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: HYBRID IDENTIFICATION FOR GLYCINE MAX AND GLYCINE SOJA WITH SSR MARKERS AND ANALYSIS OF SALT TOLERANCE
Review round: 2
Reviewer: 2

Output:
Basic reporting: Authors made an improvement in professional English along the manuscript. References are now better connected with high profile journals. The structured was ameliorated; however, the abstract (first 5 lines) goes directly to crosses; it should better describe the importance of obtaining hybrids for salinity tolerance.
Experimental design: Methods in this version are better described.
Validity of the findings: Conclusions were better stated.
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: A NEW TESTUDINOID TURTLE FROM THE MIDDLE TO LATE EOCENE OF VIETNAM
Review round: 1
Reviewer: 1

Output:
Basic reporting: There are no issues with Basic reporting, the work is very good overall. Please see comments to the author, because I have structured my review in a different way
Experimental design: There are no major issues with Experimental Design. Please see specific comments to the author, because I have structured my review in a different way
Validity of the findings: There are no issues with the validity of the findings.
Additional comments: Thank you very much for inviting me to review this important manuscript. When I was invited, the message of the authors to me said that they believe I will enjoy reviewing this work. I think it was even better. It is so rare to receive a work on fossil turtles based on so many specimens, with so good preservation, and placed within a detailed stratigraphical context. Even if the authors only described 30 out of 100 shells, I am tempted to speculate that the new species described by Garbin, Boehme, and Joyce is among the best-known fossil turtle species in the world, ever. To my knowledge, only the testudinid Stylemys nebrascensis and the combined Echmatemys spp. from USA would compete the richness of the new taxon herein, but they would still stand far from the detailed and meticulous descriptions and figurations herein, and from the precise stratigraphical context of Banhxeochelys. This work is beyond doubt a landmark paper for the entire clade of turtles. I do not know if the authors agree with this view, but if so, please make sure to comment somewhere on how unique is the material you bring to our knowledge.

Another reason that gave me joy in reading this work, is because I know fully understand the reasons behind the latest work of Garbin, Ascarrunz, and Joyce (2018; ZJLS) on the polymorphism on Geoemydidae. With the addition of Banhxeochelys I am now able to see and understand that bigger and beautiful picture that Garbin, Joyce, et al have been looking over the last years.

The authors described the 30 most complete shells of this turtle, accompanied by high-quality illustrations, extensive comparisons with relevant taxa, and a new phylogenetic analysis based on a recently published matrix. Based on this analysis, the authors propose a new taxon; I have no doubt about that. Also, they present a lot of new and important information, not only for the new taxon, but for many other extant and extinct geoemydids as well.

I would absolutely recommend the publication of this work beyond any reasonable doubt, and I would urge the authors to continue on this line and describe the remaining 70 shells as well in the near future.

I have only some specific comments to make, either as some minor ones on the pdf, or some comments that require more explanation from my part (below); these proposed changes would not alter the ms significantly. In all cases, I hope that I was able to understand the intended meaning.

Perhaps the only part that I would urge to be expanded has to do with the large polytomy of their phylogeny. Half of the tree is not resolved, but this is not the problem. The problem is that I find little effort from the authors to understand and explain why is that. Besides the superficial comment on homoplasy and polymorphism (p. 6 of the pdf), the “dangerous” phrase (if taken out of context) of p.32 that “[…] is therefore clear that the inclusion of fossils negatively impacted resolution among extant taxa”, and an unnecessary effort of creating numerous reduced consensuses to improve resolution, I do not see any meaningful efforts to solve and explain this problem. There is no doubt that there is homoplasy and polymorphism in Geoemydidae, but how and why this is supposed to be related with our poor knowledge of phylogenetic relationships of this clade is beyond my understanding; especially when we have the tools to investigate this.  Not to mention that numerous works after the landmark paper of Gauthier et al. (1988) proved the importance of fossils in resolving phylogenies of extant taxa…

In the points E and F below I try to provide my opinion on what the authors should do to address those issues properly. Briefly, I think that the authors should take a full advantage of the script IterPCR that they are already using (which actually proves that polymorphism is not issue, but conflict of characters and missing information are; see below) and should also try implied weights (which is a proved method to improve resolution and tackle homoplasy).

The authors claim in the title that the new taxon has some implications for geoemydid systematics. Well, I am not sure if it is clear which are they? It is a new species and most probably is a stem geoemydid, but these do not add any significant implications in geoemydid systematics.

Actually, the reader is left with the (wrong) impression that geoemydid phylogeny is a mess, polymorphism and homoplasy are to blame, morphology does not make sense, and that the inclusion of fossils in phylogenies causes chaos. I find it hard to believe that the authors actually would like to support these ideas and that these are the implications stated in the title (please check and revise if necessary). I had the same issues with the Garbin et al. 2018 (ZJLS) paper, and I am still seriously concerned in this ms as well.

Thank you again for giving me the opportunity to serve as a reviewer for this respected journal and especially for a ms of this quality. I sincerely hope that I helped the authors in the revision of their work.

General Comments

A| One species or more? Even if the authors say that this is a true population (which I agree), this does not necessarily support the idea of a single species. To the contrary, the identification of a true population or snapshot should start with the consideration if they indeed represent a single species or not. Even today, Vietnam is a hotspot of turtle biodiversity and of geoemydids in particular, and we have the actualistic information of the sympatry between several testudinoids in Vietnam and other places in SE Asia. So, if today we analyse a true population or a snapshot we will find more than one species of a genus, or subspecies of a species. So why not in your case? Is it possible that the variation you record could be explained by the existence of more than one species? How is the polymorphy distributed in the specimens? For example, most of the polymorphies are scored (as far as I can tell from the figures and text information) on the specimen GPIT/RE/09743; does this specimen has a distinct morphotype compared to the rest? Or it is because it is a juvenile (so its morphology should not be taken into account for resolving the relationships of the species; see D3 below). What do the other 70 specimens tell you?

I have no doubt that Ba.trani is a new species, but I naturally wonder what if you have more than one species. Several of the characters you find as polymorphic, I used them to define different morphotypes in Echmatemys and to attribute them to previously named taxa. With this concept in mind (and if you have some nice distribution of the morphotypes of neural shapes and/or hu-pec sulcus vs. the entoplastron) you might have up to 3 different species at least. I do not know how you or others would react on that, but I personally think that is more likely to have more than one species than to have ONLY ONE. As 70 specimens are yet to be described, I believe that the best approach would be to name only one species, but to distinguish a set of morphotypes of Ba.trani which could be used as working hypotheses for a future distinction of taxa (in species/subspecies level) within your assemblage. I firmly believe that your assemblage is one of the few, or the only one, where such a work could be made. I am working on a similar case (but with much fewer shells), wherein a “snapshot” or a “true population” of 15 individuals there are beyond any doubt two different genera and up to 3 different geoemydid species. I think that you have a similar case, with at least two different clades of turtles, and more than one geoemydid species.

In any case, I would definitely welcome a comment on that.

B| After reading the ms, I am not sure if the authors consider the new taxon as a stem geoemydid or a testugurian. In the systematic list, it is listed under Pan-Testuguria, in the diagnosis they say is a member of Pan-Geoemydidae, in the final tree is in the stem of Geoemydidae. I would say that there has to be a bit more consistency on that. If the final position of the taxon is not certain, then I think that the addition of a final taxonomic conclusion would definitely help the reader. I, personally, believe that the new taxon is a stem geoemydid, and its recovery in this basal testugurian polytomy is not its problem, but actually the inherent problematic position of Testudinidae from the reference Garbin et al. (2018) phylogeny (see other relevant comments I made herein).

C| Diagnosis. After seeing the diagnosis and the comparisons, I would like to suggest considering the utility of the following characters as part of the combined diagnostic characters of trani: the wide, trapezoid, cervical scute and the wide suprapygal 2. These are certainly different from the Chinese “similar” taxa.

D| Matrix/Phylogenetic analysis: I have checked the matrix overall and the scorings of the new taxon in detail.

1| There are some inconsistencies between the text file and the tnt file. Some characters that are scored as inapplicable in the word file appear as “?” in the tnt file. Please check and revise if necessary.

2| If I understand correct, there are some extant species with DNA data but no morphological data. If so, please explain this in detail in the ms (i.e. which are those taxa).

3| If I understand correct, some of the polymorphisms scored by the authors are the result of scoring both the adult and juvenile morphologies (e.g., presence, number, and position of keels) and/or scoring the anomalies as well (e.g., the number of neurals; the number of vertebrals). I would like to point out that I do not think that is a correct practice scoring those cases, as neither the juvenile nor the anomalous morphologies should be considered as useful to add anything to the solution of the phylogenetic relationships of the taxon. In fact, I am certain that scoring those cases can only add problems. The phyl. analysis of the new taxon should be focused, in my opinion, only on the adult non-anomalous specimens (considering that the authors have the privilege of working with 100 fossils, excluding some of them shouldn’t be any problem). Of course, those cases should be mentioned in the text (as the authors have done already), but simply they should not be scored and taken into account for the phyl. analysis (in that case a note should be added in the text).

4| I have some comments regarding the scorings of some specific characters on the new taxon:

Ch8: flared posterior marginals> it should be “peripherals”, right? If so, please correct it to the text as well. The new taxon is scored as 0/1, but no such information is given in the text. Please check and revise

Ch12: number of suprapygals. Scored as 0/1, whereas in the text is mentioned that all specimens have only two suprapygals [l.195]

Ch26: the new taxon is scored as 0/1, but you mention that the sixth vertebral in the single specimen that shows this morphology is an anomaly. Are you certain you should score this anomaly as a polymorphy of the taxon?

Ch27: I am not sure about some of the scorings of this character. In two of the specimens where the notch is scored as present (09735, 09738) there is some deformation involved as well on one side of the vertebral I/cervical/marginal I association. Any why 09733 is not scored as having the notch as well?

Ch29: This character is scored as polymorphic (implying that there are at least two specimens where the visceral view of the nuchal can be observed and scored). However in the text is mentioned “The ventral side of the nuchal is exposed only in GPIT/RE/09751, but it is not possible to see any characteristics due to bad preservation”. So I do not understand how this character is scored. I mean, if you truly have not observed this character it should be scored as ?; as this character has only two states, scoring as ? or 0/1 would be the same for the analysis, but it is like you imply polymorphism where actually there is missing information. Please check and revise.

6| Uploaded files: Please consider uploading the Mesquite file with the character/state names of the morphological matrix separately. Please replace the terminal taxon “testu” with the genus and species name of the new taxon herein for overall consistency. Please upload the ctf file of the MPTs of the full run. Please upload the iterPCR results, especially the part of the conflict of characters, and missing information.

E| IterPCR. I would like to kindly ask to clarify if you run the actual script or the built-in command in TNT. It seems to me that what you actually did was only the first part of the IterPCR, which is not different than the pruning taxa command; it seems that you did not complete the character/taxa evaluation which is actually the juicy part of the method. I find it hard to believe that you have been able to run the full IterPCR method on the 700.000 trees from a computational point of view. I strongly suggest running the full IterPCR on a subset of trees which reflect the topology (e.g., I selected the first 1000 trees and is the same topology more or less) and try to find out why exactly you have this polytomy.

When you run the script, the reasons of conflict are clear (please SEE FIGURE inserted in the first page of the annotated pdf). The script highlights the conflicting characters and the missing characters which if scored could help to resolve the polytomies. First of all, polymorphism is not really an issue (see cells marked in red). Only few characters scored as polymorphic in a handful of taxa are returned as conflicting. Also, the multiple positions of the new taxon (the most polymorphic of the extinct taxa) are not the result of polymorphism. trani has only one conflicting character which is not polymorphic. The main problems are the presence of several conflicting (not polymorphic) characters (marked with green) and the amount of missing information which could be useful to solve the polytomies (marked with blue). Especially half of the extinct taxa contain a large amount of missing information, which appears to be crucial for resolving their position. Also, the script analyses the jumping positions of some clades (e.g., Rhinoclemmys and Heosemys) as the result of conflicting characters; although many of these conflicting characters in the included species are polymorphic, their reconstructions on the node of these clades are rarely polymorphic.

As the problem of the missing characters in the extinct taxa appears to be a serious one, I would reconsider the necessity of adding most of the extinct taxa in this phylogenetic analysis (they should remain in the comparisons, however). In fact, our knowledge about their position has not improved after this work. We thought that they are pan-geoemydids, they are shown as pan-geoemydids or pan-testugurians herein. Why adding them in the analysis if they only create noise?

F| I am not sure if I understand why the authors went after all this trouble with the various consensuses with the various pruned taxa; also the authors notified us during the review that the new taxon was selected as not to be pruned (otherwise it would be pruned as well). I am not sure either if all these trees are necessary to be presented. I understand that this is a big polytomy, and is OK. This is the result of the current matrix. The simplest way would be that the authors present the strict consensus of the full analysis as a supplementary information, and then the most stable reduced consensus tree (even if the new taxon is not there…); it is, however, important to mark on the reduced strict consensus the various positions of the pruned taxa. Also, the authors should use the term “reduced strict consensus” when they present trees where pruned taxa are not shown, and “strict consensus” when all analysed taxa are shown.

Also, you need to be clear any time you mention characters or synapomorphies in which set of trees are calculated. If I understand correctly, they are mostly calculated on each reduced consensus tree. For that reason, it is kind of difficult to follow and even to interpret those “synapomorphies” in a meaningful way.

I would recommend trying some analyses under implied weights, which are shown to outperform other methods in terms of retrieving correct groups (see the recent paper of Goloboff et al. 2018 in Cladistics). Maybe implied weights could help to improve the resolution of your trees.

If implied weights do not work then I suggest the following:

as the full analysis does not work, I suggest that the authors focus first on resolving the position of the new taxon. In this sense, the last tree that the authors present is fine, and I am happy about that. Ba trani is a stem geoemydid.
Then they could move on and investigate the position of the other taxa in their new matrix.  Now, when all taxa are included, Ba.trani collapses to Pan-Testuguria, and the authors should try to explain why (see iterPCR). I believe that this is because of the inherent problems of the matrix regarding Testudinidae (numerous characters that could resolve the position of Testudinidae are not included, especially from the cranium, because this is shell-only, geoemydid matrix). If so, actually the inclusion of Ba.trani (a stem geoemydid) in the matrix is responsible for resolving the polytomy of Garbin et al (2018)!


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

Input:
Title: A NEW TESTUDINOID TURTLE FROM THE MIDDLE TO LATE EOCENE OF VIETNAM
Review round: 1
Reviewer: 2

Output:
Basic reporting: It is a good paper, clearly written. The literature is fine, figures and tables are good, I also appreciated the supplementary material (useful and well organized). Overall, I agree with the conclusions (see remarks for phyl. analysis and diagnosis however).
Experimental design: as it is organized, the paper is a clear taxonomic and systematic account. no problem.

supl mat. no 2 should be updated, the list of specimens studied is not complete (even if things were scored from the literature we should know which specimens or plates were used).
Validity of the findings: things are fine, just see my remark for the diagnosis that can certainly be improved, the results of the phylogenetic reconstruction could be artefactual and could be discussed a bit more (high degree of polymorphism in the fossil studied).
Additional comments: This paper describes a new genus of turtle from the Paleogene of Vietnam. The fossil record of turtles in South East Asia is not well known and this description adds up an interesting new account to what is currently known.

The description is based on a very large amount of material that has several similarities with something I described some years ago in Southern China (not too far from Loc Binh discrict actually (about 300/400 km).

It is a good paper.

Some remarks/comments that may help you to improve the ms:

1. The lack of phylogenetic relationships between Guangdongemys (or other taxa) and  Banhxeochelys two may be real or rather an artefact of the morphological characters selected and total evidence (I know you have done your best: but many of them are polymorphic in several taxa, and may make branches collapsing early in the tree...this is often the case when using total evidence methods and include fossils with polymorphic character: mostly because this polymorphic characters, as they are treated adds uncertainties; this makes distant branches collapsing and the tree looking like a long basal polytomy until molecular characters do their job). If you look at the number of character diagnosing the fossil from south china and your fossils: they are very few (and we also know that these characters can change within a single genus). I would certainly nuance even more the result of the phylogenetic analysis; even if the provision of a matrix of character was very valuable in supplementary material. Actually, I am afraid that other scientists may consider that approach as a solution for justifying easily the erection of new taxa. Note that your fossil is one of the most variable, this can explain the position that was optimised by phyl. reconstruction methods.

2. In that section and in suppl material S2, you should clarify what you consider as belonging to Palaeochelys. the specimen list I got in suppl material is incomplete and it seems the document you uploaded was a previous version (at the end of the author list there is a XXXX).

3. Intro:
I would certainly avoid to say that Palaeoemys and ptychogaster are "European lineages". The western european fossil has long been regarded as evolving independently from Asia but we have no solid ground for that (the fossil record in Asia is too weakly known...and just by looking at your results, we can speculate it is not the case ).

4. Age of Krabi is very late Eocene or very early Oligocene (Chron C13R), this is the more precise approximation in the literature so far.

5. Diagnosis should be reworked to make sure it is not ambiguous..
In the diagnosis, it is said that the taxon is assigned to testudinoidea becuase of the contact between plastral and marginal scute. This is not a clear apomorphy of crown testudinoids, since the few work concerning phylogeny of testudinoids including cretaceous and paleogene material shows that the contact between plastral and marginal scute could have occured independently in testuguria and emydidae (see Tong et al., Wutuchelys paper 2017). Furthermore, other turtle families are known to have lost these scutes (eg., pleurodires).  The presence of cervical scute should be removed from the diagnosis.

While the shape of neural 4 and 5 was interesting as a diagnostic feature, it seems that at least two specimens in the referred material did not match that (at least 10 %). I would therefore rewrite the part dealing with neurals, rather writing that neural 4 or 5 can be either octogonal and squared respectively or hexagonal. But doing that, the diagnosis fails to differentiate clearly the taxon from Mauremys (and also maybe Sacalia, and some species in the "Palaeochelys - Mauremys" waste basket of Hervet). It would be important to further differentiate Banhxeochelys from these in the diagnosis. The rather narrow and hexagnoal vertebrals (V2-V3) in adults could be something to add in the diagnosis which further underlines its resemblance with Guangdongemys.

In the same respect, it seems from figures that sometimes the entoplastron is not interesected by the HP sulcus (there is some variation here too; see line 305 of your description). Maybe you should offer a longer diagnosis with elements of comparison for taxa that could be close (Mauremys, Palaeochelys, ?P elongata, Isometremys, Guangdongemys). You do that well at the end of the MS, but a diagnosis should be the primary useful part of the taxonomic account; so I think you can improve it.

6. l. 129. I do not understand why the genus is abbreviated with the two first letters (Ba. rather than B.)

7. If this is available, it would be good to provide a better view of the epiplastral lips (visceral view of the anterior plastron) -fig 8 B is the only illustration for that, and it is not super clear- and also possibly the extent of these lips on xiphi and hypoplastron. You are not discussing the indentation on the lip (something present sometime in other species), you are also not telling whether the not so well defined "ptychogaster" pike of Hervet is present or not.

8. It is a pity that the buttress can not be observed, does that mean that they were extremely reduced ? Maybe isolated plates could help ? The bridge looks rather short and inguinal and axillary notches are very narrow, is it actually the case ? Do we know any appendicular material, vertebra that could be referred to that species or to testudinoid indet ?

9. This is not exactly the scope of the paper, but I really wonder why there is no carettochelyids in this locality. Maybe it could help to refine the age and suggest that you are rather late in the Eocene (probably later than Maoming) or taphonomic/paleoecological reasons. We have no trionychid in Krabi as well (and hundreds of shell were found).

julien CLAUDE
Institut des sciences de l'evolution
Université de Montpellier


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: DIVERSE MICROBIAL COMMUNITIES HOSTED BY THE MODEL CARNIVOROUS PITCHER PLANT SARRACENIA PURPUREA: ANALYSIS OF BOTH BACTERIAL AND EUKARYOTIC COMPOSITION ACROSS DISTINCT HOST PLANT POPULATIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is generally very well written and easy to follow. However, a few parts of the discussion were difficult to understand. In particular, lines 355-357 and 364-369. Part of this is due to the complications that surround comparing sets of taxa in a verbal way. I'd suggest that you clarify the meaning in these sections.

The literature cited is thorough and adequate. Figures and tables are informative, easy to interpret, and sufficient in number.

The manuscript is self contained while being clearly placed in the previous work.
Experimental design: The experimental design is adequate, and clearly within the scope of the journal. I have slight concerns about the research question, as this appears to be an exploratory investigation that seeks to identify the members of the community rather than question-based research. The work clearly addresses a knowledge gap, although in my mind the question of geographic variation of these communities is perhaps more interested than the question of how the communities vary as a function of the local environment.
Validity of the findings: The findings appear to be robust. The authors are careful not to over interpret their data, or to make claims beyond the findings of their work. The conclusions are clear, and speculation is left to a minimum.
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: DIVERSE MICROBIAL COMMUNITIES HOSTED BY THE MODEL CARNIVOROUS PITCHER PLANT SARRACENIA PURPUREA: ANALYSIS OF BOTH BACTERIAL AND EUKARYOTIC COMPOSITION ACROSS DISTINCT HOST PLANT POPULATIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The Introduction and Abstract were well written and there was an excellent effort throughout the manuscript to apply relevant references. The authors clearly did a thorough literature search of the subject before writing the manuscript. The manuscript was of a professional structure, although I could not find where/if the sequences/raw data are publically available. Overall, professional English is used throughout - there are just parts throughout the text (mainly the discussion) where some sentences should be more clear. I have mentioned these points in the general comments to the authors. The results and hypotheses were relevant.
Experimental design: This research falls within the Aims and Scope of the journal. The questions are well defined and very relevant, especially in fulfilling a knowledge gap in Sarracenia research. This is a gap that was desperate to be filled and the paper will definitely contribute. The authors performed a rigorous investigation; however more information is needed in the Methods section. Specifically, Line 390-395 in the Discussion was the first time that I realized that multiple pitcher samples were taken from 1 pant. Please explain in more detail in the Methods section Line 141-142. I had assumed that one pitcher sample was taken per plant, totaling 5 plants per site. Now when I look at Table 1, I realize that 3 - 4 samples were taken from one plant in each site, and then there were 1-2 samples that were from a different plant. Please justify why the sampling was done in this manner. Other information that I would like to see in the Methods section is the depth of basepair reads the authors obtained per sample. The authors should also justify why they did not take measurements of the shape (mouth opening, etc) of the leaves that they sampled during their experiment. The size of the leaf opening could affect insect prey capture, so were the 10 leaves they selected for their study all of a similar size?
Validity of the findings: The data appears to be robust. Of course, it would be nice to have more pitcher communities sequenced, and more replicates from other plants, but this study is a good first step towards identifying the inquiline community in this model study system. Conclusions are well stated, but the Discussion is quite long and confusing and would benefit from a revision. Specific comments can be found in the general comments to the authors.
Additional comments: Overall, it is a nice study that provides information that is much needed about the Sarracenia system. It is a small study, and I have some questions about the decision to select a majority of leaves on 1 plant, and then a few others on other plants, but the results still provide an indepth description of the Sarracenia system.

For the Discussion, I became very confused with the differences in the different sub-sections. The first sub-section topic is about the microbial composition of the communities. It explains the overall similarities/differences of the two populations of Sarracenia. How is this different from the “between population” part of the second sub-section of the Discussion? Overall, I find the Discussion to be overly long (about 2 pages too long) and confusing because it appears that some information is repeated. I suggest a shortening of the Discussion, and to rework the sub-sections from 1) broad similarities/differences in composition between the two populations. Why this could be: habitat differences 2) differences within the sites (between the pitchers). Why this could be: prey differences, etc. 3) Diversity 4) Bacteria function. Try to make it clear to the readers when it is the bacterial composition being discussed, when it is the eukaryotic composition that is discussed, and when it is the combined composition that is discussed. Try not to flip back and forth between the three things within a section.

Some other minor comments throughout the manuscript are:
Line 73 : Just ciliates? What about the flagellates? I suggest rewording to say “protozoa”

Line 76-77: Maybe cite also Gebühr et al. 2006.

Line 93-93: “with higher nitrogen and phosphorus resulting in narrower pitchers….” is confusing in this sentence as I am unsure if this was a result found for one of the wetland that was used in this study or if it is an overall statement of what happened to the morphology of pitcher plants.

Line 123: “based on taxonomic and metagenomics predictions” is oddly placed in this question.

Line 235: “other protists distributed across pitcher samples” is confusing

Line 409-410: This sentence seems oddly placed the way that it is currently worded.

Line 328: “within the same S. purpurea pitchers within” is oddly worded

Line 352: “have also shown” instead of “showed”

Line 353-355: Were these species observed (morphologically) by the authors in the 10 pitcher leaves that were sampled? I think this sentence should be made stronger to re-iterate just how common it is to have these species (at least identified morphologically) across the geographic range of Sarracenia purpurea.

Line 359: within “the” 10 pitchers sampled.

Line 368: TerHorst 2001 the correct reference here?

Line 391: Suggested rewording “changes in pitcher community composition over time”

Line 394: “Some similar and some very different composition between pitchers” is oddly worded

Line 390-395: This is the first time that I realized that multiple pitcher samples were taken from 1 plant. Please explain in more detail in the Methods section Line 141-142. I had assumed that one pitcher sample was taken per plant, totaling 5 plants per site. Now when I look at Table 1, I realize that 3 - 4 samples were taken from one plant in each site, and then there were 1-2 samples that were from a different plant. Please justify why the sampling was done in this manner.

Line 394-395 again: what composition and colonization are we talking about? Just the bacteria or both the bacteria and eukaryotes? The beginning of the paragraph makes me assume we are still discussing bacterial composition, but it is not clear.

Line 395: Differences in bacterial composition? Overall, the first paragraph is confusing as I am unsure when the discussion about bacterial composition stops and the discussion about eukaryotic composition begins. Without directly looking at the NMDS figure, I first assumed that the listed eukaryote species in this sentence were affecting the bacteria composition. After reading the rest of the paragraph, I think the authors are only discussing eukaryotic composition. Please make the paragraph more clear.

Line 403: “in surrounding bog” is oddly worded

Line 408-410: “and there other known aquatic and soil habitats” is oddly worded. Plus, this sentences rather abruptly ends. I think it belongs in this paragraph but as it is presented now, it seems out of place.

Line 411-412: “the greater randomness of eukaryotic prey capture”. What happens to the similarity in composition between pitchers when the data on the eukaryotic prey is removed?

Line 527: “was found to be similar to in other…” oddly worded.


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: DIVERSE MICROBIAL COMMUNITIES HOSTED BY THE MODEL CARNIVOROUS PITCHER PLANT SARRACENIA PURPUREA: ANALYSIS OF BOTH BACTERIAL AND EUKARYOTIC COMPOSITION ACROSS DISTINCT HOST PLANT POPULATIONS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Line 183: cite ANOSIM statistic

Line 186: What are distance unifrac values?

Line 225: “differences in these families were not heavily influenced by a single OTU for those families” I don’t know why it would be expected that differences at such a broad level would be impacted by a single OTU.

Line 263 and Table 1: I’m not sure all of these metrics needs to be included. Do you need all of them to tell your story?

Figure 4 and 5: Wastewaster/Eukbase can be removed.

Figure 4B and 5B: The site names can be removed. Also, the labels on the metabolic function vectors should be larger.

Fig 6: Please provide bootstrap values (or other indication of branch support) on the tree.

Line 207: The naming of the samples is confusing. Are each of the labels (like CB1p1) corresponding to one of the 5 plants in each of the two sites? If so, why not just Cedarburg1, Cedarburg2, etc or CB1, CB2, etc.?

Line 282: I don’t think the outgroup is needed except for the dendrograms.

Line 284: PiCrust does not assess bacterial function.

Line 287-288: Were these functional pathways significantly different between sites? Why focus on these? Same thing in the associated figure, are all pathways included as vectors significantly different across sites? Or were all of them included?

Line 303-312: I think this section can be removed without losing anything from the story.
Experimental design: Overall, simple but OK. However, please be more clear about your sample size – this study is on 10 total pitchers? 5 from each site?
Validity of the findings: For PiCRUST – what was your NSTI score? How confidant are you with the predictions?

Line 220: Do you believe the zero abundance is real or an artifact of the methods?

Regarding the use of 18S primers to capture eukaryotic diversity, I’d like to see a bit more about the bias introduced by these primers. For example, in figure 3, is it possible that the differences in abundance between major types of eukaryotes is due to different copy numbers of 18S rRNA in their genome? I’m comfortable with a presence/absence analysis but I think given the diversity of eukaryotes focused on here more justification needs to be provided to quell concern of amplification bias across the major groups.

Similarly, has there been any study validating the use of 18S sequencing to quantify the abundance of larger eukaryotes (like mites?). If so, it would help bolster this method to be used to assess the abundance of a diverse assortment of eukaryotes.

Line 265: How can the rarefaction curves show low coverage but Good’s coverage show nearly full coverage of the diversity?

Line 360: were the keystone species missing? Or did you not pick them up with your primers? Were the pitchers visually inspected for the presence of mosquito larvae?

Line 490: comparison with the wastewater samples is irrelevant and should be removed.
Additional comments: This manuscript presents a characterization of bacterial and eukaryotic diversity within S. purpurea pitchers in two sites in Wisconsin. In addition to the comments in other sections of this review, I think this manuscript has the feel of the thesis and not a manuscript. The same story can be told if the manuscript was cut down by 25% or more. It would benefit the manuscript for the author to streamline the story and only include those data that are useful to the story to make this manuscript feel less like a “data dump”. The data are good, but the story and presentation should be streamlined.


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: DIVERSE MICROBIAL COMMUNITIES HOSTED BY THE MODEL CARNIVOROUS PITCHER PLANT SARRACENIA PURPUREA: ANALYSIS OF BOTH BACTERIAL AND EUKARYOTIC COMPOSITION ACROSS DISTINCT HOST PLANT POPULATIONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Acceptable
Experimental design: Acceptable
Validity of the findings: Acceptable
Additional comments: Nicely done on the revision.


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

Input:
Title: MYCORRHIZATION OF QUERCUS ACUTISSIMA WITH CHINESE BLACK TRUFFLE SIGNIFICANTLY ALTERED THE HOST PHYSIOLOGY AND ROOT-ASSOCIATED MICROBIOMES
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this study, Zhang et al., evaluated how the ectomycorrhizae of Quercus acutissima with Chinese black truffle affects plant physiology using four parameters. Further, they collected the root endosphere and rhizosphere samples of those T.indicum inoculated and uninoculated plants, and profiled the bacterial and fungal communities in these samples. The methodologies used in this study could be strong enough to answer their questions, and the overall quality of the writing is OK despite some places being vague in delivering their meanings. I suggest the authors doing some changes before publishing this work, and details are provided as follows.
Experimental design: The general experimental design was good enough to answer research question of the authors.
Validity of the findings: the general bioinformatics and statistical analysis were OK, but need to be improved at some places please see detail in my general comments for the authors
Additional comments: Comments on Peer J paper

In this study, Zhang et al., evaluated how the ectomycorrhizae of Quercus acutissima with Chinese black truffle affects plant physiology using four parameters. Further, they collected the root endosphere and rhizosphere samples of those T.indicum inoculated and uninoculated plants, and profiled the bacterial and fungal communities in these samples. The methodologies used in this study could be strong enough to answer their questions, and the overall quality of the writing is OK despite some places being vague in delivering their meanings. I suggest the authors doing some changes before publishing this work, and details are provided as follows.

Title: I may suggest to change the current title according to your main findings, for example: Mycorrhization of Quercus acutissima with Chinese black truffle significantly altered host physiology and root-associated microbiomes.

In abstract, Line 37: throughout the article, I could see many phrases of ‘surrounding soil’, did you mean ‘rhizosphere soil’. Generally, rhizosphere effects are huge on soil microbial properties. I suggest to make it clear by using rhizosphere/root endosphere throughout this manuscript.

Introduction: I suggest to provide hypothesis that you were testing in this study at the end of the introduction.
Line 119, what was the size of your plastic containers
Line 130, it would benefit if providing more details about how the glasshouse conditions were controlled, e.g., temperature, moisture, and what time of the year as it matters daylight.
Line 137: please detail what soil properties you measured.
Line 140, how you cleaned the roots?
Line 144, it is important to provide more details how the mycorrhizal colonization rating was performed.

Bioreplicates: you had 60 plants for each treatment, thereby you would have 20 plants per each bilreplicate, please provide relative information at an appropriate place of the manuscript

Line 173 ‘soil samples around roots’, did you mean rhizosphere soils?

Line 177, please cite references that originally designed the primer pairs for bacterial and fungal community profiling you used here, and provide template specific primer sequences.

Line 194, which version of the SILVA and Unite databases?

Line 203, regarding statistics of the study: how you performed multivariate analysis for your community data? And in the following results, you should also provide P values demonstrating if your treatments differed from controls.
Line 209, did you collect the plant biomass production data?

Line 212, should you explain these mycorrhizae-induced differences in morphology in more details? As I see there seems to be a lot of differences between inoculated and procedure control roots in Figure 1.

Line 222, soil properties analysis, should you give the size of changes in particular soil nutrient? such as total nitrogen (+110%)…..

Line 235 Alpha diversity of bacterial community
Line 258 Alpha diversity of fungal community
Line 243-257 and Line 263-271, if possible, provide significant level for different treatments, P<0.01 or P<0.05.

Line 272, similar to the above, statistical analysis here needs to be improved.

Line 336, typo-mistakes

Line 403, typo-mistakes

Line 412: not all Fusarium species are phytopathogens

In discussion, if appropriate, you can discuss more about rhizosphere effects on root microbial community structure, that is why the endophere microbial community differed from rhizosophere community for Q. acutissima plants.

In all figures, should clarify what treatments associate with A, B, C and D, figures should be shelf-explanative.
Figure 5, it might be better if only show differences at phylum level, results at genus level can be therefore put in Supplementary results.


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

Input:
Title: MYCORRHIZATION OF QUERCUS ACUTISSIMA WITH CHINESE BLACK TRUFFLE SIGNIFICANTLY ALTERED THE HOST PHYSIOLOGY AND ROOT-ASSOCIATED MICROBIOMES
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The manuscript described an original work on the impact of truffle on root/soil characteristics. Experimental design seems to be right with respect to the aims of the performed work. Results seem to be solid basing on three replicates. However, some points have to be clarify before the publication.
In the introduction the part from line 54 to line 56 should be deleted, since it is not well inserted there.
Line 62, colonization should be better than infection.
Line 148-51, why ECM, soil, soil, roots and not ECM, soil, roots, soil?
Root activity and chlorophyll content. Why the authors have evaluated these parameters, and mainly why chlorophyll content in roots?
The sentence from line 162 to line 163 have to be clarified.
Line 367: why "could"?
In Figure 2, microstructure characteristics is not suitable...morphological characteristics could be probably better. Legend should be changed in:
a and c, transversal sections; b and d, longitudinal sections.
Check along the manuscript "T.indicum" that should be "T. indicum" and "Q.acutissima" should be "Q. acutissima". The same comment also for T. melanosporum.
Recent literature has been cited, although the authors should be check the word that need italic (such as Tuber melanosporum) in the reference list.


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: MYCORRHIZATION OF QUERCUS ACUTISSIMA WITH CHINESE BLACK TRUFFLE SIGNIFICANTLY ALTERED THE HOST PHYSIOLOGY AND ROOT-ASSOCIATED MICROBIOMES
Review round: 2
Reviewer: 1

Output:
Basic reporting: I believe the current version meet publishing standard.
Experimental design: I believe the current version meet publishing standard.
Validity of the findings: I believe the current version meet publishing standard.
Additional comments: I believe the current version meet publishing standard.


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: MYCORRHIZATION OF QUERCUS ACUTISSIMA WITH CHINESE BLACK TRUFFLE SIGNIFICANTLY ALTERED THE HOST PHYSIOLOGY AND ROOT-ASSOCIATED MICROBIOMES
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript has been improved following the reviewers' suggestions. I have only a doubt on the fact to use microbiomes or microbiota in the title. I prefer the second one, but see also what the second reviewer will say on this point.
Experimental design: Methods have been improved in the revised version.
Validity of the findings: In the revised version the critical points have been addressed.
Additional comments: The manuscript is now suitable for the publication.


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

Input:
Title: STRESS RESPONSES UPON STARVATION AND EXPOSURE TO BACTERIA IN THE ANT FORMICA EXSECTA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Line 44: It might read better if written "serve to store resources in the..."

Line 57: "Incur a metabolic..." may sound better than "cause".

Line 58: I think this is rather immunopathology than autoimmunity.

Line 65-68: I had to read these two sentences several times to understand them fully. I think that they could be written more simply, i.e. that the ability of an organism to survive an infection will likely depend on its nutritional state.

Line 77: ", which are all potential..." might read better.

Line 78: Here, I would suggest removing the names of the genes and just say you look at a subset of immune genes, then in the methods state the gene names along with their function. When I read the ms I was missing an explanation here of the gene's function, which then came later in the methods.

Line 82: "These" instead of "the".

Line 88: Were was this bacteria isolated/obtained from for the study?

Line 136: I'd move up the explanation for choosing this time point to here.

Line 154: Missing a "the" between measured and concentration.

Line 226: Adding headings for the results may be benefical.

Line 262: Can remove the comma after 'bacteria'.

Line 343: Maybe change 'can' to 'may' as the results are 100% conclusive.

Supplemental figure 1: I think you can add a more informative Y-axis label.

Supplemental data sets: I'm not 100% sure how this is handled by PeerJ, but I think you should have a 'legend' for these in the PDF that explains what the column names mean and they type of data each column contains. For example, it's not obvious that Cens is survival and that 0 = alive or 1 = dead. It might also be handy to include the PCA results as a third data set since most of the statistics are carried out directly on these and it's not necessarily straightforward for a third party to run the PCAs again.
Experimental design: 104: Honey has antimicrobial properties and so I am surprised that ants were both fed honey containing food, as well as mixing the bacteria with it. Is it possible that the honey neutralised some/all of the bacteria and whether this could explain the absence of an effect of two of the bacteria?

Line 107: I am unsure how polymorphic size is in this species, but I know it can vary greatly within some Formica. Did you control for ant size, given that this may affect the relative dose of bacteria they receive?

Line 107: Throughout, I think it would be helpful to have in brackets the final sample sizes used, as it was hard to follow as is.

Line 117: Please clarify whether this means 50 ul was added to 100 ul, or 50 ul + 50 ul. How was the food provided, e.g. in a dish? I ask because it's a known problem that the bacterial spores can sink to the bottom of larger droplets, possibly leading to less being consumed/lack of infections occurring.

Line 119: Was the old food removed before the new added? Moreover, as far as I can tell, ants were allowed to consume the food freely, rather than administering a controlled dose to each. Do you have any data on how much of the food was consumed on a daily basis and whether enough food was provided per ant (I think the amount you gives works out at about 7 ul of food per ant)? More information is needed here, especially as its known animals can avoid contaminated food.

Line 124: Was this concentration the same across the bacterial spp?

Line 126: I find it peculiar that in one group the ants are continually fed bacteria for an additional seven days. A more balanced design may have been to cease feeding bacteria in the group that continues to have food, otherwise, this group receives a higher bacterial dose than the starved comparison, which may have affected immune gene expression etc.

Line 187: It might be helpful to explain what a time-dependent factor is and why you included it this way.

Line 188: I may be wrong, but I think you also need a random intercept effect for pot since ants in the same pot are non-independent.

Line 193: It's unclear what is meant by nests as a biological replicate, please add an explanation as well as final sample sizes.

Line 212: Unless the ants were pooled (this was unclear), pot probably should be included as a random intercept effect here as well.

Line 216: Is this arbitrary scale approach have any basis in the literature?

Line 218: Was multicollinearity present between all genes or subsets?

Line 224: Please state what model assumptions were checked for the Cox and LMERs and how you assessed model stability. There are some survival curves crossing that may violate the assumption of proportional hazards.
Validity of the findings: Line 227 & Table 1: You are missing an overall effect of bacterial treatment, feeding regime and their interaction. Table 1 appears to be the summary output of the cox regression when the reference category is set to the control, which is good to show for the hazard ratios, but you need to also report the likelihood ratio or Wald statistic of the whole model - this tells us about how well the model fits the data (at the bottom of the summary output) - as well as the statistic and associated p-value for the predictors in the model. This can be done using likelihood ratio tests that compare full and reduced models with terms removed. Currently, it's unclear whether there is a significant interaction present - if not, it should be removed from the model. However, if there is a significant interaction, it's inadvisable to interpret the main effects alone. I believe this section of the results, therefore, needs to be fully revised.

Table 2: It's a bit unclear how these pairwise post hoc comparisons were carried out. Did you use the mult.comp R package where you set up your own contrasts or did you re-level the model with different reference groups until all pairwise combinations were produced? Either is fine, but the results will be slightly different. It might also be good to add to the legend that the p-values were adjusted for multiple comparisons for clarity. It might be worth stating somewhere that you used planned comparisons as you were not interested in comparing between bacteria. This makes me wonder, based on the way the post hocs presented and the graphs, whether it may be simpler to have three separate Cox regressions for the three bacteria? It may be necessary to do this in fact, depending on what the main effects for treatment and feeding are.

Figure 1: I think you should state in the legend that the control groups are the same data in each of the graphs, but that you've split up the data based on bacteria to aid visual interpretation. Could you also add letters to the ends of the lines that indicate significantly different groups? This would make the graph easier to interpret on its own.

Line 231: You could add 'continuously fed and exposed to bacteria' since it's the feeding (or lack of it) that seems to be the important factor.

Line 238: I found this section particularly hard to follow, as it's unclear what the loadings mean. For example, you state that 'all genes responded the same way' but then go on to discuss the differences between them.

Figure 2: Could you change the order of the bacteria so that they are presented in the same way Figure 1. In fact, it may be better to present this data as three separate graphs again, to make it easier to compare with Figure 1. This would also better reflect the planned post hocs in Table 4, which do not compare between bacteria. Currently, Figure 2 invites readers to compare the dots and the letters are not actually representative of a full pairwise comparison set up, so it's misleading to show them all in one. Finally, I'm a bit unsure what the CIs are if the dots are not means/medians? Please explain this more fully so that they can be meainfully interpreted.

Table 1: Again, this seems to be the summary output of the LMER. You need to show a p-value that tests the fit of the model to the data (i.e. by comparing the full model to an intercept-only null model) as well as comparisons to reduced models to give you the results of the main effects (i.e. bacteria exposure, feeding regime and their interaction). Please see this handy tutorial for more info: http://www.bodowinter.com/tutorial/bw_LME_tutorial2.pdf

Line 267: This is a bit unclear, as the pattern does not seem to be the same across treatments, e.g. gene expression is decreased in the SM group?

Line 272: Not sure you can use the word infected here, since you find no mortality effect and could not confirm infection actually took place. 'Exposed' may be better.

Line 275: Possible explanations for any lack of mortality are that the methods you used did not result in any infection. This could be because the bacteria sunk to the bottom of the food, they are simply non-infectious to the ants, they were neutralised in the crop by the ants' formic acid, the ants avoided the bacteria (hence, data on how much ants actually consumed would be handy) etc. It would be good if you could discuss some of these other possibilities.

Line 284: Is there any evidence of bacteria being used as food in insects? I wonder how you could test this in your system.

Line 325: Unclear how cuticle grooming and other external social defences would affect oral infections?
Additional comments: I'm not really sure if this is needed, by I wondered why the immune and metabolic genes were analysed as one? Would it perhaps be informative to runs PCAs on these two sets of genes separately to tease apart any trade-offs between 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: STRESS RESPONSES UPON STARVATION AND EXPOSURE TO BACTERIA IN THE ANT FORMICA EXSECTA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written, and I found it to be an interesting read. I have only minor points to the basic reporting
Line 110: I assume that the standard diet mentioned in Line 110 is without the addition of agar?
Line 288-289: from figure 1 it appears to me that gene expression in starved ants exposed to E. coli and S. marcescens increased significantly compared to the control and not P. entomophila or S. marcescens. Is this a typo?
Line 324-325: allogrooming is a poor example of a behavioral immune defense upon oral infection, as it is very unlikely to have played a role. Instead the other behavioral interactions such as trophallaxis mentioned in line 329 make much more sense. Please consider revising.
Line 348-349: I am not sure I can follow why the ubiquitous presence of multiple stresses may result in the evolution of synergies between defense mechanisms. Could you please elaborate on this?
Experimental design: no comment
Validity of the findings: Although I found the manuscript interesting there is a potential pitfall in interpreting the data. Some bacteria such as E. coli, emit a strong smell and food containing them might be avoided and only eaten at a last resort. I therefore wonder whether the continuous feeding treatment really was a continuous feeding treatment or whether a potential reluctance of the ants to feed on bacteria contaminated food might not have influenced food consumption in the Exposure treatments and thus also survival and immune gene expression. Unfortunately, the authors did not monitor food consumption. I think this is an important point and therefore the ways how this might have influenced the presented results should be thoroughly discussed.
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: STRESS RESPONSES UPON STARVATION AND EXPOSURE TO BACTERIA IN THE ANT FORMICA EXSECTA
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have done a great job responding to the reviewer's 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: STRESS RESPONSES UPON STARVATION AND EXPOSURE TO BACTERIA IN THE ANT FORMICA EXSECTA
Review round: 2
Reviewer: 2

Output:
Basic reporting: Line 274-276: replace comma with dot at the end of the sentence.

Line 331-335: I am not sure whether I agree with the logic here and I think the part on the prophylactic immune response would maybe better fit into the next paragraph. A possible formic acid ingestion would in my view have to affect bacterial survival in different ways in order to explain differences in ant host survival and gene expression.
Moreover, although the authors now included the possiblity that the ants sensed and avoided contaminated food, I miss a discussion how these might have affected their results.
Experimental design: Although I did not spot this in the previous version of the manuscript, I must agree with comment R1.24 made by the other reviewer about including a random effect of pot. As far as my understanding goes, the 20 animals in one pot are not independent and the same applies for the two pots of ingestion of bacteria (Exposure) per colony (one in each Treatment, i.e. continuous feeding or starvation). Thus, a random effect of pot would capture the interdependence of the 20 animals per pot (or the 3 animals per pot for the gene expression, but as they were pooled this is unnecessary), while the random effect of colony would capture the interdependence of the two pots per colony used for continuous feeding or starvation.
I am also curious about the way the proportional hazard test was performed on the survival model. I know this test can be performed via the function cox.zph on a coxph model call in the package survival. However, if I am running your specified model via the coxph model call with Colony as a frailty term: m<-coxph(Surv(Time1,Time2,Cens)~Treatment*Diet+frailty(Colony),data=surv) and then comparing this model with a model without the interaction: m1<-coxph(Surv(Time1,Time2,Cens)~Treatment+Diet+frailty(Colony),data=surv), I cannot get the same statistical inference you report now at the beginning of the results section for the interaction term (your report: Chi-square=7.41, df=3, p=0.06; while I get: Chi-square=7.125, df=2.9474, p=0.0654). I therefore assumed you might be using a coxme model call in the package coxme (m<-coxme(Surv(Time1,Time2,Cens)~Treatment*Diet+(1|Colony),data=surv). Doing the comparison again of models with and without the interaction gave exactly the same values as you report: Chi-square=7.4076, df=3, p=0.05998; loglik(m)=-4032.0). As far as I am aware there is currently no current equivalent to cox.zph to test proportional hazards on a coxme model. Therefore, I am wondering which model call you used (if coxme, then this should be reported in the used packages) and how you performed the proportional hazard test?
I would have also run a model including Colony and pot as a random effect but unfortunately the raw data set does not encoded a variable pot.
Validity of the findings: see comments to basic reporting and experimental design
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: DYNAMIC MULTI-SPECIES OCCUPANCY MODELS REVEAL INDIVIDUALISTIC HABITAT PREFERENCES IN A HIGH-ALTITUDE GRASSLAND BIRD COMMUNITY
Review round: 1
Reviewer: 1

Output:
Basic reporting: I found this manuscript describing the results of a multi-species dynamic occupancy model of highland grassland birds in southern Africa to be very nicely crafted and an enjoyable read. I provide below a few general comments but then spend most of my time in this review providing suggestions for clarifying the text.
Starting at line 67 and going through line 87, methods of analysis are presented before the questions being addressed are provided to the reader. Are the questions motivated by the methodological approach, or are the questions dictating the approach to answering them? If the latter, this arrangement in the Introduction should be altered to move the focus to the questions (i.e., the role of grass height and cover on species occurrence). One simple solution is moving the paragraph in lines 88-96 before the paragraphs starting at line 67.
The authors’ approach allows for estimation of detection probability, but I can find no description of those results. The effect of obs is not described, nor are species-specific detection probabilities provided. I think it would be instructive for p to be described, perhaps akin to Figure 2 and 3.
As it currently stands, the reader has no idea whether the model fits the data well. There are no goodness of fit assessments. An omnibus goodness‐of‐fit test using a chi‐square discrepancy measure on unique detection histories is available for occupancy models (MacKenzie and Bailey, Journal of Agricultural, Biological, and Environmental Statistics, 9, 2004, 300; the MacKenzie–Bailey test). Broms et al. suggest WAIC, CPO, and other methods (Broms, Kristin & B. Hooten, Mevin & Fitzpatrick, Ryan. (2016). Model selection and assessment for multi-species occupancy models. Ecology. 97. 10.1890/15-1471.1.).

Line-by-line comments
The third (3) affiliation, i.e., Ingula Partnership Project etc., seems to be missing from the article title page, but it is available in the separate abstract page preceding the manuscript.
Line 34. ‘Grazing’ to ‘grazing’.
Line 47. Is the comma after the parenthetical necessary?
Line 87. ‘set management objectives’? Is ‘set’ necessary?
Line 98. Suggestion: ‘maintain long-term avian diversity.’
Line 128. ‘with a few plots’.
Lines 134-136. Unclear. Suggested rewrite: ‘This area, previously used to support commercial livestock in summer, falls partly…’
Line 163. Is ‘lie’ necessary?
Line 169. The citational support here is incorrectly formatted.
Line 170. Only birds walking in and out of the plot were recorded? What kind of birds are these? Quail-like animals?
Line 173. ‘Each birds’? Each species? Each individual bird?
Line 174. Assuming bird should be singular, the verb tense should be ‘was’.
Line 183. ‘completion of surveys’
Line 184. Close in time or space?
Line 185. ‘a similar method’ or ‘similar methods’
Line 186. ‘This method’. No naked this.
Line 186. Throwing? Placing?
Line 216. Space before parenthetical.
Lines 221-222. Italicize Coturnix coturnix.
Lines 230-233. There seems to be a verb missing. Perhaps after ‘site i’ should be ‘site i that is assumed to be’?
Line 237. Period after Bernoulli distribution should be removed.
Line 247. i,j,t should be subscripted for γ.
Lines 248 and 249. Perhaps ‘to become’ and ‘to remain’ should be changed to ‘becoming’ and ‘remaining’?
Lines 260-266. There is no connection, as currently written, for p back to Θ. I think you require a line like 245, but written for Θ rather than z, and p rather than Ψ.
Line 260. For clarification, it would be best to insert ‘month-specific’ prior to ‘detection probability’, given that p is indexed by t.
Lines 294 onward. This section is awkward in that it bounces among the different population parameters. My initial thought to make it more sensible would be to compartmentalize the parameters into their own paragraph. For instance, the first paragraph of this section begins with occupancy, moves to a general description among the three parameters, spends a fair bit of time muddling persistence and colonization, and then circles back in the next paragraph back with occupancy. Then, halfway through that paragraph, it veers toward persistence and colonization. It’s hard to keep track the way it is written. In retrospect, maybe what it requires is a sentence ahead of the second paragraph that moves from the generalization of results to the species-specific findings, something along the lines of… “Species differed in their response to grass height and cover.”
To reiterate, because I’m having so much trouble here… two sentences in the first paragraph seem to conflict. Starting at line 296, “Across the 12 species, … colonization decreased with increasing grass height and cover…”, Starting at line 301, “Overall, colonization declined with increasing grass height and cover for a majority of the 12 species, with [3 species] being exceptions…” The first sentence suggests there are no exceptions, the section sentence says the exact same thing but identifies 3 exceptions.
Line 295. Insert ‘the’ or ‘a’ prior to ‘majority’.
Lines 306-307. ‘little’ should be moved before ‘affected’.
Line 334. I’d replace ‘monitoring’ with ‘assessing’, as the models interpret results of the monitoring.
Line 346. Cover the naked this by inserting ‘result’ after ‘this’.
Line 347. Replace ‘nest’ with ‘next’.
Line 347. Insert ‘the’ or ‘a’ prior to ‘majority’.
Line 348. Reconcile verb tense. ‘this result supports’ or ‘these results support’.
Line 353. Is ‘and’ necessary after ‘burning and grazing’? Replace with comma? And then insert a comma after ‘unburned’.
Line 369. Replace ‘resulted to’ with ‘resulted in’.
Line 395. Replace ‘first’ with ‘most’.
Line 395. Cover the naked this by inserting ‘result’ after ‘this’.
Line 402. There seems to be a formatting problem here. An errant space occurs before the period.
Line 346. Cover the naked this by inserting ‘approach’ after ‘this’, and the subsequent ‘approach’ with ‘one’.
Line 346. Cover the naked this by inserting ‘expansion’ after ‘this’.
Line 436. This sentence is muddled. Models are not a survey method, and ‘purposed’ does not work here.
Line 440. Rectify verb tense. ‘Improvements… make’ or ‘Improvement… makes’.
Figure 3. I have a hard time differentiating these colors. There is a thick black line that, I surmise, is supposed to be the independent mean of the species estimates, but this is described nowhere.
Figure legend 4 misspells ‘comparing’.
Experimental design: Nothing further to add here.
Validity of the findings: Here, beyond the comments already given, I wish to reemphasize the need for model assessment. Further, the authors should report their results pertaining to detection probability.
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: DYNAMIC MULTI-SPECIES OCCUPANCY MODELS REVEAL INDIVIDUALISTIC HABITAT PREFERENCES IN A HIGH-ALTITUDE GRASSLAND BIRD COMMUNITY
Review round: 1
Reviewer: 2

Output:
Basic reporting: Clear and unambiguous, professional English used throughout: Use of English could be improved in some places, but is generally good.  Specific comments in attached PDF.

Literature references, sufficient field background / context provided: Introduction needs substantially more background / context for scientific questions.  Use of primary literature could be improved in the discussion.  Suggestion for improvement included in attached PDF.

Professional article structure, figs, tables. Raw data shared: Some figures could be improved, particularly Figure 3.  Specific suggestions included in attached PDF. Thank you for sharing raw data.  Code used to format raw data for analysis in JAGS would be helpful.

Self-contained with relevant results to hypotheses: I had a hard time finding the take-home message.  The discussion didn't relate well to the objectives defined in the last paragraph of the introduction.  i.e., I didn't have a good sense of the response of the 12 common species to grass height and cover, or how I could use that information to inform grassland management.  Specific comments in attached PDF.
Experimental design: Original primary research with Aims and Scope of the journal: This appears to be original primary research.

Research question well defines, relevant & meaningful. It is stated how research fill an identified knowledge gap: It is not clear to me how the research fills an identified knowledge gap.  No gap is identified.  A more thorough literature review in the introduction is necessary.

Rigorous investigation performed to a high technical & ethical standard: Research appears to conform to prevailing ethical standards.  No animals are handled, and the author indicates he / she had permission to survey on private lands.  Uses state of the art dynamic occupancy models, though there is no evaluation of potential competing models.  See attached PDF for details.

Methods described with sufficient detail & information to replicate: Substantially more information needed in methods section to replicate study.  Details are in attached PDF.
Validity of the findings: Data is robust, statistically sound, & controlled: Sample size is small (~ 20 sites).  The author probably needs to use more informative priors if they want to derive meaningful inference from their data.  I need more details on study design to determine if statistically sound.  Data are not controlled in terms of burning and grazing, which seems to be an area where the authors wish to make inference.  This can be okay from a design perspective, since this is an observational study, but authors do not include fire / grazing covariates in their models.

Conclusions are well stated, linked to original research question & limited to supporting results: Not always.  For example, the authors make recommendations regarding burning and grazing, but do not include burning and grazing in their models.  Details in attached PDF.

Speculation is welcome, but should be identified as such: Some speculation in discussion, not substantiated by prior literature or identified as such.  For example, the authors speculate when describing causes for decline in occupancy on line 387, without reference to the primary literature.  Details in attached PDF.
Additional comments: See 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: IMPACT OF OLD AGE ON RESECTABLE COLORECTAL CANCER OUTCOMES
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: Line 84, the fourth of exclusion criteria: patients who survived less than one month from diagnosis. This may introduce a selection bias. How many patients were excluded? Why did the researchers exclude these patients?
Validity of the findings: 1. Line 286-287, this study concerns the prognostic risk factors of CRC. From the multivariate analysis, researchers concluded that age was an independent risk factor. However, this does not support the conclusion that current therapy standards in the elderly are insufficient because therapy is only a covariate, among many, for survival.
2. Table 3, did all of the patients receive surgery? If not, should surgery be included as a covariate?
3. Overall fitting outcomes (pseudo R2) of the models should be compared, as well.
4. Line 148, what are the methods of univariate and multivariate analysis? Logistic regression?
5. Line 163, for how long did 14,425 and 6,982 patients die of CSD and non-CSD?
6. Line 194-202, researchers concluded 70 years should be adopted as a suitable cut off age. Why was 70 years better as a cut off age, compared with other previously published studies?
7. Figure 2, what does cumulative incidence mean? Overall survival?
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: IMPACT OF OLD AGE ON RESECTABLE COLORECTAL CANCER OUTCOMES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is very clear with well done background provided.
Experimental design: no comments
Validity of the findings: no comments
Additional comments: Please check the reviewed document attached for additional comments.

Important:- not included BMI and comorbid conditions and substantiate this under study discussion section.


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

Input:
Title: IMPACT OF OLD AGE ON RESECTABLE COLORECTAL CANCER OUTCOMES
Review round: 1
Reviewer: 3

Output:
Basic reporting: The overall structure of the manuscript is good. However, the method is questionable and the policy implication is not quite sound.

Minor formatting issues:
a.	Suggest adding a sample flow chart to show how many patients were excluded by each exclusion criteria
b.	Line 92: it should be “(separated, widowed, and divorced)“?
c.	Line 127: please keep the decimal consistent throughout the context (i.e. “range 1.0-119.0 months”)
d.	Line 196: for the other previously published studies, please add citations
e.	Table 1: suggest adding a row to clarity which part is before PSM and which part is after PSM
f.	Table 2 and Table 3: please add total sample size, or clarify in the title that Table 3 is after PSM.
Experimental design: 1.	The objective of this study is stated as “to identify a reasonable cutoff age for defining older patients with colorectal cancer (CRC) and to examine whether old age was related with poor colorectal cancer-specific survival (CSS) and increased colorectal cancer-specific death (CSD)”.
The cutoff age is chosen based on CSS and so age will definitely be associated with CSS. You may want to point out to examine independent effect of older age after controlling for other characteristics.

2.	In Figure 1, the turning point looks considerably earlier than 70 years old. Can the author provide some detailed outputs from the Chow test, especially for age 60-70 years old.

3.	The statistical analysis part is a little confusing. The author mentioned that the primary end point is cancer-specific survival, and the secondary is cancer-specific death and non-cancer-specific death. For COX model, both death (yes and no) and survival time (months/days) are required for the model, so the endpoints are actually the same. I understand that in the first COX model the author censored the non-CSD, whereas in the second model, the author did PSM first and then treated non-CSD as competing risk. But keeping the second model should be sufficient.

4.	Even though the author adopted PSM, the matching didn’t seem to work very well. Quite a few characteristics still showed significantly different distributions across younger and older groups. Ideally, the characteristics should be well balanced between two groups that you only need to run COX model between Age group and CSD after matching.

5.	Has the author considered adding insurance status to the model?  Medicare may be highly correlated with your age measurement. But can try an “insured vs. uninsured” indicator or "public vs. private vs. none".
Validity of the findings: Age is widely known as one of the most important predictor of survival/death. Especially for older age patients, whose health status sometimes decreases disproportionally. However, I am not quite sure how much this cutoff age can contribute to current clinical practice. The author suggested stronger treatments to the older patients. However, the adjusted model showed that chemotherapy is actually harmful to the patients. (HR of CSD (receiving vs. not receiving chemo =0.84 (0.80-0.88)) I also suggest adding an interaction term between age group and CT/RT to see whether CT/RT affects younger and older patients differently.
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: IMPACT OF OLD AGE ON RESECTABLE COLORECTAL CANCER OUTCOMES
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: The fourth of exclusion criteria: patients who survived less than one month from diagnosis. This may introduce a selection bias. How many patients were excluded? Why did the researchers exclude these patients?
It has been addressed.
Validity of the findings: 1.this study concerns the prognostic risk factors of CRC. From the multivariate analysis, researchers concluded that age was an independent risk factor. However, this does not support the conclusion that current therapy standards in the elderly are insufficient because therapy is only a covariate, among many, for survival.
It has been addressed.
2.Table 3, did all of the patients receive surgery? If not, should surgery be included as a covariate?
It has been addressed.
3. Overall fitting outcomes (pseudo R2) of the models should be compared, as well.
It has been addressed.
4. what are the methods of univariate and multivariate analysis? Logistic regression?
It has been addressed.
5. For how long did 14,425 and 6,982 patients die of CSD and non-CSD?
It has been addressed.
6.researchers concluded 70 years should be adopted as a suitable cut off age. Why was 70 years better as a cut off age, compared with other previously published studies?
It has been addressed.
7.Figure 2, what does cumulative incidence mean? Overall survival?
It has been addressed.
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: IMPACT OF OLD AGE ON RESECTABLE COLORECTAL CANCER OUTCOMES
Review round: 2
Reviewer: 2

Output:
Basic reporting: Sufficiently addressed
Experimental design: Rigorous investigation performed
Validity of the findings: no comments
Additional comments: Study is meaningful and useful for further investigation


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: IMPACT OF OLD AGE ON RESECTABLE COLORECTAL CANCER OUTCOMES
Review round: 2
Reviewer: 3

Output:
Basic reporting: The author addressed all related comments.
Experimental design: Method:
Please add what models you used for your subgroup analyses (e.g. COX model).

Result:
PSM: balance test of covariates is important after PS matching. A poor prediction model can result in unbalanced covariates after matching. I wonder if the author looked into the model performance (C index). Prior studies have recommended adding interaction terms to improve the model performance.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3144483/

If the PS matching does not work and the author still needs to control for the covariates in the final model, why not just run a multivariate regression with the unmatched sample?
Validity of the findings: Data interpretation and conclusion

In table 2 and 3, the reference group of chemotherapy (CT) is "Yes" and the HR is 0.84 (0.80-0.88), which should mean patients not receiving chemotherapy had lower risks of death than patient receiving chemotherapy. In other words, receiving chemotherapy is harmful. In the supplemental figure 2 where the author added age interaction, the coefficients are also <1. Why is the conclusion then "favorite chemotherapy"? Please clarify your reference group in the comparisons.
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: SHIFTING HEADLINES? SIZE TRENDS OF NEWSWORTHY FISHES
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Overall I love this paper.  The methodology is sound and the paper is overall well written.  I have read over the paper several times now looking for any comment or suggestions to make but have nothing to offer.  I say this so that this review is not seen a light review but rather the paper is sound.  I offer the following as thought and discussion and maybe worth of inclusion?

1.  Do you think the lack of pattern reflects low sample sizes and the fact that even in subsets that several species are grouped together? Perhaps this blur any intraspecific patterns?
2. The shifting baseline requires two criteria.  The first one describes an overall decline in average size a shift in the distribution.  The second criteria is focused on extremes, i.e. the rare event.  Although the overall shift in the size distribution may be occurring it does not mean that these already rare events, both the existence of a record holder and its capture, will not happen.  You need simply a single individual to escape this pressure.  Does the fact the two criteria focus on different aspects of the size spectrum suggest they many not align?
3. It does appear in some of the graphs that the frequency of smaller individuals being reported is increasing even if mean reported size is not.  I would suggest potentially running a quantile regression to see if these patterns could be recovered in the lower quantiles.  Perhaps this is a draw of the recent as social media and internet have allowed us to report more.

***I had gotten excited about doing this and was going to attach r code and the figure to show you how many of your analyses would likely have significant regressions in the lower quantiles (<25%).  However, when I downloaded the data, I was unable to replicate Figure 1.  According the the text relative size is reported length divided by Fishbase max length (reported.length.cm / fb.max.tl.cm).  This needs to be clarified in 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: SHIFTING HEADLINES? SIZE TRENDS OF NEWSWORTHY FISHES
Review round: 1
Reviewer: 2

Output:
Basic reporting: very good
Experimental design: good
Validity of the findings: dubious
Additional comments: This paper is extremely well written and nearly flawless in its presentation.  However, the authors used excellent methods and sophisticated statistics and obviously did an exhaustive search of non-scientific literature to analyze questionable, unreliable, dubious, and perhaps incomplete (only literature in English) data.  Although the goal of this manuscript is laudable and very important, a manuscript resulting from good methods applied to unreliable data should not be published in a scientific journal. Perhaps some other venue would be more appropriate.


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: SHIFTING HEADLINES? SIZE TRENDS OF NEWSWORTHY FISHES
Review round: 1
Reviewer: 3

Output:
Basic reporting: I don’t have any concerns with the basic reporting categories
Experimental design: As a retrospective study, there’s no experimental design per se.  The research question is a worthy one: to test for the presence of a shifting baseline in media reports of size in marine gamefish and “charismatic megafish”.
Validity of the findings: Here I do have some concerns with the conclusions, particularly with respect to the charismatic megafish, rather than the gamefishes.
On line 200, the authors report that relative length of gamefish did not change over time, but that mass increased significantly.  This is an odd finding since length and mass are so tightly correlated.  Similarly, but in reverse, the relative length of charismatic megafish declined significantly over time, but their relative mass did not. No explanation is given for these unusual results, but they really leap out at the reader so it seems some speculation at least is warranted.
My greater concern is in the interpretation of the results relative to the charismatic megafishes and, specifically, the generalization of well-established reductions in fish length and mass over time among gamefish (refs on line 270) to apply to the megafaunal species for which no such reductions are yet in evidence. I can only speak out of experience with the megafaunal species, but I’m only aware of one published instance that documents decline in size of whale sharks, and that’s the Bradshaw and Holmberg papers cited on line 329-330, which document decrease in length of whale sharks at one site in Australia over time. I don’t think there’s any other whale shark site we’ve been following long enough to detect a change in size over time and I’m not aware of any similar reports for molids, basking sharks or manta rays, so I don’t think the authors can substantiate a pattern of scientifically proven decline in size among megafaunal species as they can for the gamefishes, and thus interpreting changes in their representation in media is tricky.
There’s a second problem with interpretation of the results concerns taxonomic confounding among the megafishes, specifically manta rays and Mola spp.. Up until recently, both mantas and sunfishes were considered monospecific, but we now know that there are probably three manta ray species and at least four Mola spp..  In both cases, the body size varies considerably between species, so how do we interpret historical reports of body size of a “manta ray” or “sunfish” without knowing which species we’re talking about? This does not apply as much to the gamefishes, who have been well studied and are on the whole more easily identified.
Third, something bugs me about the difference between the way gamefishes and megafaunal species come to be represented in media.  Gamefishes are deliberately fished, which is an activity that explicitly prizes and seeks to catch the largest individuals.  By contrast, the megafaunal species tend only be reported when they are stranded, entangled or caught as bycatch, all methods that are essential neutral to body size, at least relative to targeted gamefishing.  How this difference might be expressed in the way the species are recorded in media isn’t clear to me, but it seems like something that should be pointed out.
Finally, in the analysis of changing size relative to IUCN RedList status, the authors chose to compare to the current status of each species, but populations of these species might have been considerably different at the times when media reports were made.  Even accounting for this, it occurs to me that the RedList status and relative size ought to be negatively correlated because, as the population shrinks, both tails of the distribution move towards the central tendency, reducing the ratio of average size relative to the maximum.  I don’t know how else you would investigate relationship between size and conservation status, but it seems an inevitable consequence of reducing population size that relative size would decline, even if average size does not.
Additional comments: None


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: SHIFTING HEADLINES? SIZE TRENDS OF NEWSWORTHY FISHES
Review round: 2
Reviewer: 1

Output:
Basic reporting: I am happy with the revisions and feel the authors have adequately addressed the valid concerns of all three reviewers.
Experimental design: I am happy with the revisions and feel the authors have adequately addressed the valid concerns of all three reviewers.
Validity of the findings: I am happy with the revisions and feel the authors have adequately addressed the valid concerns of all three reviewers.
Additional comments: I think the authors have done a fine job of responding to the authors and I commend them on the additional efforts and analyses.


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: SHIFTING HEADLINES? SIZE TRENDS OF NEWSWORTHY FISHES
Review round: 2
Reviewer: 2

Output:
Basic reporting: no additional comments
Experimental design: no additional comments
Validity of the findings: no additional comments
Additional comments: I'm satisfied with the responses to my concerns except the one about taxonomic uncertainty.  While the sensitivity analyses are great, the statements about taxonomy of Mola and manta rays are inaccurate, probably due to an over-reliance on Fishbase rather than the taxonomic literature around these two megafaunal groups.  Fix that, which is pretty easy, and I'm happy to see this published. PLEASE SEE MY COMMENTS IN THE REBUTTAL FILE IN BLUE