIC PATIENTS—A RETROSPECTIVE DESCRIPTIVE STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: I commend the authors for having revised the article well.

A few typographical errors in the revised document were noted.
Line 55; capitalization of other after Furthermore,
Line 90; sbiopsy – biopsy
Line 151 & 157, the sentences “there was no significant difference between the incidence of…..” should really read “there was no difference in the incidence of ….. between the three groups.”
Experimental design: The concerns mentioned in my previous review have been satisfactorily addressed.
Validity of the findings: The conclusion section is much improved. Although I feel the final sentence can be made to have a much bigger impact.

Suggestion – Given the large percentage of NDRD features identified through biopsies in our cohort of Diabetic patients with renal disease, and given that there were very few differences in the clinical presentation between the DN and NDRD groups, the study strongly supports the need for early renal biopsy in diabetic patients which can affect the long term management of these patients.
Additional comments: Many of the suggestions and concerns have been adequately addressed in this revised version and the article is much improved. Please see the minor revisions suggested above.

I feel mentioning the title as a ‘retrospective case series’ might unnecessarily bring down the value of this article as this is more than a case series. It would be better to call it – a retrospective descriptive study.

I feel the article is now in a sufficiently suitable standard for publication once these minor revisions are made.


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: PLAYING BY THE RULES? PHENOTYPIC ADAPTATION TO TEMPERATE ENVIRONMENTS IN AN AMERICAN MARSUPIAL
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript ““Playing by the rules? Phenotypic adaptation to temperate environments in an American marsupial” analyses central points in macroecological studies, i.e., the Bergmann, Allen and Gloger rules. The work was performed with a good number of samples and analysed a large area of the distribution of the species Didelphis virginiana. With no doubt this work is original and of scientific relevance, being of interest for macroecologist and biologist. Meanwhile, I have some concerns and suggestions that I consider important. The figs and tables are correct.
Introduction: Authors should explicit their hyphoteses and predictions for each of the rules. I consider this point the weakest of the work. This is a central point, since the choice of the variables will depend on the hyphoteses presented. Authors can not chose a large number of variables and test all of them to see which correlates more with the response variable. I consider that the work would benefit if the authors present the alternative hypotheses for each of the rules and the variables corresponding to the rules. An example of this approach is Torres-Romero et al. (2016): "Bergmann's rule in the oceans? Temperature strongly correlates with global interspecific patterns of body size in marine mammals"
Line 58-60: Authors should give a better explication of the fundaments of each of the rules and the different nivels of analysis: i) intraspecific and (ii) interespecific (assemblage and cross-species).
Experimental design: Authors should make available body size data in some repository or supplemental material for other biologists to perform other studies.
Authors should clarify which variables were used to test which hypothesis
Line 192-195: Why did they not analyse males and females separately?
Line 211: An analysis of spatial regression (SAR sor GLS) is more appropiate for this study. Not taking into account the spatial correlation can lead to increase type I error (look Legendre, 1993,2002; Diniz-Filho et al. 2009).

Diniz-Filho et al. "Blackwell Science, Ltd Spatial autocorrelation and red herrings in geographical ecology"
Legendre, P. (1993) Spatial autocorrelation: trouble or new paradigm? Ecology, 74, 1659–1673.
Legendre, P., Dale, M.R.T., Fortin, M.J., Gurevitch, J., Hohn, M. & Myers, D. (2002) The consequences of spatial structure for design and analysis of ecological field surveys. Ecography, 25, 601–615.
Validity of the findings: From the results, the conclusions are appropriately. Meanwhile, analysis taking into account the spatial autocorrelation are necessary.
Minor consideration
Line 346-347: “Our data suggests Allen’s rule also applies to American marsupials”. The study is intraspecific, the authors can not make this generalization.
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: PLAYING BY THE RULES? PHENOTYPIC ADAPTATION TO TEMPERATE ENVIRONMENTS IN AN AMERICAN MARSUPIAL
Review round: 1
Reviewer: 2

Output:
Basic reporting: If I am honest, I enjoyed reading this manuscript. Reading was like a story, easy to follow, clear and objective. Language and writing style are clear throughout the manuscript, making it easy to read. Information provided in the Introduction and M&M sections is sufficient and necessary to follow the study aims, and they cite relevant to the study, and both new and classic papers are cited. They provided all the raw data and background analyses results in supplementary files. Figures are necessary but not excesive.
Results reporting is appropriate and they are discussed accordingly.
Experimental design: All the items requested in this category are fulfilled. Although the question proposed is not new in biology, it was not answered for the study organism before and it is clearly stated in the introduction. The study absolutely follows high technical and ethical standards. Methodology is clear, even the statistics are well explained, and easily replicable.
Validity of the findings: This is a “clean”, “tidy” study. Data is actually robust, statistically sound, and controlled.
Conclusions are well stated, linked to original research question and limited to supporting results, although some hypotheses are suggested to be tested to complete  the study findings.
Additional comments: I think this is the first time it happens to me that I enjoy a manuscript when reviewing from the beginning to the end. I believe this is a good contribution for the journal and for life sciences, and I can only suggest some minor modifications. The design is simple and clear, sampling is wide enough, methods are appropriate, and findings are discussed accordingly. However, I would like to ask the authors why they used grouped latitude instead of using it as the continuous variable it is. I can see they have a break at some point of the distribution, but that should be evidenced using linear models too (see minor comments about it). Also, you used hindfoot length as a proxy for body size, after a R = 0.54. That is not a “high correlation”, and I suggest you to keep body size as size variable.

Minor comments:

L150- I am sorry to say I cannot recall any author in order to make a strong statement, but I am quite sure that an R value of near .500 is rather a moderate relationship instead of “high”. I suggest you to maintain body length as a measurement of size.
L206- Is there a reason to make these groups? If that so, please explain why you need to form groups (although arbitrary, from my point of view). Otherwise, I suggest you to perform linear (lm function in R) models which allow you to include categorical and continuous variables in the same analysis.
L210- Even though we all know the main core packages in R, I suggest to cite them.
L235- Did you check for correlation between environmental variables and latitude/longitude? If so, please mention it in the text
L278- In the M&M section you mentioned that as body size and hindfoot length were correlated you decided to use the later as a proxy for body size, but here you analyzed both. Can you please clarify either the methodology or the results?
L335-337. This sentence is a bit disconnected, I suggest to move it after 339 sentence.
L346-347- This sentence is redundant, you may delete it for the sake of brevity.
L377- Independently?
L392- I do not see the relationship between cheeks color as a diagnosis character and sexual selection of this trait.
Fig. 6A- May be you can rename the variable as “thermal amplitude”, as temperature range high/low looks confusing in the figure.


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: PLAYING BY THE RULES? PHENOTYPIC ADAPTATION TO TEMPERATE ENVIRONMENTS IN AN AMERICAN MARSUPIAL
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have made a great effort to incorporate most of the criticisms and suggestions. The work " Playing by the rules? Phenotypic adaptation to temperate environments in an American marsupial ", presents relevant results for the hypotheses presented in the introduction.
Experimental design: Methodologically, only one point worries me, the spatial autocorrelation. The method used is not the most appropriate, since its response variables have spatial autocorrelation, so the residuals of the models will have spatial autocorrelation. If they want to keep the RandomForest method they can follow the approach used by Stuarth-Smith et al. (2013). Stuarth-Smith et al.(2013) uses random forest, but to see if autocorrelation affects his results he did the following: (i) determine how far the spatial autocorrelation decreases and (ii) use only points with distances greater than this distance in the models.
Validity of the findings: The work is novel, important for the understanding of the ecogeographic rules, being an important contribution to the knowledge of the forces that affect in the phenotypic variations along the environmental gradient.
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: PLAYING BY THE RULES? PHENOTYPIC ADAPTATION TO TEMPERATE ENVIRONMENTS IN AN AMERICAN MARSUPIAL
Review round: 3
Reviewer: 1

Output:
Basic reporting: The work is adequate and well done. Only, I ask the authors to incorporate an I Moran analysis of the residuals of the model, to be reassured that the model was adequate to deal with spatial autocorrelation.
Experimental design: Is ok.
Validity of the findings: Is ok
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: TEMPERAMENT AND CHARACTER EFFECTS ON LATE ADOLESCENTS’ WELL-BEING AND EMOTIONAL-BEHAVIOURAL DIFFICULTIES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The writing is good except for a few typos and awkward phrases. Specifically,
 page 7 of 37 in the pdf, line 52 should be "an underlying", not "un underlying".  Line 55, trait, not traits.  Line 69, no comma is needed.  On page 8 of 37, line 88, refer to propositional or insight learning, not prepositional learning. On page 9 of 37, line 103, the word differentiated is unclear; perhaps you mean correlated?  On page 10 of 37, line 134, "prevents from" is awkward, perhaps yo could change this to "makes it difficult to ascertain in the same subjects..."

The literature review is excellent and the article is well organized.
Experimental design: The study is cross-sectional with self-report on multiple instruments. The limitations of this are adequately discussed.  Methods are clearly described.  The authors rely on linear regression with individual scale scores.  Future work could be enhanced by considering multidimensional profiles of traits, but what was done is adequate for the limited sample size.
Validity of the findings: The results are reasonable and extend prior findings.  Conclusions are justified and clearly stated except that the authors consistently minimize the associations they observed for Cooperativeness.  Specifically, CO was correlated with Personal Growth (PG) so it is false to say that Co was not associated with well-being on page 15 of 37, line 246.  Likewise, on page 16 of 37, authors should add a statement that CO had significant associations with adjustment, including Total, externalizing, and Prosocial behaviors.  Therefore in the discussion the paragraph about Cooperativeness needs to be revised to indicate that Co had effects primarily related to personal growth and prosocial behaviors.  It is possible that a composite measure of (SD+CO) would be a stronger predictor than either alone because this is a validated indicator of character maturity and absence of personality disorder.
Additional comments: This is a well-done cross-sectional study in an important area, the well-being of adolescents.  There are only one issue about interpretation about Cooperativeness that needs revision and some minor awkward language and typos that can be easily corrected.  I hope you continue this line of investigation and encourage you to consider profiles of traits as well as individual traits.


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: TEMPERAMENT AND CHARACTER EFFECTS ON LATE ADOLESCENTS’ WELL-BEING AND EMOTIONAL-BEHAVIOURAL DIFFICULTIES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The comments are included in the "general" section
Experimental design: Sample
More information on the sample (background variables) would be needed.
Measures
Speaking about “behavior” should be done with a caution because just self-reports have been utilized. After having read the “measures” a reader is still more convinced of an inaccurary between the content of an introduction and an implementation.
Data analysis is very traditional and would benefit from more advanced approach. A low number of subjects is, of course, an evident disadvantage
Validity of the findings: The findings per se are in no way novel but available to be derived from the previous literature. Therefore,  some new approach or advanced statistical model would be needed.
Additional comments: Temperament and character effects on late adolescents’ well-being and emotional-behavioral difficulties

This study examines associations between personality and psychological and subjective well-being. Several aspects of the study need reconsideration.
Introduction
“Goodness of fit” between the introduction and the study problem is not the best one, i.e. the introduction doesn’t lead to this very research problem  in the best way but describes findings which do not help the reader to get the focus of this study. Actually there are references to previous literature which are more likely to mislead the reader than justify the present study (or a refining the study problem is needed). The most relevant literature in this context has been in many respects passed over. A distinction between psychological well-being and subjective well-being is factitious and therefore, not clear. Actually, the overlapping is high resulting in strange claims on a role of personality in PWE and SWE (i.e. claims on a different role of a personality in PWE from a role in SWE).  Other concept used in the present study should be clarified, too, for instance a lack of symptoms is not identical with well-being and well-being with psychosocial adjustment. The concepts to be used are far from clear. – More specified hypotheses are possible to be derived from the previous literature.
.

Discussion
There are major concerns in discussion. At least the following revisions would lead to remarkable improvements.  Using the concepts should be consistent.  Extroversion shares elements with novelty seeking, but however, novelty seeking cannot be in midstream called extroverted behavior.  Inconsistency is true with most of the concepts. It is not always easy to see, whether the authors speak about the findings of the present study or whether they speak about literature. There is a large amount of speculative interpretations, i.e. interpretations which are based on secondary sources (a researcher finds a correlation between reward dependence and positive emotionality. Literature has documented a correlation between positive emotionality and social adjustment. The researcher writes that his or her findings have shown an association between RD and adjustment). The discussion also includes statements derived from concepts which have not been used in the present study. The discussion should be a more coherent wholeness; in its present form it is more likely to comprise a long list of random correlations, most of those correlations being well-known, not novel.  A significance of those associations would need more clarification. At the end of the discussion there are two slightly strange suggestions. First, the authors suggest that instead of self-reports, one’s personality could be assessed by others, teachers or peers. This is not possible, then it is no more one’s personality but observation on his or her behavior. Second, the authors suggest that physiological measures like heart rate variability could be used to understand  relations between TCI and subjective wellbeing


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: POLLINATION IMPLICATIONS OF THE DIVERSE DIET OF TROPICAL NECTAR-FEEDING BATS ROOSTING IN AN URBAN CAVE
Review round: 1
Reviewer: 1

Output:
Basic reporting: - The manuscript is well written, logical and easy to comprehend.

- The context and the literature references are sufficient

- The structure and the number of tables as figures seem appropriate. I would suggest nevertheless to move Table 1 to the supplementary materials, as it is not fundamental for understanding the results.

- Raw data is shared. Please consider changing the name of the file in Supplementary Info so it will be easier to understand its contents.

- Please consider being more detailed about the aims of the paper in the abstract.
Experimental design: - The research questions focus on two very different aspects - one methodological and one ecological. The methodology cannot be consider so much a novelty, so please consider giving more focus on the issue of bat pollination of exotic (invasive?) and commercial plant species. Seed dispersal of invasive plants by native animals is a timely a very relevant issue and you could exploit it better using your data.

- The ms. would benefit from information on food availability for this species. This could be inferred e.g. from the flowering season of each species. Notice that the importance of plant species based only on its occurrence during the sampling period is highly deceiving. A plant species can be preferred by this species, but if it is not easily available (because it started blooming only at the end of the sampling period) or it is too far away it will show as unimportant.

- Please consider including some information on how the different Chao 2 estimators presented differ and how those differences may be of relevance to the results.
Validity of the findings: - The authors state that the methodology employed facilitated the detection of plants that were not previously reported. It would be relevant to discuss also why previous studies recorded several species that were not detected with this novel method. Again, discussing a bit further the issue of flower availability (see above) may be fundamental to fully clarify some of the lines discussed.
Also relevant to mention if all the previous studies were performed during the same season, otherwise any comparison between studies may be less informative. Please consider including this aspect also in the Discussion.
Additional comments: 'no other 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: POLLINATION IMPLICATIONS OF THE DIVERSE DIET OF TROPICAL NECTAR-FEEDING BATS ROOSTING IN AN URBAN CAVE
Review round: 1
Reviewer: 2

Output:
Basic reporting: This submission is a well-written manuscript using new techniques to bring new information to a long-studied topic: pollinator diet breadth. This study focuses on the diet of a nectarivorous bat species common to SE Asia, E. spelaea. Unlike previous studies, which have relied on visual identification of pollen samples, this study identifies plant resources via DNA from fecal samples. They also use their findings to examine the extent to which this common bat pollinator uses exotic versus native plant species, given that their study area was primarily surrounded by an urban landscape (with many introduced/cultivated plant species). I think this manuscript will provide useful information to the scientific community primarily for the new methodology (that is, relatively new in the field of pollinator foraging/diets), and will also be of interest to more specialized audiences (bat or pollination or urban ecologists). That being said, I also think this manuscript can be strengthened by addressing a number of issues.
Experimental design: The data collection/sampling is a bit vague, please provide more detail.
Line 117: 100 mL total? Over how many days were samples collected?
Line 126: how many samples per week?

[Note: I have limited knowledge of DNA metabarcoding, and therefore cannot assess the authors' use/description of these methods.]
Validity of the findings: My first main concern is the authors’ discussion of which plant species are “important” to the diet of E. spelaea. First of all, it can be misleading to use presence/absence data to estimate importance. A plant species may be detected every week, but it might only comprise a small percentage of the total volume consumed. Alternatively, a plant species may only be detected 2 or 3 weeks, but it might have comprised the large majority of the bat’s diet during that time. Secondly, the authors only collected samples for essentially two months (January and February). So it’s important to state that these were the most commonly encountered species during the study period, but resource use will likely differ in other months, given that available floral resources fluctuate over time (ie, different plant species flower during different times of year).

My second main issue is the discussion of their species richness results. Their analyses estimated 65-69 plant species. This is the predicted number of plant species consumed during the study period. Or you can also think of it as the predicted number of plant species consumed if the floral community did not change over time. But floral communities do change across months. If the authors were to collect samples throughout the entire year, they would likely encounter the DNA of several more plant species, and the estimated species richness would likely be greater than 65-69. This is because a large percentage of plants (even in the tropics) do not flower year round. So the calculations are not incorporating all of the species that bloom between March and December. Likewise, the reported 0.912 sampling completeness ratio is for the study period, not for the entire year.

My third main issue is more of a request, which is that the authors at least mention the possibility that not all species detected in the fecal samples are intentionally consumed. Especially the ferns, and the plant species detected only once or twice. An alternative explanation is that the bats brush against ferns (or other random plants) during foraging and their fur picks up spores/pollen, which they then ingest during grooming. Again, I wish metabarcoding could provide quantitative data, because it would be really interesting to see the percentage of each plant species in the diet.
Additional comments: One other suggestion about Lines 287-288: One idea is to find info about fruiting/flowering times of each plant species. Then you could hypothesize whether bats were eating floral resources (nectar/pollen) or fruits or leaves (if the species wasn’t flowering or fruiting during the study period).


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: POLLINATION IMPLICATIONS OF THE DIVERSE DIET OF TROPICAL NECTAR-FEEDING BATS ROOSTING IN AN URBAN CAVE
Review round: 1
Reviewer: 3

Output:
Basic reporting: See General Comments.
Experimental design: See General Comments.
Validity of the findings: See General Comments.
Additional comments: The manuscript by Lim and colleagues employs DNA metabarcoding to identify the diet of a primarily nectar-feeding species of bat roosting in urban caves in Peninsular Malaysia. The authors were able to identify 55 species of plants, from scat samples collected on the cave floor where the bats were roosting.  They make the assumption that all of these plant species are part of the diet of the bat.  The plant species are a mix of native and exotic species, many of the latter with economic importance.  The study and the manuscript are well done and should be published in PeerJ.  However, the following points should be addressed before the paper is ready for publication.

1) Metabarcoding investigations have not been restricted just to bat diets and the authors should site some additional broad and high-profile papers on using DNA barcodes to elucidate animal diets (e.g., African herbivores; neotropical insect herbivores).

2) Why were only two of the four most common plant DNA barcode markers used in this study?  Both matK and trnH-psbA could greatly help in providing identifications to the species level.  The authors need to justify their use of only rbcL and ITS2.

3) It is not clear why the authors assume that the DNA barcodes were recovered from digested nectar?  Does nectar even contain DNA?  Or is it more likely that the DNA is being recovered from pollen, fruits or other plant parts consumed and excreted by the bats?

4) The cave floor is hardly a “sterile” environment, even if it is swept clean on a daily basis.  Could there be a source of contamination in the samples collected in the cave?  Some of the plant species reported hardly seem like bat diet items (e.g., Bidens?).

5) A more appropriate title for the paper might be along the lines of “Evidence for pollinators from the diverse diet of tropical nectar-feeding bats inhabiting an urban cave”

6) The citations in the text need to be checked to the references (e.g., Brandon-Mong et al, 2015 absent in references).

7) BLASTing to GenBank will only bring up species with previously sequenced barcode data, which may not be the case for many tropical native species in Peninsular Malaysia.  The authors may therefore be underestimating the native plant species in the bat diets.

8) There is much redundancy in the text.  The authors and editors should careful edit out, especially in discussion section.  For this reason the Conclusion section could be omitted as it provides nothing new.

If the authors can address these points and revise the text accordingly, the paper should be acceptable for publication in PeerJ.


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

Input:
Title: POLLINATION IMPLICATIONS OF THE DIVERSE DIET OF TROPICAL NECTAR-FEEDING BATS ROOSTING IN AN URBAN CAVE
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have responded to all reviewer comments, and I think the manuscript is much improved.

One last minor comment: Does Ceiba pentandra really flower year-round in Malaysia? We only observed it flowering from Nov-Feb in southern Thailand (Stewart & Dudash BIOTROPICA 50(1): 98–105 2018), and other studies have also reported it as mass-flowering.
-	Flowers in August in Brazil. Gribel et al. Journal of Tropical Ecology (1999) 15:247–263
-	Flowers in June-Aug in Samoa. Elmqvist et al. Biotropica (1992) 24:15-23
-	“individuals that flower are highly synchronized and do so within a relatively short period of six weeks (Frankie et al., 1974; Gribel et al., 1999; Lobo et al., 2003). Along the Pacific coast of Mexico and Central America flowering occurs at the beginning of the dry season in January and February (Lobo et al., 2003).” – Lobo et al. Am. J. Bot. February 2005 vol. 92 no. 2 370-376

It might be a good idea to double-check the flowering phenology info.


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: POLLINATION IMPLICATIONS OF THE DIVERSE DIET OF TROPICAL NECTAR-FEEDING BATS ROOSTING IN AN URBAN CAVE
Review round: 2
Reviewer: 2

Output:
Basic reporting: In this paper the authors examine the diet of Eonycteris spelaea roosting in an urban cave in Malaysia by identifying plant material present in bat feaces.
From my understanding this is a second review of the paper, which I did not revise previously. My understanding is that the authors answered most of the concerns of the previous reviewers and, for this reason, I feel pleased with the majority of their text and findings.
Experimental design: The experimental design seems adequate. However, the authors include information on what they refer is food availability for Eonycteris spelaea, but truly is just information on the phenology of plants that potentially belong to its diet. While I see no substantial problem with this, and understand the difficulty of getting data on food availability, the authors should be more explicit about this in their methodology.
Validity of the findings: Findings are robust and rather interesting, although the methodology is not particularly novel.
Additional comments: It would be rather relevant for the authors to suggest management actions to potentially reduce the consumption of exotic species by Eonycteris spelaea, while promoting the consumption of native species.


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

Input:
Title: BREAST CANCER IDENTIFICATION VIA MODELING OF PERIPHERALLY CIRCULATING MIRNAS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comments
Additional comments: Breast cancer is the second leading cause of cancer-related cell death in females. The scientists in this study addressed one of the most critical concerns of modern-day research studies, i.e., limiting the study samples or patients demographically. More diverse sample inclusions and investigations are needed to make research outcomes and projected cures relevant for distinct population subsets. The present study highlights the importance of increasing the sample size. Further, authors excellently identify the requirement of rapid, sensitive and specific biomarkers for early detection of breast cancer; and employ a better modeling tool, i.e., neural network cascade (NNC) for accurately predicting the robust miRNA biomarkers for breast cancer detection. The study is well-written, easily comprehensible, relevant; and contributes to rapid and accurate detection of breast cancer. Though paper from Shimomura et al., 2016, have addressed related research questions before, the present group further worked on optimization section and identified previously unreported and more robust miRNA biomarker by using NNC model. I have following comments:

1.	In line #29, author begins to conclude that the better model helps in reducing the no. of required miRNA biomarkers for accurate and early prediction of BC. It is not clear how reducing the no. of miRNA biomarkers helps in early detection of BC?
2.	Does miRNA-8073 serve as a diagnostics biomarker for initial stage breast cancer patient?
3.	Authors used large dataset, but demographically samples were not diverse. It would be scientifically strengthening to confirm the current findings across distinct populations subsets. The concern of reproducibility that arises due to small sample size and geographically restricted results still stands unaddressed.

Overall, the work is carried out meticulously, and presented in a logical flow. I highly recommend accepting the manuscript.


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

Input:
Title: BREAST CANCER IDENTIFICATION VIA MODELING OF PERIPHERALLY CIRCULATING MIRNAS
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this paper Cui et al. have reported three miRNAs which can be used to detect breast cancer using machine learning models. However, manuscript is descriptive and needs further improvements.
Experimental design: Breast cancer has distinct subtypes. How this model performs in breast cancer detection for different subtypes?

Authors report that 70% of miRNAs are highly predictive of breast cancer patients which is a very high number. How steps authors performed to check if their model is not overfitted? Which regularization techniques were performed to avoid overfitting?

Authors have performed ROC analysis on 2540 miRNA and identified non collinear miRNAs with highest AUC. It is not clear how this ROC analysis was performed.

Figure 1B is not informative. Number of edges should be reduced to only significant collinear relationships.

It is not clear how normalization of miRNA dataset was perfomed?
Authors identidied 8 non-collinear miRNAs and then used only three of them for generating a combined model. What is the rationale for selecting three miRNAs?
Validity of the findings: Authors haven’t shown performance of their model on other available miRNA datasets for breast cancer detection. A comprehensive analysis of performance of their model on all the available miRNA data will be useful
Additional comments: What is the advantage of using miRNA data over other omic datasets (mRNA gene expression, CNV, mutation)?

Conclusion is verbose and doesn’t give insights about the advantage of using miRNAs in detecting breast cancer

The writing is poor and should be improved.


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: BREAST CANCER IDENTIFICATION VIA MODELING OF PERIPHERALLY CIRCULATING MIRNAS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The authors, if possible should add updated references to recent literature involving miRNA's in breast cancer in the introduction section.

The figures were not annotated properly in the text. Figure 1A and Figure 2B. The way the authors wrote the results related to Figure 1A was as if it was written for methods section. They need to restructure the statement related to Figure 1A.
Experimental design: The authors have a done analysis utilizing data from large number of patients. The methodology, NND based analysis has been explained in the discussion.

The authors have shown AUC data for 3 miRNA's that have been the output of their NND analysis. I would suggest the authors to mention about various reports if any were published citing these miRNA's as prognostic biomarkers in cancers or other dieseases. For eg: miR1246 has been suggested as biomarker in pancreatobiliary tract cancer utilizing salivary exosomes (Machida T, et al, Oncol Rep. 2016 Oct;36(4):2375-81).

The authors should probably add one more analysis (survival curves, progression free survival) to see if the miRNA's  serve as prognostic biomarkers in breast cancer.

If possible the authors should add some negative controls (miRNA's) that do not support the analysis and include the data in figures.

The authors if possible can add additional analysis of predicted targets for these miRNA's which will help strengthen their signature.

The authors are not consistent with the annotation of the figures in the text (results section).
Validity of the findings: patient number use din the analysis is robust.

Conclusions are good, could be a little elaborate.
Additional comments: The authors have done analysis utilizing large patient volume,  but should add some control miRNA's in the analysis.


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: BREAST CANCER IDENTIFICATION VIA MODELING OF PERIPHERALLY CIRCULATING MIRNAS
Review round: 2
Reviewer: 1

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


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

Input:
Title: BREAST CANCER IDENTIFICATION VIA MODELING OF PERIPHERALLY CIRCULATING MIRNAS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Manuscript is highly improved as compared to their first submission. Authors have addressed all of my concerns.
Experimental design: NA
Validity of the findings: NA
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: BREAST CANCER IDENTIFICATION VIA MODELING OF PERIPHERALLY CIRCULATING MIRNAS
Review round: 2
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have identified miRNA signature using a large breast cancer patient set. However the authors failed to segregate the patients by category (Luminal, Basal, or ER+, PR+ or TNBC). The authors have also failed to identify the targets of the miRNA enriched in the signature which could be easily done either from previous studies or using miRNA target identification software. This analysis would have added additional impact to the manuscript


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

Input:
Title: FEMALE HARBOR SEAL (PHOCA VITULINA) BEHAVIORAL RESPONSE TO PLAYBACKS OF UNDERWATER MALE ACOUSTIC ADVERTISEMENT DISPLAYS
Review round: 1
Reviewer: 1

Output:
Basic reporting: advertisement displays”

The manuscript describes the response of captive female harbor seals to male harbor seal roars and control sounds.  I like the question posed by the authors and the overall design of the study.  The paper is well written and easy to follow.  I am a bit concerned about the foundation on which the study rest and I also believe that there are other interpretations to the findings made by the authors and that as such the conclusions are an overreach.  I have smaller comments regarding the methods.

Foundation
The theoretical framework began very promisingly in the first paragraph.  However, the study relies on the results of an unpublished MSc thesis.  [I realize that theses are peer-reviewed by faculty, yet I also realize that faculty have a stake on seeing theses finished, unlike anonymous reviewers of a manuscript.]  I read the thesis by Nicholson (2000) and have serious concerns about the work.  Relevant to this manuscript, I do not know how she determined that wild harbor seals were males and females, adults and sub-adults.  It is not an easy task, sometimes outright impossible, and she did not describe at all how she determined age-sex classes.  I am also not convinced that she was able to unambiguously ascertain whether a particular vocalization came from a specific male with just one recording hydrophone.  My concerns about the thesis do not demerit the manuscript, but they do indicate that the theoretical foundation is not as strong as it appears in the manuscript.  So my suggestion would be to present Nicholson’s findings as a hypothesis rather than as a fact.  In addition, Nikolich et al. (2016) indicated that roars in their study site form a continuum, rather than a dichotomy of short versus long duration and high versus low frequency calls, so I think a brief discussion on the implications of these results to the framework in which this manuscript was placed and to its discussion is needed.
Experimental design: Methods
The authors posit that female harbor seals reacted more to male vocalizations than to control noise, something with which I agree; then they posit that roars are important in male-female vocalization.  Although this could be the case, one could argue that females are reacting to male or even seal sounds given that the experimental design did not test for other types of vocalizations such as growls or the fact that roars can represent a continuum (see above).  I realize that the design included unusual variations of the roars but it did not include other types of vocalizations and, as I mentioned before, the results from the second year indicated that only 50% of the sample size reacted according to the predictions of the hypothesis.  Because females are in a captive environment, because of individual variation and context (something that the authors discussed for one of the subjects) and because of the limited sample size, I wonder how much the relatively ambiguous results (see above in interpretation) are a result of the novelty of a seal sound rather than the specifics of a roar.  How would they have reacted if they heard a growl, for example?  Given all these issues, I suggest that authors to tone down their conclusions.

The paper is very well written, but I was unable to figure out the experimental design regarding playbacks and trials (lines 165-168).  It seems to me that more detail or a different way to provide the information is needed.

From where did the females come?  Did they come from Elkhorn Slough?  If not, what is the justification that they will react to roars from seals from another region?  This is important given that seal sounds can vary at the individual and population level.  How long were they in captivity?  For how long were they exposed in the wild to harbor seal sounds?  I believe more information is needed about the provenance of the females.

Less importantly, it is unclear to me if the measured levels of 149-156 dB were also applicable to the water controls (lines 182-183).
Validity of the findings: Interpretation
I believe the authors give strong conclusions to their results that are not warranted by the data.  In year 2, the results of Pinky and Tater are very similar to those for year 1, so only 50% of the sample size did not approach manipulated roars and controls between the years, as predicted.  Further, the differences in response between what are termed subordinate and dominant male roars were only one approach or contrary to predictions (60%).  Given that the test was not significant, similar to the results of Hayes et al. (2004), I suggest that the authors provide alternative explanations.  It is possible, like they suggest, that their predictions could still be correct; however, maybe the answer is not as straightforward as a high/short and low/long roar and it is more complicated, with the female response based on roar nuances and other characteristics.  So, my suggestion is to present alternative interpretations and tone down the conclusiveness of the results.
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: FEMALE HARBOR SEAL (PHOCA VITULINA) BEHAVIORAL RESPONSE TO PLAYBACKS OF UNDERWATER MALE ACOUSTIC ADVERTISEMENT DISPLAYS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The Methods, results, and discussion need to be clarified and re-organized.
Figure 1 is not helpful and needs axis labels and figure caption
Table 1 7 2 needs captions and I believe including which subjects were in estrous is needed.
Experimental design: Methods and analysis need much work/reorganization. They, themselves are fine, but the reporting of it needs improvement
Validity of the findings: My concern when answering this is that I am unclear based on some clarification needed through revised methods/analysis reporting.

Conclusion should go into more depth
Additional comments: The research question is interesting and the general work well done.  The paper needs major revision in my opinion but I would like to see it published after revisions as something of this nature can add to the overall information in the field. Lab and field work complement each other - but this paper, as written, only scratches the surface or what I want to read and leaves me with more questions than answers in how the design was carried out.

-Please see all specific comments in the attached 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: FEMALE HARBOR SEAL (PHOCA VITULINA) BEHAVIORAL RESPONSE TO PLAYBACKS OF UNDERWATER MALE ACOUSTIC ADVERTISEMENT DISPLAYS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript was well written and presented before, and it continues to be the case in this revised version.
Experimental design: I want to commend the authors for the revisions they made to their manuscript. The revised introduction makes the paper intriguing, with a framework that offers a more honest intellectual justification than the previous version.
Validity of the findings: The authors are upfront and candid about the limitations of their study, particularly the sample size.  In this regard, the conclusions are for the most part excellent.  However I believe two changes are important:

1- The abstract does not match the conclusions.  The impression the reader has after reading the abstract changes after reading the paper, including the conclusions.  I agree that females responded to male calls more than the control.  Taking into account both years and all females, I am not quite convinced that there is preliminary evidence that females prefer LL male calls, I would say that results did not invalidate the hypothesis that females prefer LL male calls. I think it is up to the reader to make up her/his mind about that.  Yet, the abstract presents the results on female approaches to LL calls first than the results of female responses to control and in stronger terms than in the conclusion.  My suggestion is that the abstract follows the conclusion regarding the findings: female approaches to LL calls comes after female approaches to calls over control and qualify the statement on female approaches to LL calls.

2- I think the authors should either balance out or cut down the discussion (lines 292-328).  The results did no support the hypothesis of female response to LL calls (both by looking at the figures and by running the statistical tests).  They did not refute it either (as I said before).  Yet the main thread in the discussion is about the hypothesis being correct or potentially correct and why that could be.  The overall read I got from those lines was they were an overreach so at the very least they should be cut down.  Personally, I would like to see a discussion of what if females actually do not respond to LL calls, what would that meand and why?  It would certainly be speculative but so are lines 292-238 in the discussion.
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: QUANTITATIVE TRAIT LOCI ASSOCIATED WITH SOFT WHEAT QUALITY IN A CROSS OF GOOD BY MODERATE QUALITY PARENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: •	the manuscript is written clearly and in good english
Experimental design: •	The size of the population is quite small, unusual for QTL studies nowadays
•	The choice of genetic markers and the number of markers used in this manuscript is not suitable for QTL studies nowadays
•	The phenotypic data is old, from 2002 to 2004 and grown in very small plots (only one row)
•	In general, there is no reason not to use old phenotypic data but you would rather combine it with new genetic data or at least a current statistical method, but this is not the case in this manuscript
 M&M part has no novelty impact to the current scientific questions in QTL studies
Validity of the findings: •	The low resolution of the map makes QTL location impossible, traits can only be associated to a chromosome, and this is not the state of the art anymore.
•	A search for QTL quality in soft wheat in google scholar results in newer literature with greater populations and higher amount of genetic markers and therefore a better genetic resolution
•	Conclusion within the discussion are missing
•	“The take home massage is that you would just need to identify the better parent of a cross and select for the allele of the better parent”
o	this is not a novel assumption
Additional comments: Introduction: General comments
•	Explain abbreviations within the introduction
•	Be consistent with the abbreviations, is it LA or is it LA SRC (65-67)
•	Your introduction is quite detailed concerning the traits under investigation but you do not write anything about QTL mapping in your introduction
•	Please include a section about QTL mapping, population size, model selection, choice of parents for crosses in your introduction

Material and Methods: General comments
•	M&M in general is quite short
•	115: it is not evident, if you had 2 replications in 2004 (in 127 you say you pooled the grain samples of both reps in 2004), please be more precise
•	121: is Pioneer 26R46 still the cultivar with the highest quality in soft winter wheat? Be more precise and critical with the choice of parents at that time when the population was constructed, especially, because your population you are using is quite old.
•	137: Phenotypic means? To my knowledge, this is not a statistical term, please explain how you calculated means. Why did you not use LSmeans calculated in SAS, this is statistically verified
•	140: please check punctuation
•	143: and environment
•	146: formula does not fit to the results, include environment
•	159: please check punctuation
•	165 please check grammar

Results: General comments
•	170: either include figure in supplementary data, or delete the sentence, if you do not show the data then you cannot prove your statement
•	182-184: part of discussion

Discussion: General comments
•	222: eight chromosomes
•	241: Language
•	271: which trait?
•	Further Conclusion within the discussion are missing
•

Table 1, Table 2:
•	Please sort traits in alphabetic order
•	Please have the same number of digits after the value column wise


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: QUANTITATIVE TRAIT LOCI ASSOCIATED WITH SOFT WHEAT QUALITY IN A CROSS OF GOOD BY MODERATE QUALITY PARENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1. The manuscript is well written and readable. However please correct the subject -verb or subject article agreements as in line 74; 76, 104; 151, 169,
2. Table 1: should include the best RILs
3. Include the association of quality traits with agronomic traits in the result section
4. In Table 4, I could not see the columns for the years though it is titled across years. It should be average over the years.
5. List the best transgressive RILs in terms of quality as compared to the best check.
6. Show the frequency distribution in graph of  the RILS in relation to the two parents for the important traits such as FY, FP, LA.
Experimental design: characterize the environments ( soil type, PH, Temperature, rainfall)  in a Table as these factors affect quality traits in wheat. .
Validity of the findings: The experiment confirms the importance of chromosome 1B and 2B for soft wheat quality.  It also reports the identification of new QTLs on chromosome 1A.

However, this should be validated further.
Additional comments: 1. The abstract is too long.  Please summarize it and just indicate the important part of your methodology, key findings and recommendations.
2. In the discussion part, please review  the list of previously reported genes and references in a Table.
3. Check again some of the missing words/articles in the sentences.


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: QUANTITATIVE TRAIT LOCI ASSOCIATED WITH SOFT WHEAT QUALITY IN A CROSS OF GOOD BY MODERATE QUALITY PARENTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: In general, the english is fine

please change: trait-marker associatin = marker-trait association
Experimental design: The research question, the population design and especially the choice of markers is not relevant to this time anymore
Validity of the findings: no comment
Additional comments: no comment