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: BIODIVERSITY AND TEMPORAL PATTERNS OF MACROZOOBENTHOS IN A COAL MINING SUBSIDENCE AREA IN NORTH CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall this is a well-written ms testing clear hypotheses with well-organized structure. The introduction and background clearly set up and justify the study. However, the results section needs significant clarification, and the methods also need some minor clarifications. The raw data only for the the species abundances are included, however, the environmental data has not been made available. Additionally there are a number of minor comments which need addressing, listed in the general comments section.
Experimental design: This ms fits the aims and scope of the journal, and the research question is clearly defined. The analyses seem appropriate, however, I have highlighted some points in the general comments to the author that need to be addressed.
Validity of the findings: The validity of the findings appears to be sound, but clarification in the methods, and a re-written results section is needed to fully evaluate the discussion of the findings.
Data appear to be robust, however, as mentioned in the basic reporting, the environmental data are not included, and there is some confusion about the number of samples and aggregation of environmental data.
Additional comments: 1. Your most important issue is in the results section. There are a number of places where percentages are used, but it is unclear what they are referring to. e.g. L199-200: "...molluscs accounted for 20.59% of the community..." Is this percent referring to numerical density, species richness, biomass? The statistical test also needs to be clarified in the text. e.g. L 206 - I assume this is this Tukey HSD test? please clarify.  There are also some typos and misstated results. e.g. L 225, I believe that "abundance" should actually be "richness".
I recommend including a table of results to help clarify this.

2. Your second most important item is some clarification needed in the methods. Particularly the index of relative importance subsection, and a clarification of the environmental variables used in the CCA.

Specific comments:
L55-56. I disagree with these characteristics applying to all macrozoobenthos. Particularly, the "long life" and "slow movement". Many insect taxa have short generations and have active adult dispersal phases, making them able to rapidly colonize habitats, as you point out in the discussion (L295)
L 107. Species names should be italicized.
L 130-132. Please clarify "broad coastal vegetation". Does this include the 2 species you list, or does it mean something different?
L 133. What is meant by "homogeneous monogenic plant community"? Is this referring to macrophytes, riparian or emergent vegetation?
L 138-139. Please clarify your sampling of environmental variables. If they were only collected in 2 seasons, are the results in table 1 an average between the 2 sampling times? Was there any significant seasonal variation in environmental variables?
L 147. Clarify lowest possible classification unit. e.g. Species or Genus for everything? Species for some groups, other taxonomic level (e.g. Family) for other groups?
L 163-169. Here you describe the equation for the index of relative importance, but I do not see any results of these analyses, or discussion of them. Was this analysis used? If it was, it needs to be clearly articulated in the results section. If not, this subsection needs to be removed.
L179. Here it states that the relationship between the community and environmental factors were assessed using CCA. Which environmental factors were assessed? Table 1 contains 11 variables, but figure 5 only has 4 variables on the plot. Were these 4 variables determined via some model selection? If so, that process needs to be explained. Or if they were the only variables used, this needs to be clearly stated and justified in the methods.
L 192-195. Were only the abundance data averaged? What about biomass and richness data? It's unclear exactly what you're testing here. e.g. "... abundance data were averaged from three ponds and then averaged from four sampling seasons"

Results: as mentioned above, this section needs significant clarification. Please clearly indicate exactly what the percentages are referring to, and which statistical tests are being conducted. I would also recommend clearly defining terms and making them consistent throughout results. For example you mention abundance and density. Are these referring to the same things? Or absolute abundance and relative density?

L 199-202. You state that the main group is molluscs with 14 species and 20.59% of the community, and then say that insects had 48 species and 70.59%. Shouldn't insects be the "main" group then? Or are you defining molluscs as the main group for some other reason?
L 219. I recommend replacing "P=0.000" with "P < 0.001".
L 220. What does "the highest record" refer to?
L 225. You state that the abundances significantly vary, but the P-value for GC is 0.444.
L 227. What does the "highest values" refer to? A specific FFG, or total abundance or richness?
L 233. a P-value of 0.995 for the PR FFG indicates they are not affected.
L 236. Recommend changing sentence to" "Significant changes in SC occured only between MS and LS, where relative densities in MS were significantly higher that those in LS.
L 246. Please clarify which environmental factors were used, or if there was a model selection process to select only the 4 listed in Figure 5.
L 248-249. Is "environmental factor" supposed to be plural? e.g. all factors?
L 246-253. I have a hard time following the results here. Granted, I have little experience with CCA, but a brief explanation of what the eigenvalues, and correlation coefficients represent, and how the percent explanation of variance for the 4 factors were calculated would be helpful.
L 273. Clarify what is meant by "irreversible degraded state".
L 275. What other secondary habitats are you referring to?
L 277. Are there few natural habitats because they have been removed from land use changes, or are there few in general because of homogeneous habitat?
L 277. How are "low-quality ponds" defined
L 298. Clarify what higher density refers to. E.g. higher density than what, LS or IS MSWs?
L 315. there is an extra period after the Cristina et al. 2016 reference.
L 315-317. I don't understand what this sentence means.
L 327-328. This sentence is circular and doesn't make sense. E.g. what is the effect of seasonal changes, and what is it exacerbated by?
L 334. WATERKEYN reference appears to be wrong (authors are all capitalized)


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: BIODIVERSITY AND TEMPORAL PATTERNS OF MACROZOOBENTHOS IN A COAL MINING SUBSIDENCE AREA IN NORTH CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The paper presents the diversity and temporal patterns of macrozoobenthos in coal mining subsidence wetlands. It is a topic of interest to the researchers in the related areas. The findings are interesting to a wide audience and of importance for future development of biodiversity conversation in post-mining landscape. The paper provided sufficient introduction to concepts and citation of relevant literature, and was written in a clear and concise language.

Line 28, 29, 105- change ‘hectares’ to ‘ha’.
Line 65- references should be added in this line.
Line 92- the paper misses a citation for Figure 1. Please add a citation for Figure 1 in this paragraph.
Line 107- two plant species in this line should be italicized.
Line 188- ‘H'’ should be italicized.
Line 219- change ‘subsidence’ to ‘the time of subsidence’.
Line 284, 288, 299- since the paper mainly focused on the macrozoobenthos, the macrozoobenthos list table(at least to famlily level) is very necessary as online APPendix. Please add a citation for the macrozoobenthos list table in this line.
Line 302- change ‘farmland’ to ‘i.e. farmland’.
Line 315- ‘. .’, remove first ‘.’.
Line 317- references should be added in this line.
Line 336- the author described the effect of seasonal precipitation on the water quantity of MSWs. I think the author should add the introduction of precipitation season in the 90 Materials and methods (i.e. Study area).
Some of the figures should be beautified.


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: BIODIVERSITY AND TEMPORAL PATTERNS OF MACROZOOBENTHOS IN A COAL MINING SUBSIDENCE AREA IN NORTH CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have clearly addressed all of my comments and concerns, and I believe that the manuscript is now suitable for publication in PeerJ. However, I have noted a few minor comments below which should be addressed.
Experimental design: No comments
Validity of the findings: No comments.
Additional comments: I recommend adding some description to the figures. Namely clearly indicating what the letters in Figs. 3-5 represent (e.g. Tukey HSD, PERMANOVA, etc).

Please double check that all of the references are correct and consistently reported. e.g. Ref in L 571-573 has title in all caps.

I think there is a small typo in L 405. e.g. "We believe that can we see..."


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: MAT THICKNESS ASSOCIATED WITH DIDYMOSPHENIA GEMINATA AND CYMBELLA SPP. IN THE SOUTHERN RIVERS OF CHILE
Review round: 1
Reviewer: 1

Output:
Basic reporting: Please see attachment.
Experimental design: Please see attachment.
Validity of the findings: Please see attachment.
Additional comments: Please see attachment.


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: MAT THICKNESS ASSOCIATED WITH DIDYMOSPHENIA GEMINATA AND CYMBELLA SPP. IN THE SOUTHERN RIVERS OF CHILE
Review round: 1
Reviewer: 2

Output:
Basic reporting: •  The English in the manuscript will need some editorial work to align single/plural, subject/verb, and editing some unclear statements. Replace weak verbs (i.e. is, are, were, be, etc) with active verbs to bring clarity and improve meaning in each section of the manuscript.  Consider this an important edit. This will add more meaning to each sentence and will help you remove the repetition of ideas.
•  Introduction: The most effective changes you could make to the introduction would be to bring in some literature to build a case for why we might care about mat thickness. Take the time to expand the information you allude to currently in the introduction. The strong case for your study that then emerges from this will draw your reader in more, and even broader the applicability of the study. Consider describing what we know about how mucilaginous mats for Didymo or other species changes flow, nutrient dynamics, insect emergence, and surface area available for epiphytes. Then, what might it mean if a mat is thick or thin.
•  Is there a reason you might prediction interactions between diatom species that produce mucilage? How? Why?  Anything unusual about Didymo here?
• Tables and Figures.  In general these are Okay. Consider the following edits to improve clarity:
         o	Fig. 1. Captions should be stand alone. Be clear what the letters A, C, D represent (Even though it might seem intuitive). Does the black box in B represent the area zoomed in on in A?  Be clear. In (C), doe
         o	Figs 2 and 3. – Italicize genus/species names in axis titles.
         o	Fig. 3. Remove repetition. For example  …   “ Mat thickness as a function of cell density of (A) Cymbella sp. and (B) Didymosphenia.  Dropping one ‘l” in cell does not reduce much space. Instead use both l’s and add the ‘s’. For example “cells/mm3”
         o	Table 1 caption. – Line 3. “The percentage of the importance of a variable….”.  Define your acronyms (for example, what does Vel fond” mean…velocity..??. Not clear what “not participate” means.  Watch your subscripts for things like SiO2. Be consistent with use of capitals vs. small capitals in headings (i.e. MS residuals vs Var. Explained). Be clear that depth represents water column depth
      o	Table 1. Reduce clutter by putting units (like %) in the column header. This will also allow you to right align the numbers to allow for easier comparison between large and small numbers.  Reduce the repeated column labels down to one column (this will also allow easier comparison).
Experimental design: 2.	Experimental Design - needs a few details
•	L92 – You state that each sampling point was “analyzed” – please clarify what it was that you analyzed.
•	L97 – Provide some details for how you subsampled each sample. Typically mucilaginous mats need to be blended. So how confident are you in your subsample. If samples were blended, did you conduct any microscope analysis of the samples prior to subsampling (i.e. to assess where the stalks were attached for each taxon etc.).
•	40x is a pretty low magnification for diatoms (but adequate to identify Cymbella and Didymo cells), so be clear that only the large Cymbella and Didymo cells were identified, but not the others.
•	Since you later try to build the case for an interaction with Cymbella and Didymo, do you have any image evidence to show how Cymbella used Didymo stalks? Did you measure average stalk length in the different mate scenarios?  This might make that argument more convincing.
•	Provide a little more detail for nutrient and other elemental collection and analysis. I.e. were the samples taken near the mats? Above the mats? Below the water surface? Kept cold? Frozen? Analyzed within X number of hours, etc.
Validity of the findings: Results
•	To improve clarity throughout the results, remove repeated phrases and replace “weak” verbs with active verbs. For example….” Of the 36 samples, detection of cells by microscopic counts occurred for D. geminata in 13 river reaches in the spring (___%) and 17 in the autumn (____%), and for Cymbella in 14 river reaches in the spring  (___%)  and 18 in the autumn (___%). However, of the ## of sampling points…..”…etc.
•	Line 138. Report the range of mat thickness for mat >1cm.
•	Line 140:  Clarify what the 36 represents. (The 36 that contained Didymo?? or both? or….  Mats , of a certain thickness…or of the 36 river reach samples??)
•	Results should be in **past tense.
•	It also helps to follow the same “structure” within a paragraph. For example in L144 to 150, it looks like you want to talk about mats with Didymo alone, Cymbella alone, or both together.  Thus, L147 states…..  “…with the absence of both genera….”, so the next sentence, L149 should read “However, each taxon alone (C/A or A/D) did not differ from mats with both taxa absent (A/A) or both present (C/D)”.  Present in this ‘parallel’ fashion throughout the results.  Acronyms can be helpful, but the message is more effective if you refer to the mats with a taxon alone or present together and put the acronyms afterwards if it helps.
•	Lines 144 to 150.  Be clear on mat content. For example. “….in the presence of Cymbella sp. alone…”.
•	Line 152, Add units after the 0.
•	Line 155: “….in the presence of both genera (C/D)
•	Line 153.  Put this summative statement first…then follow with the details.
•	Line 162 – Move the interpretation of the results to the discussion.
Discussion
•	The discussion needs more literature comparison. This lack of discussion with other literature weakens the strength of this section and reduces the breadth of readers the manuscript might reach. Consider this a one of your top edits. This section needs some attention.
•	Go through the discussion to align grammar and subject verb agreement. For example. Line 196 –remove the “s” from present or changed to “presented”. It will also help to replace weak verbs (such as is, was, were, etc) with active verbs throughout. (i.e. L197. – just state “In the presence of both taxa, mat thickness doubled. However mats typically occurred as thin (< 0. 5 mm), less visible biofilms with Cymbella sp alone, in contrast with the visible, thicker (median 3 mm) mats more commonly present with D. geminata alone.”
•	You make several bold statements about what you think your data state about Cymbella, but the evidence is not that strong. If you want to make an argument for a few scenarios that might stem for your data, then back the statements up with supporting literature. For example.
o	***L200 Your data does not assess that your Cymbella sp. does not have the ability to produce massive growths. Perhaps it would be helpful to shed some light on your observations here by comparing with the literature. Cymbella can produce mats in other systems, so it certainly is quite capable.
o	L207.  Given that Cymbella was present in thin mats, this implies that they are present in early colonization stages, so it is not clear why you think that Cymbella might not be a colonizer. With respect to a certain cell density required for mat formation – is there some evidence of this in other taxa? A mechanism that might be at work? Etc.
o	You attempt to build a case for the role of mucilage in increasing surface area for Cymbella. Any evidence to support this? The taxa that typically are reported to colonize Didymo stalks are often small (as you mentioned), and very visible under the microscope. Perhaps include an image plate showing stalk structure with Didymo alone, Cymbella alone or both.
Additional comments: The ideas in the manuscript will be of interest to those interested in Didymo and other stalk forming diatoms. Some care editing around language and time spent really setting the stage for the role of mucilage will help
Misc. General
References: Do a careful check for italics of genus and species names (for example Furey et al. ref.;  Ladrera et al. ref.; Kilroy et al. ref.).
Do a spell check for D. geminata vs. D. geminate. If your sentence begins with “D. geminata”, write out Didymosphenia in full (i.e. Line 39 in abstract). Check also for italics (i.e. L 73)
Correct typo in title (…associated..)
Replace the word “community” with algal biofilm (or some other word) if you are only referencing algae. Community suggests more than one trophic level. (I.e. Methods – L92.


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: MAT THICKNESS ASSOCIATED WITH DIDYMOSPHENIA GEMINATA AND CYMBELLA SPP. IN THE SOUTHERN RIVERS OF CHILE
Review round: 1
Reviewer: 3

Output:
Basic reporting: The reporting is professional with some minor grammatical issues, otherwise this paper is well thought out and written. Please correct. See the list.

Minor grammatical issues:
1.	Line 47 D. geminate is misspelled should be geminata
2.	Line 53 mats producers should mat producers
3.	Line 61 Cymbella should be italic.
4.	Line 65 Cymbella should be italic.
5.	Line 86 – on two occasions
6.	Line 126 D. geminate is misspelled should be geminata
7.	Line 127 one and two way ANOVAs were…..
8.	Line 195 Spell out Didymosphenia
9.	Line 199-200 correct grammar.
10.	Line 201 due should be do
11.	Line 213 doubles should be double
12.	Lines 237-238 I would not use dashes after the numbers.
13.	Line 239 thick should be thickness check grammar.
14.	Check all taxa to ensure the names are italic.

Question: Were there any dams or impediments upstream from the blooms? Were the rivers regulated in any way?
Experimental design: The experimental design is appropriate.
1. The methods can be replicated.
2. The research question is relevant and interesting.
3. The methods are described sufficiently.
4. Very nice maps and details.
Validity of the findings: Data is sufficient and related to the authors questions. Question - What Cymbella taxa did you find in the different location samples?

Data is robust and sound.
Additional comments: Important issues:
1.	Recommend a couple of images of Didymosphenia geminata and Cymbella sp. cells. LM and only if possible SEM if available.
2.	Recommend 1 or 2 photos of the mucilaginous stalks laid out or being held to see the length and 1 photo of the stalks on the rocks.
3.	Why Cymbella sp.? Can’t you ID the different species? Don’t make sp. italic if you continue to use sp.
4.	Recommend that you use sp. only when you are unsure of the species (Khan-Bureau at al. 2014).
5.	I would recommend to write Cymbella taxa instead of sp. unless you do not know which Cymbella species are present.
6.	Boulders – you may want to say how large those boulders are. This is why I would have a photo.
7.	It is important to distinguish the Cymbella taxa. You could also mention whether the Cymbella taxa that you studied are native and which taxa are not.
8.	 Were all the Cymbella taxa that were mentioned found in all of the samples? If not distinguish which Cymbella taxa were in the different samples.

This paper is interesting and appears that the experimental design and methodology is appropriate.
I find your conclusions regarding water temperature and nutrients interesting. Typically Cymbella janischii or Cymbella taxa blooms at different times under different conditions than D. geminata. (Khan-Bureau et al. 2014, 2016) However with that said habitat are diverse and continually changing (i.e. climate change and adaptation etc.). I do agree that further work needs to be done to determine if your conclusions of mucilage production are representative of river systems with the presence of both D. geminata and Cymbella taxa.

Please correct your use of sp. in your manuscript. Sp. is used when a species cannot be verified although can be identified to genus level. Some scientists use cf. when comparing like species. I recommend that you distinguish which Cymbella taxa were found in each sample and recommend writing Cymbella taxa instead of Cymbella sp. I recommend that you provide a photo of the mucilaginous stalks of Didymosphenia geminata with Cymbella taxa on the same rock, substrate or location. I recommend that you have LM and if possible SEM images of D. geminata and Cymbella taxa cells. These items should be corrected prior to acceptance.


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

Input:
Title: MAT THICKNESS ASSOCIATED WITH DIDYMOSPHENIA GEMINATA AND CYMBELLA SPP. IN THE SOUTHERN RIVERS OF CHILE
Review round: 2
Reviewer: 1

Output:
Basic reporting: While the questions addressed in this manuscript are interesting, it suffers from a poor translation into English.  With the Introduction, Methods, and Results I have tried to make as many grammatical comments as I could.  But with the Discussion I had a very hard time following the author’s points and I did not want to inadvertently change the intended meaning of the text.  Rather, you will need a friendly reader to go over that section to clarify your points.  Until then, I am not able to fully judge the merits of this paper.  Given the very short turnaround time given to review this manuscript, this is the best I could do.
The Intro seems well-referenced with many of the latest related studies.  Although at one point the author mentions that no studies have been conducted on the stalk production for the genus Cymbella- While I cannot provide additional references, I believe that such papers exist and would encourage the authors to try another search to find them.
The overall structure of the paper seems fine.
The figures and tables seem good in general.  I have made some comments below on a few specific points.
The raw data provided seem in order and appear to support at least the main points (as I understand them) of the manuscript.
Experimental design: This work is original and within the scope of the journal.  The research question is interesting, well defined, relevant and meaningful. The methodology seems sufficiently rigorous.  And the method (in most cases) are provided with enough details to replicate the findings.
Validity of the findings: As a reviewer, I had trouble (due to poor application of English grammar) assessing some of these points.  But in general, the authors took an interesting approach to an understudied natural phenomenon that could lead to management implications.
Additional comments: -It is clear that a lot of work went into the development of this manuscript.  I am hopeful that the English language can be improved so that some of your conclusions can be more clearly understood by a wider audience.  This manuscript would benefit by the authors going over it again with an English editor.  In many sections, I am not always sure of the authors intent and so I am reluctant to suggest edits that might change the author’s meaning.
-The way you cite references in the text is not standardized and often has many mistakes.  If you are citing a paper with more than three authors use et al. after the first author!
-Please explain in the method why these specific rivers were chosen for the study.  How typical are these rivers to others in the region?  Do other rivers seem to have more or less Didymo associated with them?  Why or why not?  Were the same sites samples during spring and fall?
-please provide more details on how the algae samples were actually collected.  As written, I do not understand the procedure at all.
-Please provide more statistical information.  Include the type of permutations used along with the software (including version) used.
-In most cases, when giving the mean value of a parameter you have measured, its range should also be reported.
-you mention total richness of taxa in the results but we need more details on how this was calculated in the methods.  What was the minimum number of algal cells counted before it was determined a taxa was absent?  Were other taxa identified and counted to determine the “total richness”?  If so, how many were counted?  If not, do not call this variable “total richness”.
Specific comments:
Line 18- change to “have shown chemical…”
Line 26- change to “… sites with Cymbella spp. Presence showed a spring maximum.”
Line 38-change to “…mats can…”
Line 41- change to (Bray et al., 2017) but also check this reference since as reported it is not in the literature cited.
Line 45- change to Larned et al, 2011)
Line 47-48- I cannot tell what you are trying to say with this sentence.
Line 49- suggest changing to “the presence of nitrogen-fixing cyanobacteria (Novis et al, 2016) and levels of dissolved reactive phosphorus (Bothwell et al., 2014 and Bray et al., 2017) would favor D. geminata blooms…”
Line 55- “This problem” –not sure what you mean.  “who have begun to warn by others possible bloom maker microalgae”-I have no idea what this means.  Please clarify.
Line 61- change to “been reported”…
Line 91-94-“one algal sample of 1ml of mat was taken”-Did you mean to report an area (such as 1cm2) here instead of a volume?  I don’t understand this.  Please elaborate on these methods!  Within a reach, how was the specific site(s) selected?  This is especially important since it seems that in some cases just one sample was taken for an entire river reach.  Please clarify the information for the rest of this passage and give a final concentration for the Lugol’s solution in the samples.
Line 105-change to “the laboratory within 48hours.”
Line 109-My understanding is that there is more than one way to conduct these permutations.  If that is the case please provide more info.  Also be clear about what two dependent factors you are using.
Line 110- Which “non-parametric Tukey test” was used. Please be specific.
Line 115- REML? -please reference any software mentioned- along with the version used.
Line 116-change to “different plots”…
Line 120- delete “in the first place” and change to “To relate physical…”
Line 124-125-  What was the name of the test used?
Line 125-129- As written, these lines are very hard to follow.  The grammar is especially poor here.
Line 134- change to …”evaluated with R2”.  But also need more information here.  What R2s were considered not significant?  Does this need to be justified?
Lines 135-142,  Good! But much of this information should be included as soon as a specific test is first mentioned.  Again, include package version and version of R used.
Line 142- change to “macroscopic photos…)
Line 152-157. Please consider reporting this data as a table rather than in text.
Lines 159-162-Please report if any of these differences were significant.
Lines 162-167.  Was this the twoway ANOVA? If so, were there any significant interactions?
Line 169- change to “inverse relationship”
Line 177-change to “density was always relatively high”…
Line 182- I suggest NOT reporting f-values.
Line 188- change to “detected significant differences…”
Line 215- “total richness of taxa”  How was this calculated?  I don’t think that this was mentioned in the methods.
Figure 1-good figure!  It may be helpful to have the rivers on the map marked with darker lines.  Its hard to see them.


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: PROTEIN SIGNATURES LINKING HISTORY OF MISCARRIAGES AND METABOLIC SYNDROME: A PROTEOMIC STUDY AMONG NORTH INDIAN WOMEN
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: 1. How many patients were included per group - please provide details.
2. Please statistics analysis of these four group of clinical characteristic of patients, including maternal weight, age, height, BMI, blood pressure, etc. in a Table.
3. Please include the internal standard protein (like β-actin or GAPDH) in Western Blot analysis, by the way, if the number of samples is less than three, how can you caculate the P value?
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: PROTEIN SIGNATURES LINKING HISTORY OF MISCARRIAGES AND METABOLIC SYNDROME: A PROTEOMIC STUDY AMONG NORTH INDIAN WOMEN
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The article entitled " Protein signature linking history of miscarriages and metabolic syndrome: A retrospective proteomic study among North Indian women" want to identify the proteins signatures to understand the connection between the history of miscarriage and metabolic syndrome. These results showing some new findings, however, there are several points need to be improved and revised before further consideration.

>The text must rewriting, because current text is too redundant.
-For example, In Abstract
The sections of Background and Methods must be simple and clearly.
The section of Results do not need repeat the words in the text. It is better to describe the key new findings. What is the “in the three case groups”? What is the “in the two case groups”? Which is the control?

>What are the standards for grouping? Miscarriage and MeS based on what? Must give more information to explanation.

>The quality of 2-DE gel needs to improve, for current image it’s hard to say about the accuracy of the results.

>The number of the differentially expressed proteins is too few; I cannot concluded any significance thighs from Fig3.

>Why the western blot in Fig6 have any control band? The results of validation are not right. In the other hand, the quality of the blot is very low.

>Table 2
This table must give the p-value of each differential expression result.


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: PROTEIN SIGNATURES LINKING HISTORY OF MISCARRIAGES AND METABOLIC SYNDROME: A PROTEOMIC STUDY AMONG NORTH INDIAN WOMEN
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is very well written and clear.  The authors have conducted the right experiments to support their hypothesis and cited appropriate references throughout the manuscript.
Experimental design: The experimental design of the study is appropriate and well thought. The methods reported in manuscript is well described.
Validity of the findings: Data reported in manuscript is meaningful. The study reports proper control and replicates.
Additional comments: In this study, entitled "Protein signature linking history of miscarriages and metabolic syndrome: A retrospective proteomic study among North Indian women" authors investigate the presence of protein signatures in premenopausal women cohorts. The authors undertook 2D-gel electrophoresis and mass spectrometry approach to determine the differential expressed proteins in experimental and control cohorts. Based on the data provided authors suggest that, they have identified 18 differentially expressed proteins in experimental groups and they have also validated the up regulated TTR by various protein assays. The study is significant in profiling the protein signatures on human samples of miscarriage and metabolic syndrome, however following things need to be addressed before publication

1: There is no term like single Mendelian Population. Author should change it to “Mendelian population of same gene pool”.

2: In figure 6, it is not clear whether the authors have compared group A with other three groups or three experimental groups are compared with control group (Group B). Figure legend needs restructuring.

3: Did authors follow up on individuals with increased TTR for their cardio vascular parameters? It is important to know if they show such sign of CVD disorder.

4: Discussion section is too long. It can be shorten a bit.

5: While citing fig in manuscript author should follow one consistent pattern of as advised by journal guidelines. Presently, both round brackets (... ) and square brackets [... ] are used.


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: PROTEIN SIGNATURES LINKING HISTORY OF MISCARRIAGES AND METABOLIC SYNDROME: A PROTEOMIC STUDY AMONG NORTH INDIAN WOMEN
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors not address all my concern and questions.


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: PROTEIN SIGNATURES LINKING HISTORY OF MISCARRIAGES AND METABOLIC SYNDROME: A PROTEOMIC STUDY AMONG NORTH INDIAN WOMEN
Review round: 2
Reviewer: 2

Output:
Basic reporting: No Comments
Experimental design: No Comments
Validity of the findings: No Comments
Additional comments: The authors have done a commendable job in answering this reviewer questions and in revising the manuscript. No more 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: PROTEIN SIGNATURES LINKING HISTORY OF MISCARRIAGES AND METABOLIC SYNDROME: A PROTEOMIC STUDY AMONG NORTH INDIAN WOMEN
Review round: 3
Reviewer: 1

Output:
Basic reporting: accept
Experimental design: accept
Validity of the findings: accept
Additional comments: accept


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: EMBRACING HETEROGENEITY: COALESCING THE TREE OF LIFE AND THE FUTURE OF PHYLOGENOMICS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Fulfills all standards
Experimental design: Fulfills all standards
Validity of the findings: Fulfills all standards
Additional comments: Resulting from an international Tree of Life workshop, the authors give a “state of the field” address, and summarize current issues, developments, and future avenues for phylogenomics. In some ways, they are simply summarizing what is common knowledge among in-depth practitioners in the field, but I think such a summary will probably serve as a useful introduction for students, and a touchstone citation for those needing to refer to myriad issues that “everyone knows,” but are often lacking from the literature.

There are a few places where I disagree with how the authors characterize certain issues (some are listed below), and I suspect that most readers will feel this way about certain parts. This is probably endemic to a large group effort to summarize an entire field, and isn’t necessarily a condemnation of the authors. Three criticisms in particular:

1) The authors focus heavily on how population-genetic processes affect phylogenetic inference, but not as much on the nature of the pop-gen processes themselves, or how they arise in natural populations and interact with our conception of species and speciation.

2) The authors don’t take a broad time horizon. Despite talking about the Tree of Life, they focus mostly on the present day, with little discussion of fossils, ancient DNA, or paleobiology. This is consistent with a focus on genomics, but doesn’t represent the whole of the Tree of Life.

3) The authors state problems that face our collective efforts, but don’t really address the underlying structural issues that give rise to those problems, such as institutionalized focus on impact in developing nations and many western institutions. Some parts read simply as a list of problems, and then the statement “this should change!” What concrete steps could we take to, for instance, foster an international dedication to free and open data sharing, while preserving novelty and impact for new datasets?

Specific sentences that might be improved:

"Phylogenomics and macroevolution represent two ends of a research spectrum, with one end focusing on building phylogenies and the other end on using them.”

This statement seems problematic; I don’t think most researchers would find any dichotomy or opposition between phylogenetic inference and phylogenetic comparative methods. They are also very close to each other compared to, say, macro ecology. Could this be phrased differently?

"More generally, evolutionary biologists have not yet thought much about the type of new questions that we are going to be able to address if we are given genomic data at the tips of all species from a phylogeny.”

This also seems unwarranted; I’m certain that very many people have thought very deeply about this. Perhaps its more accurate to say that a large literature does not exist to give a framework for this perspective?

"While such approaches elicit a culture clash between those who laboriously build trees and those that simply use them, there are other approaches stemming from macroevolution that are less offending to phylogeny builders.”

Again, I’m not exactly sure what the authors are trying to say here, but perhaps it could be phrased more delicately? First, I’m not sure that there’s a huge divide between “builders” and “users;” certainly, they are commonly the same group, with very few people assuming only one of those labels. Second, it seems like the authors are implying that Jetz, Tonini, and Kuhn are “users,” and that imputation offends “builders?” I assure you that all three groups are builders; Tonini was my doctoral student, and my lab is known for building trees if nothing else. Imputation is simply a stop-gap measure to make full-scale phylogenetic datasets available for “use” in a way that compartmentalizes phylogenetic error to the taxonomic level.

Perhaps I’ve misunderstood the intent here, but it could be written differently?

Finally, in this section the authors mention extinct species, but there’s very little, if any discussion devoted to fossil-bearing trees, or tip-dating. The authors might discuss Pyron (2011), Ronquist et al. (2012), or many of the recent Slater, Matzke, and Wright papers on including fossil tips in molecular phylogenies to estimate the “true” Tree of Life through time, and not simply the present-day living slice. I realize this is a paper on genomics, but researchers will still want fossil-bearing trees even with genomic data. The authors mention DNA from old museum specimens; this begs discussion of ancient DNA and potential fossil-genomics.

Finally, I’m a bit confused by the Dickens quote to open, which refers to the French Revolution and Robespierre’s Reign of Terror. Is this really the worst of times for phylogenomics? Or do we simply have a surfeit of data that we haven’t quite figured out how to exploit fully? Do the authors plan on throwing off the shackles of an entrenched aristocracy and leading royals to the guillotine? If not, perhaps another quote is better?

Perhaps Shakespeare’s _The Tempest_: For phylogenomics, “hell is empty, and all the devils are here!”

Or Mark Twain’s _The Horse’s Tale_: “Herodotus says 'Very few things happen at the right time, and the rest do not happen at all. The conscientious historian will correct these defects.’"


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: EMBRACING HETEROGENEITY: COALESCING THE TREE OF LIFE AND THE FUTURE OF PHYLOGENOMICS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This perspectives piece on “Embracing heterogeneity: Building the tree of life and the future of phylogenomics” provides well rounded summary on current approaches and limitations in phylogenomics and proposes areas of research that need development over the next few years. It will appeal broadly to those working in the field of phylogenomics.
Overall the perspectives piece is well balanced, written and referenced. It gives a good overview of the field and thus I have no major criticisms to offer.

Instead I have some minor comments which will help with the overall readability as well as minor comments on specific examples/topics which could be expanded or included.
Experimental design: no comment as this is a perspectives piece.
Validity of the findings: no comment as this is a perspectives piece.
Additional comments: •	The introduction [57-102] is verbose and needs further editing so that it is more concise and better summarises the topics will be discussed for the remainder of the perspectives piece.
•	The survey methodology paragraph is not necessary as the details are covered in the acknowledgments.
•	There are several acronyms used throughout this perspectives (ILS, MSC, GDL, ARG, and HTS) which makes the content difficult to quickly digest for the reader. A standalone text box that summarises the main acronyms used in the paper would be a helpful addition.

•	III data generation and data types in phylogenomics [114-170]. This section does not follow the title heading. A discussion on collection of data types and sequencing approaches was expected but instead the paragraph vaguely discusses taxon versus marker size. Editing this section so that it more adequately reflects what is about to be discussed in the sub headings is advised.
•	The statement referring to “large-scale phylogenetic trees are cobbled together from disparate existing sources, even taxonomy, but often without hard data being the placement of many species” needs further clarity [122-125]. It is generally acquisitive without clear examples from the literature.
•	A comment on technical errors that accumulate in sequences due to different sequencing chemistries is advised as well as commenting on varied sequencing depths across species which impacts the ability to reconstruct the genome and reliably call nucleotides.

•	Data generation and marker development [171-278].
Avoid using the word “impossible” in the following statement “the non-coding genome is difficult if not impossible to align and analyse” [line 183-184]. The MultiZ vertebrate alignments available through Ensembl and UCSC demonstrate that alignments of reasonable proportions of the non-coding regions are possible. Rather than focusing on what cannot be done now, the authors could discuss advances that are underway in understanding the genetic code of the non-coding genome and mention that it will take development of new methods and approaches to interpret the evolutionary history of these genomic regions. For example, while there is low levels of sequence conservation, regulatory conservation and conserved 3D structures show higher levels of conservation and could be used for comparative genomics purposes in the future (see Berthelot C et al 2018,doi:10.1038/s41559-017-0377-2, Villard D et al 2015 (doi: 10.1016/j.cell.2015.01.006) and Pope et al 2014 doi:10.1038/nature13986).
•	An expanded comment on the limitations of transcriptomic data is needed [185].  One of the major shortcomings is that the transcriptome is subject to tissue specific splicing and tissue specific expression making it difficult to compare across species.

•	More taxa versus more loci [238 - 276]. In this section while the authors mention that there will be a jump in the size of phylogenetic datasets, they do not give specific examples of some of the ongoing efforts to increase WGS of taxa e.g. Genome 10K or the BGIs plans to sequence 1 million plant, animal and micro-ecosystem genomes.

•	Filtering heterogeneous phylogenomic data sets [277]. Mention that balanced taxon sampling will help overcome the effect of outliers.
•	Furthermore, there are systematic methods available to detect spurious species (see work by Siu-Ting et al (2015) https://doi.org/10.1093/sysbio/syu066)

•	Heterogeneity and Intra individual state polymorphisms [295-378]. The authors discuss markers of phylogenetics which could include rare genomic changes, gene order and synteny, indels and transposition and copy number variations. It would be beneficial here to mention the benefits in congruence across multiple markers. (Rota-Stabelli et al (2011) discusses this ( doi:  10.1098/rspb.2010.0590))

Finally, it would be beneficial to comment on recent specific examples in HTS. PacBio provides long reads which will significantly improve our ability to identify large structural changes in genomes. Advances in sequencing technology such as the HiSeq X or NovaSeq allow for a significant reduction in cost of sequencing which can result in more taxa at a higher coverage. Finally, the Naopore is as hand held device which can be used in the field. These technical advances will have a significant impact on the increase in genomic loci and taxa available for reconstruction of the tree of life.


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: EMBRACING HETEROGENEITY: COALESCING THE TREE OF LIFE AND THE FUTURE OF PHYLOGENOMICS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The review is an extensive and very broad overview of genomic data and the development of Multiple Species Coalescent models, with a particular focus in its uses in biodiversity research (species delimitation, phylogeography and species sampling) in phylogenomics. I think it is timely and it will be of interest mainly to biologists and bioinformaticians that have certain base knowledge of the methods (I wouldn’t say it is intended for a novice audience). It is within the scope of the journal (as a Literature review).

There has been a few recent reviews on this topic, but more into the actual phylogenomics methods (supertrees, supermatrix and models of nucleotide substitution in phylogenetics). The present review focuses primarily on multispecies coalescent models, and in this particular topic there is another recent review (more like a opinion piece) made by one of the authors (S. Edwards) published in Molecular Phylogenetics and Evolution in 2016 (https://doi.org/10.1016/j.ympev.2015.10.027). But the focus of both differ substantially, with the 2016 paper addressing a criticism made by other authors on transcriptomic used in MSC and current work being an actual literature review.

The authors address who their target audience is and their motivation for the paper. The only criticism I could raise on this point is that it is not entirely clear who they mean in the phylogenomics community, as the paper mainly concerns the Multispecies Coalescent model. For a phylogenomics review, I feel that this is lacking of a very important component: the traditional methods and the vast number of models that have been made in this topic of research, as well as other latest developments in different aspects that are of importance to current phylogenomic analyses (alignments and supermatrices methods of phylogenetic reconstruction and models used in these). The "Concepts and models in phylogenomics" and “Bypassing full likelihood models by relying on summaries of the coalescent process” sections are heavily focused on Multispecies Coalescent Models, and dismiss the traditional methods and models still very widely used and comprise the vast amount that lead to the field of phylogenomics in the last 15 years. For instance, recent advances in supermatrix models and methods include the use of codon models of evolution in Maximum likelihood (see for example IQ-tree), also there’s the CAT model implemented in Phylobayes (Lartillot and Philippe 2004) with its MPI version; also when talking about heterogenous models of evolution there’s P4 (Foster 2004), just to mention a few. It seems to me they try to “get off the hook” from covering the other methods with the statement: "Our goal is not to provide a complete overview of phylogenomic and phylogeographic research, but rather present a number of conceptual and practical aspects that we feel are essential to keep the momentum that these fields have gained during recent times."  At the moment this statement would mislead an audience that works traditionally with supermatrix methods in phylogenomics, as MSC is not all of phylogenomics. I think it should be stated from the very beginning (including the title and abstract) that the focus of the paper is about the future of multispecies coalescent methods in phylogenomics.

Another point: the use of the term “heterogeneity”. I think this could also lead to some confusion to anyone who works in phylogenomics because there are also heterogenous models of evolution, compositional heterogeneity, site heterogeneity (by the way, neither mentioned in this review). I know, after reading this review, this is not what was meant, but perhaps it would be worth making a small annotation somewhere in the introduction that they do not mean any of these other topics.

Another issue I would raise is that most of the focus of the paper is on evolution at the tips of the tree (or relatively recent divergences), with very little mention on how this could affect deep level evolutionary relationships. In fact, there’s several recent advances (some cited in the first part of this review) addressing deep nodes and their divergence times that even with large-scale data remain controversial. All of these use genomic scale data.

The section on "Tree-free methods of character evolution" - I think it moves the paper out of the scope of phylogenomics here. It's nicely done, don't get me wrong but there’s no relation of this to genomic data and, I just think that it is a bit out of place in an already very broad paper.

In terms of structure and citations, sources are adequately cited and paraphrased as appropriate as far as I could see. The review is mostly well organized into coherent paragraphs and subsections. I would point out here that all the sections starting from “Heterozygosity and Intra-Individual Site Polymorphisms” to “Copy Number Variations” should be listed under a new different subsection with its new name (not Data generation and marker development) where it currently is.
Experimental design: I have no comments.
Validity of the findings: The conclusion identifies unresolved questions and future directions, namely on curation of metadata associated to specimens and sequencing data, potential new ways to integrate other types of data in the future. Having made such a thorough review on the types of genomic data in the beginning, it lacks any mention of it in the end.

In my opinion, the review mainly focuses on 3 topics: Types of genomic data and their caveats (mostly on the MSC), Multiple Species Coalescent models and some potential uses in biogeography and expanding the species sampling in the tree of life. The authors have done a very nice job to collect an exhaustive amount of information and point out numerous aspects in these topics, some very interesting remarks there too, but it feels like they tried to put too many different things together and these are so numerous, that they become inconsequential and lost in the paper (for example the literature review to show the increase in number of loci vs number of species and the other methods that are not MSC). There’s barely any mention of this in the end and it makes me wonder why you would go through such trouble when it is barely mentioned again. In addition to that, the amount of topics is so broad that it becomes a bit difficult for the reader to pin down what are the main messages here. There is an attempt to bring it together, but I missed the point of discussing the different caveats of genomic data along with the methods, and then along with the tree of life. I think there is potential for improvement in connecting those main ideas and rounding this paper.
Additional comments: Overall I think it is a great effort done to try to put together many topics that can impact MSC in phylogenomics, and the future of how this could extend to biodiversity. Many interesting points raised. I am of the opinion it should be published and that it will make a nice contribution to the field of phylogenomics.

I have raised some points above, that are made with the hope that it will improve the manuscript and that it won't be misleading (in reference to dismissing other methods apart from MSC). I have also listed some minor corrections that need to be addressed in an attached pdf.


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

Input:
Title: EMBRACING HETEROGENEITY: COALESCING THE TREE OF LIFE AND THE FUTURE OF PHYLOGENOMICS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I’ve reviewed this again and consulted the other reviews and response, and I still have some lingering reservations about the structure of the review. It would be easy to nitpick a review of this length forever, and I’m not trying to do that. But I still want to re-iterate my concerns, and hope the authors can address some of them.

In no particular order:

First sentence; is it really an embarrassment of riches? Isn’t one of the points made that we lack the full datasets (i.e., whole genomes) that would allow for easy a posteriori marker selection? Do we really need a “snappy” quote in the introduction at all?

The authors stated that they didn’t want to review population genetic processes, because they are focusing on phylogenomics. However, as noted by another reviewer, it seems like they want to have it both ways. The authors talk about how these processes might mislead phylogenomic analyses, AND they talk about species delimitation and concepts. Yet, they still don’t discuss HOW the population-genetic processes interact to bridge these scales. There’s a lot of talk about the population-phylogeography-phylogeny continuum, but it comes off as a bit shallow since the actual mechanistic effects aren’t introduced to link HOW population processes actually affect genealogical signal.

Related to the above, the citation patterns are a bit odd; not citing Avise et al. 1987 or Edwards and Beerli 2000 (among other classics) in the intro section, but waiting until much later.

Also related to (2), the authors focus on the MSC because it forms the basis of many current methods, but that’s a small slice of the relevant pop-gen literature. I also feel like there’s not a detailed enough description, again, of HOW the various pop-gen processes mentioned actually affect the outcome of these methods. Part of that is due to it not being known. But it leaves the reader wanting, I think, for a fuller understanding.

The issue regarding pop gen and the MSC is part of a larger issue here, I think, which is that the authors are trying to summarize too broad a range of material, without sufficient depth in parts of it. I realize this piece originated from a wide-ranging workshop, but the really valuable depth is concentrated in a few sections, while the other leave much to be desired. My main suggestion here is to consider trimming several of them. I’ll highlight the ones that seem, to me, to be most superfluous:

3.3.2-3.3.3: This material is rapidly becoming irrelevant as we move closer to whole genomes. It also illustrates the false dichotomy of taxa vs loci, as the number of loci is fixed (i.e., the genome), and is being rapidly approached.

3.3.4: it seems like there’s very little detail or depth here; the latter part is simply a list of methods and citations with no discussion of how they function.

3.5 This short section again just simply lists several sequencing technologies…

Section 4-4.3: THIS is the really valuable meat of the review. There’s a lot of detailed information here, reflecting the expertise of the authors. I found this whole section to be immensely valuable; just reading through it during review has already changed my perception of the direction of the field, illuminated some patterns in my own datasets, and altered the course of my research program.

Section 5: This material seems disconnected from phylogenomics, and is primarily just reiterating information found in numerous other reviews. The only exception is 5.1, talking about genomes and phenotypes. But do we really need another review discussing OU and BM models?

Section 6: This is a high-variance section for importance and quality. For one, the authors are still criticizing data imputation for building large trees, but then champion the Open Tree of Life, which is imputed!

6.3 what does mapping have to do with phylogenomics?

6.4.1 This section has a lot of sentences that seem obvious and redundant, without offering much that is new for this review. For instance: "In general, we advocate for following best practices of data management and publication to ensure the quality and utility of phylogenomic data and their associated biological information (see Costello & Wieczorek, 2014 for a review).”

Do we really need a sentence where the authors say that they feel practitioners in the field should follow best practices? Was that in question?

Similarly, and I don’t want to seem petty, but: "Recent genomic techniques now allow successful results in obtaining valuable DNA data from museum specimens (e.g., Staats et al., 2013; Hykin, Bi & McGuire, 2015; McCormack, Tsai &mFaircloth, 2016; McCormack et al., 2017; Ruane & Austin, 2017), and here, we advocate for routine use of these resources to enhance research in phylogenomics and phylogeography and increase awareness and usefulness of natural history collections.”

This sentence just says that biodiversity scientists should use available natural history collections and molecular methods to conduct phylogenomic research… Does that really need to be said?

I feel like my original concern still stands; that this section is a list of “good ideas” without any good ideas; there are few, if any, really strong suggestions for HOW any of these problems should be addressed.

It’s also unclear how this relates to the MSC and phylogenomics; it’s almost as if there are two or three distinct, almost unconnected reviews being conducted simultaneously. The section 6 material is certainly not reflected in the abstract or the introduction.

My suggestion would be to trim a great deal of material, focusing on developing Sections 1, 2, and 4. I don’t want to stand in the way of this publication; I’m not trying to stall it out. Hopefully, editorial guidance will provide a clear path forward.


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: EMBRACING HETEROGENEITY: COALESCING THE TREE OF LIFE AND THE FUTURE OF PHYLOGENOMICS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The article has improved from the previous version I read. I think it reads more clearly, and the new sections that they have organised it into helps to group the topics better. I like the box with definitions added.
Experimental design: No comment.
Validity of the findings: My opinion is that the article just needs a few minor things to modify/ address before being accepted for publication.

1) First sentence: "Phylogenomics, the practice and molecular methods focused on building the Tree of Life (ToL), is currently suffering from an embarrassment of riches. " -- Well, I guess this is the authors' choice, but I wouldn't see having so many options in phylogenetics methods and data a hindrance, on the contrary, that's how scientific rigour should be!

2) P11: "This a posteriori selection would be carried out after assessing desired phylogenetic and biological properties of a wide array of markers for which the data are already in hand." -- Just to make it all homogenous, and as done with the "a priori" and in the response to the review, you should add the small definition here with parenthesis after a posteriori, i.e: "a posteriori (after data generation)".

3) P12 end - P13 top: "Some researchers favor “horizontal” data matrices, wherein the number of loci far exceeds the number of taxa, whereas other researchers favor “vertical” matrices, where many taxa are analyzed at just a few (1-5) loci. Whereas the PCR era of phylogenetics was often dominated by vertical matrices, HTS is allowing data matrices to become more horizontal (Fig. 2)"  -- It would be good if the authors added just a statement about the problems that this brings with missing data issues and poor overlap all contributing to either misleading or poor phylogenetic resolution, given the numerous discussions revolving this issue across all phylogenetics.

4) P23 - "loci consistent with the MSC model can be identified (e.g., separated from loci with horizontal gene transfer) using the CLASSIPHY (Huang et al., 2017). "  -- Looks like the word "the" before "CLASSIFY" is redundant, or did you miss something here?

5) P37 - "Another point of possible improvement is in dealing with new sequences to be added to a previously large dataset: should the analysis start from scratch, or could there be substantial time gains by letting those sequences find their placement in the phylogeny ‘on the fly’ (e.g., Siu-Ting et al., 2014)?"  -- Sentence should end in "."

6) Figure 3 legend. "This implies that tree building without considering the multispecies coalescent could, in this case, lead to erroneous estimation of tree topology and divergence times."  --  There is an issue with the last sentence here, it doesn't follow logically from what is explained in the rest of this caption, which is all about violations to the MSC. I would suggest removing it.

7) typo of of the word "homoeologous" in several instances.

8) Authors should check that all citations in the text are included under the Literature Reference list.

9) In my last review, I raised the following issue:

"Another issue I would raise is that most of the focus of the paper is on evolution at the tips of the tree (or relatively recent divergences), with very little mention on how this could affect deep level evolutionary relationships. In fact, there’s several recent advances (some cited in the first part of this review) addressing deep nodes and their divergence times that even with large-scale data remain controversial. All of these use genomic scale data."

Response received from authors: "Following a similar comment by reviewer # 1, we have now added a section extinct taxa, fossils, and tip dating to cover that dimension that is beyond the reach of genomic data. We focus this paragraph on how the integration of both sources of data can be used toward the Tree of Life."

-- I would like to clarify that I did not mean any of the issues that you mention in the response and that you have now added as a new section (namely including fossils and unsampled taxa). I actually meant that what was lacking was a mention of how useful could including genome data, or including more genes or more taxa used in a MSC context actually help when addressing deep nodes in the ToL. Is it applicable to use at that level of divergence (deep nodes)? Numerous studies which you have cited in your introduction and section 3.3 (and works that these papers cite) feature these unresolved/disputed areas in the ToL (for example the sister group to animals, the sister group to arthropods, the position of turtles in the reptile+bird group, just to name a few) in spite of the increasing amount of data that these works include (i.e. either more taxa sampled or more genes included). I think that this is missing somewhere here in the review, and it could be a pertinent point to add in the 3.3 section, perhaps in the "3.3.3 More taxa versus more loci" or the "3.3.4 Filtering heterogeneous phylogenomic data sets" sections of this paper.
Additional comments: The article has improved from the previous version I read. They have addressed the majority of my questions and comments and what perhaps was my biggest concern, which was to clarify the audience and the type of methods they intended to cover (mainly phylogenomics and mostly in the realms of MSC). I think it will make a great contribution to the current literature in phylogenomics as it addresses pertinent and timely problems. It's nearly there, just a few minor things that in my opinion will improve 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: ADDITIONAL SAUROPOD DINOSAUR MATERIAL FROM THE CALLOVIAN OXFORD CLAY FORMATION, PETERBOROUGH, UK: EVIDENCE FOR HIGHER SAUROPOD DIVERSITY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is generally well-written and structured. There are a number of unsubstantiated statements in the Introduction which require adding in some references, and some identifications of previously described remains are outdated (i.e. there is more recent literature re-interpreting the affinities of these elements).
Experimental design: No comment
Validity of the findings: Please see General comments for the author
Additional comments: This manuscript describes two previously unpublished sauropod caudal vertebra from the late Middle Jurassic of the UK. Our knowledge of sauropods from that time interval is generally poor, and so although these specimens are incomplete, this is still a welcome contribution. Currently we have no unambiguous evidence for the derived sauropod clade Neosauropoda in sediments older than the Late Jurassic, and yet this MS presents evidence that these two caudal vertebrae belong to the neosauropod clade Diplodocoidea. I think that the Description and Figures are good and detailed, and the paper is generally well-written, but I have a number of issues with the content. The main ones are summarised below, and I have also provided an annotated PDF of the MS.

(1) I think the authors should be cautious about interpreting these remains as a neosauropod, given that we have no unambiguous record of this clade pre-Late Jurassic (see comment #2), and that the two vertebrae are highly incomplete. Although some features do indeed seem to suggest that these remains could represent a neosauropod (e.g. a ventral keel and shallow lateral fossa on the anterior caudal; ventrolateral ridges on middle caudal centra), I would still be a little wary of this interpretation. An anterior caudal centrum of the Middle Jurassic non-neosauropod eusauropod ‘Bothriospondylus madgascariensis’ also has a subtle midline ventral keel and lateral fossa, for example. The Chinese Middle Jurassic mamenchisaurid Chuanjiesaurus also has ventrolateral ridges in some of its middle caudal centra.

One feature used to support diplodocoid affinities is: “the high projection on the neural arch of the diapophyseal laminae suggest the existence of a ‘shoulder’, which would make the transverse processes wing-shaped”. However, I don't think that you can make this inference based on what's preserved: for it to be wing-shaped, the dorsal margin of the rib should be deflected such that it has a dorsolaterally oriented dorsal margin.

In addition, the data matrix used is primarily focused on evaluating the phylogenetic interrelationships of diplodocid sauropods, and so this is not really the most appropriate matrix to use to try and determine the placement of new specimens. It would be much better to use a matrix that includes a wide array of sauropod taxa (and thus characters) from across the tree (e.g. the most recent Carballido matrix [Patagotitan]). If analysis of that matrix indicates diplodocoid affinities, then it would be appropriate to incorporate it into a diplodocoid-focussed matrix.  Finally, if you are to include it in a diplodocoid-focussed matrix, the more recent Tschopp and Mateus (2017) matrix (Galeamopus paper) would be better as it includes a wider array of diplodocoid taxa, as well as updated scores.

I should clarify that I have no problem with neosauropods being present in the Middle Jurassic: these newly described remains might well belong to that clade. Given that we have derived members of Neosauropoda distributed fairly globally in the Late Jurassic, it’s almost certain that the clade radiated prior to the Late Jurassic. But we should be careful when extending this range back in time, especially when based on very incomplete material.

(2) Throughout the MS, previously described Middle Jurassic sauropods are stated as representing neosauropods (including specimens from the same stratigraphic unit as the newly described vertebrae), but nearly every single instance has been refuted in the literature over the last decade. As such, the authors should be careful that they are reflecting the most recent taxonomic opinions on these often fragmentary specimens. The updated IDs are commented upon in the annotated PDF.

(3) In several places it’s stated that caudal vertebrae have been neglected in phylogenetic studies, e.g. in the Introduction: “Moreover, caudal vertebrae have rarely been given appropriate attention, as only recently have caudal characters begun to be recognized as taxonomically diagnostic (e.g. Mocho et al., 2017; Holwerda & Liston, 2017)” I don't agree with this at all. I think if you look at character lists in recent papers by Carballido, D'Emic, Tschopp, Whitlock and myself (as well as older papers by Wilson, Upchurch, and others), you'll see that there's actually quite a lot of caudal vertebral characters out there, and that such emphasis on this part of the vertebral column didn't begin in 2017. The last sentence of the Discussion states: “This shows the importance of paying close attention to caudal characters, as phylogenetic information might otherwise be missed…”. However, no new caudal characters are devised in this work, and the very fact that you're able to resolve the position of these vertebrae in an existing data matrix, without adding further characters, runs contra to this argument that this work somehow captures information previously missed.

(4) One of the conclusions of this MS is that these and previously described specimens from the Oxford Clay indicate "an equivalent richness of sauropod groups from this Middle Jurassic marine formation, to the classic Late Jurassic terrestrial Morrison, Lourinhã and Tendaguru formations”. This is a bit of a leap! The Oxford Clay has Cetiosauriscus and then a bunch of additional indeterminate remains, at least some of which are different to Cetiosauriscus. But there isn’t evidence for a brachiosaurid (anteriormost caudals) and camarasaurid (a tooth) in the formation – those are outdated identifications (see point 2) – and that distal caudal sequence cannot be confidently attributed to a diplodocid. Furthermore, although the two vertebrae described in this contribution come out in different places in the tree, this doesn’t necessarily mean that they represent different taxa: they’re not overlapping, which makes it less likely that they would cluster together, and certain derived features might only be present in the middle caudal. If you split up any fragmentary taxon and scored two it's vertebrae as separate OTUs they probably wouldn't cluster together. So, I don’t think you have good evidence for lots of taxa in the Oxford Clay – taking a conservative measure, maybe three at most (Cetiosauriscus and two indet. taxa, one of which might be a diplodocoid).

(5) Finally, there are several statements in the Introduction about the timings of sauropod diversifications and the group’s fossil record, but none of these are supported with references.

Best wishes,

Phil Mannion


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

Input:
Title: ADDITIONAL SAUROPOD DINOSAUR MATERIAL FROM THE CALLOVIAN OXFORD CLAY FORMATION, PETERBOROUGH, UK: EVIDENCE FOR HIGHER SAUROPOD DIVERSITY
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a nice, tidy analysis of some interesting isolated specimens: the study is succinct and the analysis and conclusions are well explained and done well.
Experimental design: Everything seems fine and satisfactory.
Validity of the findings: Everything seems clear, well explained etc. See general comments for more.
Additional comments: After analysing the specimens concerned, the authors conclude that several different taxa – belonging to markedly different positions within Sauropoda – are represented. This conclusion may well be valid. But – given that we are talking about isolated caudal vertebrae alone – I would expect there to be at least some brief caveat crediting the possibility that the specimens might not carry sufficient phylogenetic value to justify these conclusions. In other words, there should – in my opinion – be a brief discussion where the authors either add caveats, or credit the possibility that the specimens might possibly be misleading as goes their phylogenetic position, and that one or more of them might actually belong to the same taxon.

The manuscript needs some minor tweaking as goes grammar and sentence structure. There are, for example, a few places where a semi-colon is needed instead of a comma (e.g., line 79), and quite a few sentence where re-wording and re-structuring is advised (e.g., lines 82-86, lines 89-91).

Line 34: I am slightly uneasy these days as goes referring to a taxon as ‘derived’; it has now become shorthand for ‘advanced’ and is not what the authors mean anyway. What they mean, specifically, is that the taxon ‘belongs in a deeply nested position within the clade in question’ (this being Eusauropoda, in this case). See further comments later in this review.

Line 63: taxonomic pedantry… given that pliosaurs are part of Plesiosauria, it can be argued that talking of ‘plesiosaurs and pliosaurs’ is unsatisfactory, and that better wording would be something like ‘pliosaurids, cryptoclidids and other plesiosaurians’. Also, ‘marine crocodylomorphs’ is better than ‘marine crocodiles’ (the animals concerned are not ‘crocodiles’ at all).

Line 87 (and also line 439): the authors who write about Turiasaurus and kin have named the respective clade Turiasauria, not Turiasauridae, meaning that the vernacular term should be either ‘turiasaur’ or ‘turiasaurian’.

Linex 98-100: I don’t think it’s at all true that caudal vertebrae have only recently “been begun to be recognised as … diagnosable”. Look, for example, at the several studies on titanosaurian caudals [Le Loeuff on Iuticosaurus, the discussion provided by Wilson and Upchurch 2003 and so on] and their claimed value in distinguishing taxa. Or… are you specifically referring to material from the Middle Jurassic here?

Line 151: double space present.

Line 164: ‘shallowly concave’ or similar might be better than ‘mildly’ concave.

Line 215: do you need to say that it is “an isolated element” given that the paper is about isolated caudal vertebrae?

Line 286: as a vernacular term, mamenchisaurids should be written with lower case first letter. Rather than describing the specimen as ‘more derived than mamenchisaurids etc..’ (since ‘more derived’ has connotations of ‘more advanced than’), it might be better to describe the specimen’s position with regard to which clade it belongs to. But, in any case, does this description match what you show in the tree? In Fig 4, Cetiosauriscus is not “more derived than mamenchisaurids”: it is part of the same clade, and in fact is a mamenchisaurid according to some phylogenetic definitions of that clade. Or have I missed something? Given that Cetiosauriscus is recovered here as a possible mamenchisaurid, it might be appropriate to cite other studies that found this too: Rauhut et al. (2005) did so, and Naish and Martill (2007) discussed this possibility as a result of Rauhut et al.’s (2005) conclusions. Naish and Martill (2007) should probably be cited somewhere in the present study, given the reviews provided there of Cetiosauriscus and other Oxford Clay sauropods.

Lines 288-290: you describe the position of R272 as being “more derived than Haplocanthosaurus, but basal to Zapalasaurus and all derived neosauropods”. Firstly, I would recommend against saying that any phylogenetic position makes a specimen or taxon “more derived” than another – you mean, instead, that the specimen is more nested within the given clade (Diplodocoidea) than is Haplocanthosaurus. In this case, I would say something like “R272 is recovered as being closer to diplodocids than is Haplocanthosaurus, but outside the clade that includes rebbachisaurids and remaining diplodocoids”. There is a trend in tree descriptions to prefer wording of this sort, and to refer more to tree shape, sister-group relationships and clade membership. Secondly, you’ve recovered R272 as a diplodocoid here (since Diplodocoidea is defined as the branch-based clade that includes all neosauropods closer to Diplodocus than to Saltasaurus… you didn’t include Saltasaurus, but I think we have to assume that Saltasaurus and other titanosaurs would be on the same lineage as Brachiosauridae. You might want to comment on this). In describing R272’s position, you should therefore be describing its position relative to other diplocoids, not other neosauropods.

Lines 295-297: similar comments apply here. Rather than describing the position of G.418.1956.21.0 as “more derived than” etc and “basal to…” etc, I would recommend something like “ we recover G.418.1956.21.0 as part of a clade that includes Barosaurus and Diplodocus but excludes Galeamopus, and as the sister-taxon to a Barosaurus + Kaatedocus clade”. Note that you have not found to be “more basal” than “Barosaurus and all other diplodocids”, as per your description of the tree.

Line 332: I think it’s more typical to use ‘flagellicaudatans’.

Line 413: ‘recovers’ is a better term than ‘retrieves’.

References

Naish, D. & Martill, D. M. 2007. Dinosaurs of Great Britain and the role of the Geological Society of London in their discovery: basal Dinosauria and Saurischia. Journal of the Geological Society, London 164, 493-510.

Rauhut, O. W. M., Remes, K., Fechner, R., Cladera, G. & Puerta, P. 2005. Discovery of a short-necked sauropod dinosaur from the Late Jurassic period of Patagonia. Nature 435, 670-672.

Wilson, J. A. & Upchurch, P. 2003. A revision of Titanosaurus Lydekker (Dinosauria – Sauropoda), the first dinosaur genus with a ‘Gondwanan’ distribution. Journal of Systematic Palaeontology 1, 125-160.


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: ADDITIONAL SAUROPOD DINOSAUR MATERIAL FROM THE CALLOVIAN OXFORD CLAY FORMATION, PETERBOROUGH, UK: EVIDENCE FOR HIGHER SAUROPOD DIVERSITY
Review round: 1
Reviewer: 3

Output:
Basic reporting: Dear Editor and authors.

It was a pleasure to review the present manuscript entitled “Additional sauropod material from the Peterborough Oxford Clay: evidence for higher sauropod diversity”, and in the attached pdf you can access part of my comments and suggestions. The English seems ok for me.

The sauropods of the Middle Jurassic are particularly unknown and any information can be valuable in order to understand these fauna. Furthermore, the dinosaur material from UK have been a classic disaster, taxonomically, and it is great to have people working on that. However, I believe this work fails on the approach. The material is too fragmentary, and the characters used to support diplodocoid affinities are not well-supported, and in some cases, not properly interpreted (in my opinion). A more accurate comparative study with the Middle Jurassic specimens of England is needed, and a clear comparison with key specimens, such Cetiosaurus oxoniensis, Rutland sauropod and Cetiosauriscus are necessary to really improve our knowledge on the sauropods from the Middle Jurassic of England, and consequently, the present manuscript (figuration could be a great improvement, including more specimens and being a more broader view about the caudal anatomy shown by sauropods of the Middle Jurassic of England, e.g., Cetiosaurus leedsi, rutland specimen, the posterior caudal of the NHMUK). I also think that is important to have a more conservative position counting the possible number of taxa. The comparison with the Morrison, Tendaguru and Lourinhã needs to be developed and explained in a better way. "Cetiosaurus leedsi" is different from Cetiosauricus and Cetiosaurus oxoniensis?

The phylogenetic analysis is for me unnecessary, especially when you are using a data set specifically focused on diplodocids. Improve your comparative study. Did you have good characters to include in future phylogenetic analyses, e.g. the deep crpf are curious? the heart-shaped morphology of the anterior articulation can be traced phylogenetically? In conclusion, do you have some good tail specimens in the Middle Jurassic, used them.

And please, reconsider the orientation of the anterior caudal vertebra described herein.
The incorporation of more specimens will be important in order to justify this paper in a PeerJ.

I will suggest this paper for publication with major revisions. I will be glad to review a second version. I really see potential in this work

Sincerely
Experimental design: See above
Validity of the findings: See above
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: ADDITIONAL SAUROPOD DINOSAUR MATERIAL FROM THE CALLOVIAN OXFORD CLAY FORMATION, PETERBOROUGH, UK: EVIDENCE FOR HIGHER SAUROPOD DIVERSITY
Review round: 2
Reviewer: 1

Output:
Basic reporting: Overall I don't have much to comment here, but I think that the Description might benefit from some subheadings to separate each set of elements (i.e. Dorsal vertebrae; Anterior caudal vertebra; Middle caudal vertebra).
Experimental design: No comment
Validity of the findings: Please see General comments for the author
Additional comments: The manuscript is greatly improved from the original submission, but I still have some problems with aspects of the revised MS. These are provided as an annotated version of the MS (including typos and grammatical errors), and below I have summarised some key issues:

(1) A couple of identifications in the Description are problematic. One of the dorsal vertebrae is described as having parapophyses situated on the very base of the neural arch (partly on the centrum), and the other is annotated with the parapophysis in the same place. However, they are interpreted as posterior dorsal vertebrae. The parapophyses on middle-posterior dorsal vertebrae of all sauropods are situated high on the neural arch. If correctly identified in the newly described dorsal vertebrae, they must be anterior dorsal vertebrae, approximately Dv3. This would also affect many character scorings, as most dorsal characters pertain to middle-posterior dorsals. Less of a problem, but the tentative identification of prespinal and postspinal laminae in the anterior caudal vertebrae is also very unlikely - if correct, this would mean that these laminae extend all the way down to the neural canal opening, and there would essentially be no neural arch region. As the authors note, there is another possibility, i.e. that they represent a TPRL/TPOL, hyposphene, and I think that they should go with this as a much more plausible identification.

(2) The MS seems a bit confused by exactly what the conclusions are regarding the identification of these vertebrae. Sometimes they're definitely neosauropods, whereas at other times they might be, and at other times it's very ambiguous. I would recommend plumming for the middle option, and standardising this throughout the MS.

(3) The final section of the Discussion ('Phylogenetic signal and implications for biodiversity') contains a number of claims for other Middle Jurassic neosauropods (lines 514-515). I wrote comments about the updated ID of two of these last time, and pointed out that the third reference didn't state anything about neosauropods, and yet these points have been completely ignored (they also weren't refuted in the response document). I've repeated my comments in the annotated MS. Lines 517-521 briefly comment on other taxa, but it's unclear what the focus of these sentences is - it seems like a random assortment of taxa from various geographic regions.

Best wishes,

Phil


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

Input:
Title: ADDITIONAL SAUROPOD DINOSAUR MATERIAL FROM THE CALLOVIAN OXFORD CLAY FORMATION, PETERBOROUGH, UK: EVIDENCE FOR HIGHER SAUROPOD DIVERSITY
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript is well presented, is well written, and fairly cites existing literature and the work of others.
Experimental design: The project's aims are clearly stated and the relevant methods used are well defined.
Validity of the findings: The conclusions are well stated and obvious and the article represents a valid contribution to knowledge.
Additional comments: Lines 97-100: the sentence structure here is complex and, I suggest, needs revision. I would say: ‘In addition to Cetiosauriscus, four anterior vertebrae are known from the Oxford Clay Formation. These were previously ascribed to a brachiosaurid, but were more recently reidentified as an indeterminate non-neosauropod’.
Line 101, the sentence should be started with something different from ‘Also’.
Line 192: shouldn’t the ammonite be a common ammonite _of_ the Oxford Clay Formation?
Line 203: I feel that better wording would be ‘… is known. However, the King’s Dyke pit…’.
Line 209: remove ‘back to’.
Line 322: did you really mean ‘bone matrix’ here?
Lines 522-525: I am slightly uneasy as goes the use of ‘nested with’ and ‘nested in’. When describing phylogenetic results, I personally would only use ‘nested’ when referring to an OTU that is found to be deeply embedded within a given clade; what is being described here is a simple grouping with a given OTU or membership of it. I would therefore say.. ‘recovers four trees where PETMG R272 groups with Cetiosauriscus in Diplodocimorpha…’, and ‘… being within Diplodocinae or sister to Rebbachisauridae’ (line 524-525). Also, given that PETMG R85 and LEICT G.418.1956.21.0 are not named, it might be better to refer to (in line 523 and 55) them as ‘sister to Diplodocidae/Rebbachisauridae’ (respectively), not ‘sister-taxon’.
Lines 645-646: the Mannion et al. citation has been accidentally italicised.
Line 655: remove comma after ‘present’.
Line 732: it may be appropriate to cite Taylor 2017 on Xenoposeidon, since it now appears to be an additional Early Cretaceous rebbachisaurid, and possibly an especially early one…
Taylor, M. P. 2017. Xenoposeidon is the earliest known rebbachisaurid sauropod dinosaur. PeerJ PrePrints 5: e3415.
In Fig 6, some clade names are written in technical style (eg, Diplodocoidea), and others in vernacular style (eg, Rebbachisaurids). I assume that all of these terms should be written as technical names.

Darren Naish
eotyrannus@gmail.com


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 EARLY PLIOCENE EXTINCTION OF THE MEGA-TOOTHED SHARK OTODUS MEGALODON: A VIEW FROM THE EASTERN NORTH PACIFIC
Review round: 1
Reviewer: 1

Output:
Basic reporting: See attached PDF.
Experimental design: No comment.
Validity of the findings: See attached PDF.
Additional comments: I suggest the following changes.  1) Three different types of stages are used and each should be documented in every case; 2) upper, lower, middle, and late, early, middle are not capitalized unless they are formally defined as one of those terms.  In the case of this manuscript that would only apply to Late or Upper Pleistocene (see http://www.stratigraphy.org/index.php/ics-chart-timescale); 3) Plio-Pleistocene is not an age, use Pliocene-Pleistocene; 4) Formation names used outside the type area and not directly correlated lithologically should be referred to in quote or ‘of authors’ (i.e., “Monterey” Formation or Monterey Formation of authors) 5) In figure 1 use a lower case e in early; 6) In figure 9 the Palos Verdes Sand does not occur around Newport Bay and these sediments should be referred to as unnamed Pleistocene sediment; 7) In figure 10 it might be nice to show a bar where the the authors believe Otodus megalodon went extinct.; 8) In table1 Ages should be listed as ICS Stages as that is what is mentioned in nearly all of them.

In addition one reference to Otodus megalodon was missed.  That is by GD. Hanna (1926, Calif. Acad. Sci. Proc., 4th ser., vol. 14, No. 18, pp. 434–435).  It should be included and is likely early Pliocene in age.


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 EARLY PLIOCENE EXTINCTION OF THE MEGA-TOOTHED SHARK OTODUS MEGALODON: A VIEW FROM THE EASTERN NORTH PACIFIC
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors do a comprehensive review of the occurrence of Otodus megalodon from California and Baja California.  Their literature is quite extensive and cited papers are relevant, and the entire paper is written in a clear, straight forward manner. The total number of figures may be reduced by reducing sizes of some of the imaged teeth and combining two or more figures together. Also, parts of each figure are labeled “A”, “B”, “C” etc. in capital letters, whereas the figure captions give “a”, “b”, “c” etc. in lower case, that should be standardized.  All small editorial suggestions can be found in my two-part reviewed mark-up copy in PDF, and the authors must do a thorough job revising the manuscript accordingly.  My biggest concern is Table 1, where the author states that their sample size is a total of 145 teeth in Line 104 but Table 1 lists only 33 specimens.  The table should be comprehensive and the sample size for each rock unit must also match up with the list of specimens in Lines 147-159.  In addition, each list of specimens must be cross-checked; for example, Line 486 says “14 partial teeth” but I count only 12 specimens in the same sentence. Although not critical, the authors may consider adding the following paper regarding the estimated body length for O. megalodon:
Shimada, K. 2003 (date of imprint 2002). The relationship between the tooth size and total body length in the white shark, Carcharodon carcharias (Lamniformes: Lamnidae). Journal of Fossil Research, 35(2):28–33.
Experimental design: The paper deals with the iconic ‘Megalodon’ shark and consideration about its demise; thus, it should be of general interest and is very appropriate for PeerJ.  Although their analysis is rather qualitative, their methods and procedures are well described that their interpretations can be checked by others (i.e., sufficient to replicate, provided that Table 1 can list all 145 specimens they examined).
Validity of the findings: Their arguments against previous work cited as well as their findings and propositions are scientifically sound and valid
Additional comments: Although they focus on the occurrences of Otodus megalodon from California and Baja California, the authors do a good job discussing and incorporating the 'last occurrences' of the species on a global scale.  I would like to see this article published in PeerJ so that I can use some of the data and discussions presented in the paper for my own work.