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: OBAMA CHEZ MOI! THE INVASION OF METROPOLITAN FRANCE BY THE LAND PLANARIAN OBAMA NUNGARA (PLATYHELMINTHES, GEOPLANIDAE)
Review round: 1
Reviewer: 2

Output:
Basic reporting: First at all, I want to congratulate the authors for this important and relevant piece of work. The manuscript is original and provided many important information regarding the biology of an important alien species of European soils.
All the basic requirements are met. However, some important works are missing (e.g., Boll & Leal-Zanquet, 2016; Lago-Barcia et al., 2015) and many previously known facts are presented without referring to the appropriate previous work. Please, find more comments on this topic in the section “General comments”.
Experimental design: All the requirements are met, especially for the citizen science stuff of the manuscript. However, there are many errors and things which are unclear in the molecular part of the manuscript. It is unclear if the use a subset of the sequence of the species in Europe or all the available sequences (some key sequences are missing, see the “General comments section” for more information) and also the length of the sequences used in the analyses.
Validity of the findings: The results obtained in this publication will have an important impact on the study of exotic terrestrial flatworm biology, which represent an important concern for local soil fauna biodiversity conservation. Although the information from the citizen science project is in my opinion beautifully worked, the molecular part of the work is far more less novel and is flawed by some methodological and interpretation problems. Thus, the molecular part of the work critically needs a throughout revision before publication.
Additional comments: I really liked this manuscript. Please, let me congratulate you for the large amount of material you were able to collect and the impressive way you engaged citizen scientists to work with you. My recommendation is the publication of the manuscript after the authors perform a throughout revision. I will structure my review in two main parts: “major” and “minor” concerns. Major concerns are important errors that must be corrected before publication. Minor concerns are suggestions and minor comments that the authors should fix.
MAJOR CONCERNS
1. In the abstract the authors stated that they analyzed the COI variation of European specimens of the species collected from France, Italy and Switzerland. Thus, some parts of the distribution range of the species were not covered. However, in line 275, they said they used all available sequences on GenBank. Please, clarify which option was used. There are also published sequences of the species from Spain and Portugal (Álvarez-Presas et al., 2014; Lago-Barcia et al., 2015 and 2019). In my opinion, sequences from specimens from every part of the species distribution range (including native and invaded places) should be used. Please, add them and add the correct reference for each sequence.
2. Abstract and elsewhere: “This suggests that a single clade from South America invaded Europe, and that this clade had its origin in Argentina”. This statement is wrong and repeated many times in all the manuscript. As Lago-Barcia et al. (2019) demonstrated, the European specimens belong to both clades Argentina 1 and 2 (see major concern 3 for clarification regarding the nomenclature of the populations), and European populations were formed by at least 2 independent invasions of members each clade. Correct in every part of the manuscript.
3. The literature regarding the clades (=populations?) of Obama nungara is extremely confusing since at least three unrelated research groups worked independently on them and applied different nomenclatures without taking into account other previous work from other researchers. As an author of 2 of the articles dealing with this species in Europe, I am responsible of part of this mess, which I humbly accept. I think this interesting manuscript by Dr. Justine and coauthors brings a great opportunity to fix this problem in a definitive way. Here, the authors applied new names for the 3 previously known clades of Obama nungara (see Lago-Barcia et al., 2019 for more info): Obama nungara clades “Argentina 1”, “Argentina 2” and “Brazil”. Previously, the very same clades have been named as Obama nungara “network 3”, “network 1” and “network 2”, respectively. Álvarez-Presas et al. (2014) named “Argentine 1” and “Argentine 2” as “Obama sp. A” and “Obama sp. B”. Lago-Barcia et al. (2015) identified as Obama marmorata members of “Argentine 1”. Carbayo et al. (2013) named the members of the Brazilian clade as “Obama sp. 6” and later described Obama nungara using sequences from all the three lineages in Carbayo et al. (2016).
I understand the new nomenclature provided by the authors is far more attractive than “networks 1, 2 and 3”, so I encourage them to stick to this nomenclature, although it is new. However, I think they should properly refer to the previously literature identifying all these clades and also provide a synonym list for them to avoid more confusion in the future with this species. This is especially relevant for Table 1, where an incomplete list of synonyms is provided for Obama nungara and for understanding why so many sequences inside the Obama nungara clades of figure 16 are labelled as “Obama marmorata” and other names.
4. If the most fitting model was Tamura 3-parameter model with Gamma, why did the authors provide K2P genetic distances instead of uncorrected distances (p-distances)? Please, provide uncorrected distances for distance-based inferences. Also, use the most fitting model for the neighbor-joining analyses or p-distances, but not another model. How did you test if it is the proper model? State the software and methodology. Also use the same model for the ML reconstruction.
Please, be aware that in the results section (L. 268-272) the p-distances are provided, but in the material and methods is not stated that they were calculated.
I would say that the “evolutionary history” was assessed when using coalescent or other similar methods, which are more “historical” phylogenetic methods. Can you instead indicate “the phylogeny was inferred” instead.
5. Please, provide a full description of your haplotype networks. How many haplotypes did you find? Were they equally abundant? How many mutations were present between the networks and haplotypes inside the same network? Did you find the same number of haplotypes in the native and invaded regions? Did you find private haplotypes for any of those regions? Use all this information to discuss it in the context of the results obtained with the same methodology by Lago-Barcia et al. (2019).
6. “Interpretation of trees and network for the origin of invasion in Europe”. This section does not represent result but interpretation of them. It should be placed in the discussion. Besides, the results are biased since they did not use several Iberian sequences belonging to the Argentina 2 clade published by Álvarez-Presas et al. (2014) as Obama sp. B and later used by Lago-Barcia et al. (2019), grouping inside network 1 (see major concerns 2 and 3).
7. Authors should also properly acknowledge the previous literature. For instance, in L. 333-239 (as currently written), the authors attribute to themselves the same results obtained previously by Lago-Barcia et al. (2019). Besides, the last sentence is wrong, since Lago-Barcia et al. (2019) identified at least 2 different invasions events of Europe from two different populations coming from Argentina (networks 1 and 3).
8.I would not go so far on the arguments based on sexual and asexual reproduction used to explain the genetic variability of Obama nungara. Species with sexual reproduction might have extremely low levels of COI variation, even with a single haplotype described although many specimens sequenced (many examples currently described in the literature). The mutation rate could be not equivalent for the same marker in different species (or subfamilies!!!). Asexual species with large genetic distances is also possible, since the increase of multiple neutral genetic mutations are expected to occur in asexual organisms due to the absence of genetic recombination and the accumulation of mutations (see Ament-Velasquez et al., 2016).
If the mitochondrial hereditary is exclusively matrilineal (is it in plathyhelminthes? does exist studies on that?), the mitochondrial genome is not expected to recombine, so sex is not producing genetic variation for mitochondrial markers by itself. On the other hand, mitochondria usually have weak or inexistent mutation reparation mechanisms, so genetic variability might perfectly arise and transferred to clones in asexually-reproducing species.
The absence of genetic variation in some species of alien terrestrial flatworms in the invaded areas might be better explained by the number of invasions and the number of individuals involved in those invasions. For instance, if a single fertilized female of Platydemus manokwari, a sexually reproducing species according to the authors, was the origin of the invasions in the remaining world (e.g., a single individual taken from the native area which reproduced in a garden center and them spread to others by plant commerce with the mechanisms outlined in L. 369-371) and assuming matrilineal inheritance, the observed pattern might be explained. For answering this question, in my opinion, other markers with a faster evolutionary rate (microsatellites? SNPs?) should be used. On the contrary, invasions might also have occurred one or several times with a more diverse number of individuals, producing a different pattern of diversity for COI. We also need to take into consideration our knowledge on the genetic variation of these species in the native areas, which commonly is unknown or poorly known for alien terrestrial flatworms. Sadly, it is the case of Obama nungara.
I suggest authors delete the whole paragraph or provide a better discussion using multiple references on sexually- and asexually-reproducing groups of species. If the second is followed, please do not restrict the reference to Platyhelminthes.
Since I was not formally trained as a genetist, I would suggest the editor to ask other reviewers their opinion if this part of the discussion is maintained in subsequent review rounds.
9. I do not understand how it is possible that the support values of the clades from the ML analysis are so low in this manuscript when using the same methodology Lago-Barcia et al. (2019) obtained far better results. In the current state, the phylogenetic tree of figure 16 reads as a basal polytomy for all the clades involved and even the clades they describe are not supported. Please, review your analysis and update them. Also consider the missing sequences of Obama sp. B from Álvarez-Presas et al. (2014).
10.  Information in table 1 regarding the synonyms of Obama nungara is incomplete. Specimens from the Argentina 1 clade were referred as Obama marmorata in Lago-Barcia et al (2015). Specimens of both Argentina 1 and Argentina 2 clades were cited as clades A and B by Álvarez-Presas et al. (2014). I think this article give the authors a great opportunity to clarify all this nomenclature.
Obama nungara clade Argentina 1. Synonyms. Obama sp. A sensu Álvarez-Presas et al. 2014. Obama marmorata sensu Lago-Barcia et al. 2015. Obama nungara network 3 sensu Lago-Barcia et al. 2019.
Obama nungara clade Argentina 2. Synonyms. Obama sp. B sensu Álvarez-Presas et al. 2014. Obama nungara network 1 sensu Lago-Barcia et al. 2019.
Please, also keep in mind that many species were transferred to the current genus by Carbayo et al. 2013 and they might been recorded with other name in earlier publications. Those names should be reported as synonyms in this table.
11. Figure 17. Argentina 2 clade also includes individuals from Spain (see Lago-Barcia et al. 2019 for more information).
12. Information from Table 2. Also include other records of the species, such as those from Lago-Barcia et al. 2015 and Ávarez-Presas et al. 2014. I might forget more works reporting specimens, so this should be complemented with a more exhaustive literature search.
13. Please, revise the results from Table 2. They seems to be a great overlap between minimum and maximum interclade distances and when I did similar calculations with the similar matrix from Lago-Barcia et al. (2019) (unpublished results) I obtained a very different result. Also provide the results in percentage, are easier to read.
MINOR CONCERNS
L. 25. “Obama nungara has invaded several countries of Europe (Spain, Portugal, France, Belgium, UK, Italy)”. Please add “and” between “UK” and “Italy”. Remove the comma.
L. 45. “The present findings strongly suggest that Obama nungara is a highly invasive species and that the population which has invaded several countries in Europe comes from Argentina.” This conclusion is not novel from this work, so the authors should change this phrase to something like “The present findings strongly supports” or add “as previous research have shown”. Keep in mind that there is no single invasion of Obama nungara in Europe: there are 2. See the major concern number 2 and 3 for more information.
L. 58. Coenoplana coerulea is not rare at all, at least in Spain (unpublished observation of my own, but see the large amount of individuals sequenced by Álvarez-Presas et al., 2014). Please, reconsider this statement.
L. 61-64. Please refer to the specific works reporting this species in each of the listed places. They will help the readers to locate specific literature. Please, keep in mind that for some countries there more than an article dealing with them and have them compiled here would be very much appreciated for some readers (for instance me!  ). If you think this would make this paragraph less attractive to read, you can also add a table for that.
L. 66. Is there any previous research on abundance of the species in Europe? If so, please refer it.
L. 71-74. I do not get what you want to explain in this phrase. Can you reword it in a more clear way? Also, the placement of the reference seems to me maybe a bit misleading.
L. 75-76. Substitute “the name Obama nungara itself was assigned to the species as recently as 2016 (Carbayo et al. 2016)” by “the species Obama nungara Carbayo et al. 2016 was recently described” or a similar sentence.
L. 81-82. Remove. This is a conclusion of the work, not part of the introduction. Besides, the statement regarding the origin of the European populations is wrong (see major concern 2).
L. 86. Same methodology?
L. 87. Twitter.
L. 117. photographs.
L. 118. I think researchers usually need to get used to time consuming processes! Although I acknowledge all the time you spend making sure the rights of the authors of the photographs were fully respected, I do not see the necessity to add this phrase.
L. 124. (Switzerland and Italy).
L. 130. they were EUTHANATISHED in hot water and preserved in 95% ethanol.
L. 136-138. Are you renaming the pair of primers (JB3 and JB4.5?). Please, stick to the original nomenclature.
L. 138. “(Bowles et al. 1995; Littlewood et al. 1997)”. If those references refer to the both pair of primers in a respective way, please add “respectively”.
L. 139. “3Mm MgCl2”. I do not understand this measure.
L. 250. Substitute “plot” by “chart”.
L. 252. Space between the number and the “m” or not? Homogenize.
L. 307. If you use the Spanish sequences from Álvarez-Presas et al. (2014) and Lago-Barcia et al. (2019), you will see this statement is wrong.
L. 348. Reference missing.
No specific lines. In general, the discussion is weakly supported by references to other previous works which find/suggested the same. For instance, the plant commerce is commonly suggested as an invasion mechanism for soil fauna. The text would be stronger if the use previous literature to support the authors views and not present them as original thinking from the authors, especially if they cite also other researchers.
I personally love the section “Geographical and temporal biases in citizen science data: a warning” from the discussion. If possible, please provide more references on biased data from similar studies involving citizen scientists.
L. 423. 1,000,000 times
L. 427-428. “period when amateur gardeners spend more time in their garden”. Was this inferred from your observations, from your communication with citizen scientists or it is a suggestion from the authors?
L. 446. Correct the error regarding the geographic origin of the both Argentinean clades found in Europe.
L. 447-449. This information is not exclusive from your study. Rewrite.
L. 452-453. What exactly means the most important species? Careful: a less abundant species with a more specialized diet might have more important impact on native soil fauna by triggering local extinction of some species.
L. 454-458. Boll and Leal-Zanchet (2016) studied the diet of several species of land flatworms in their native area. Obama nungara was also assessed, showing a generalist predatory behavior. Please, include this information here, evaluate the putative impacts this kind of diet might have on native soil fauna and cite the article.
Figure 2 caption. Please, also include here the name of the person who identified the snail.
Figure 13 caption. Please, substitute “Mountainous parts (yellow on the map) were not invaded” by “There are not known records in the mountainous parts (yellow on the map)”.
Figure 14 caption. Please, substitute “The color shows the intensity of the invasion” by “the intensity of the color shows the density of recorded individuals by citizen scientists”.
Figure 16 caption. “The percentage of trees in which the associated taxa clustered together is shown next to the branches”. Is this an weird way to explain what bootstrap is? I do not fully understand it, please rewrite.
114 sequences. Remove “nucleotide” from here since it confuse the reader.
“150 positions in the final dataset” Do you mean nucleotides? In the material and methods longer sequences are described! This might be the origin of the low support values found in this study respective to Lago-Barcia et al. (2019).
Figure 16. Redo the analysis including the Álvarez-Presas et al. 2014 sequences of the Obama sp. B. You will see that also Argentina 2 specimens are present in Europe.
Figure 17 and figure 17 caption. Same comment as for figure 16. Redo and correct.
Figure 18 and figure 18 caption. Same.
Table 5. What means 20 days? 20 days in may? 20 days of total sampling? Clarify. Also provide how many days each month was sampled.
All the text. Please, provide the correct reference for Lago-Barcia et al. (2019), currently cited as Lago-Barcia et al. (2018, the online first version of the article). You can find here the correct bibliographic details: https://link.springer.com/article/10.1007/s10530-018-1834-9
REFERENCES (only listed if not currently present on the manuscript):
Ament-Velasquez, SL; Figuet, EJ; Ballenghien, M;  Zattara, EE; Norenburg, J; Fernández-Álvarez, FÁ; Bierne, J; Bierne, N & Galtier, N. (2016) Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea). Molecular Ecology. DOI: 10.1111/mec.13717.
Piter Kehoma Boll, Ana Maria Leal-Zanchet. (2016) Preference for different prey allows the coexistence of several land planarians in areas of the Atlantic Forest. Zoology http://dx.doi.org/10.1016/j.zool.2016.04.002
Carbayo, F., Álvarez-Presas, M., Olivares, C. T., Marques, F. P. L., Froehlich, E. M., and Riutort, M. (2013). Molecular phylogeny of Geoplaninae (Platyhelminthes) challenges current classification: proposal of taxonomic actions. Zoologica Scripta 42, 508–528. doi:10.1111/zsc.12019
Lago-Barcia D, Fernández-Álvarez FA, Negrete L, Brusa F, Damborenea C, Grande C, Noren˜a C (2015) Morphology and DNA barcodes reveal the presence of the non-native land planarian Obama marmorata (Platyhelminthes: Geoplanidae) in Europe. Invertebr Syst 29:12–22.


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: OBAMA CHEZ MOI! THE INVASION OF METROPOLITAN FRANCE BY THE LAND PLANARIAN OBAMA NUNGARA (PLATYHELMINTHES, GEOPLANIDAE)
Review round: 1
Reviewer: 3

Output:
Basic reporting: A very interesting, well-researched and well-documented and well-written study. All figures are necessary.
Experimental design: The use of citizen science data is very good and up-to-date. It is very commendable that the authors also performed a molecular study for tracing the place of origin of the invasive species.
Validity of the findings: Findings and conclusions are supported by the data.
Additional comments: On a print-out of the manuscript I have made hand-written annotations (see attachment). Most of these concern suggestions for typographic and linguistic improvements, as well as a few corrections of references. I presume that these hand-written comments will be legible as well as intelligable to the authors. Attaching a pdf with my annotations considerably shortens the review process (for which reviewers were only given 9 days!). Providing these annotations in digital format would have greatly increased the necessary time for reviewing this manuscript. I hope that the authors will forgive me and will appreciate my detailed reading of the manuscript and the suggestions for improvement.


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: OBAMA CHEZ MOI! THE INVASION OF METROPOLITAN FRANCE BY THE LAND PLANARIAN OBAMA NUNGARA (PLATYHELMINTHES, GEOPLANIDAE)
Review round: 2
Reviewer: 1

Output:
Basic reporting: See below.
Experimental design: No comment.
Validity of the findings: See General comments below.
Additional comments: Justine et al. 2nd review. Hugh Jones.

Much improved! Should be published. A couple of minor points follow.

Methods
Delete ‘five and a half year”. This is duplication since it is stated that the survey was conducted from “mid-2013 to the end of 2018”. Suggest giving the months and year of the survey, eg. July 2013 to December 2018.
This has consequences for Figures 20 and 21 (suggest make this more clear in each Figure legend).
In Figure 20, the 2013 the data is from only half a year, for the other years it is from 12 months (this is commented on in the legend as “half of the year” – give months, presumably July to December).
In Figure 21, the data for January-June covers five years, that from July-December covers six years. Could be given as mean+-SD error bars for each month.

Results.
Page 224. The dark brown form is stated as the most abundant form, “most abundant” covers everything from 51% to 99%!!!!

Table 1 and References. “Jones 1999” should read “Jones HD & Gerard BM. 1999”

Caenoplana bicolor should be called Caenoplana variegata.


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: OBAMA CHEZ MOI! THE INVASION OF METROPOLITAN FRANCE BY THE LAND PLANARIAN OBAMA NUNGARA (PLATYHELMINTHES, GEOPLANIDAE)
Review round: 2
Reviewer: 2

Output:
Basic reporting: Everything is correct. I would also like to point out to the high quality of Suppl. material 2. The idea of adding both files, both in FASTA and in MEGA format, the last one including the grouping of each sequence, is glorious. Supplemental file 3 is also very useful to researchers willing to further research in this topic.
Experimental design: Everything is correct.
Validity of the findings: Everything is correct.
Additional comments: First at all, I want to give a very positive feedback to the authors, since the manuscript (which was very interesting in the previous version) is now greatly improved. I also acknowledge the time and efforts that the authors invested in providing excellent specific answers for all the reviewers´ comments. My recommendation is the publication of this brilliant piece of work. Happily, I only have a few minor suggestions that might improve the quality of the manuscript. “L. X” refers to the lines on the PDF reviewing file.
L. 28. cytochrome c oxidase 1
L. 60. (European_Union 2019). What is this? A citation?
L. 224-227. Do authors think the light and dark brown collorations have anything to do with the size of the specimen (i.e., larger specimens get more pigmented and change the colour). This question is more about personal interest than a comment for the manuscript.
L. 228. Living adult specimens range in length from 52 mm to 108 mm.
L. 289-290. If the authors have this information, it would be interesting to state if the 2019 observations refer to the same period of the year than the 2014 (May to August).
L. 308. (ML, 96 %; NJ, 99 %). Also applies to L. 315, 319 and 320.
L. 327. Delete “independent”, it is redundant referring to “clades”. Other alternative is substitute “independent clades” by “independent groups”.
L. 336. You might mean “individuals” or “samples” here, instead of sequences.
L. 336. I am not sure if “large network” is a correct expression.
L. 339. What does “the largest haplotype” mean? Maybe “the most represented”?
L. 341. Among the less represented groups.
L. 353-356. Please, provide more data in this part regarding the number of specimens found.
L. 371-372. Please provide your hypothesis or a citation explaining why it is clarified that the invasion is not from Brazil.
L. 382. In my opinion, making this effort to clean up the lower quality sequences increases the value of your interpretation!
L. 383. “Argentina 2”. Please, clearly state from where the nomenclature outside this work came from. I totally understand the meaning, but other readers less familiarized with the Obama nungara literature might find themselves totally lost here. Please, also relate your new nomenclature to the one from Álvarez-Presas et al. (2014) and Carabayo et al. (2013) explained in my previous report.
L. 386. The most represented network?
L. 389. COI sequences with.
L. 424. an estimate of 1000 adult individuals/day/hectare in these gardens.  [Maybe other kind of area or in other place might produce less or more individuals]
L. 435-436. However, it could be argued that cities are warmer than the countryside surrounding them, likely providing better conditions for the species in winter. [Do we know which are the best conditions for these animals to live?]
Fig. 17. I think the sequence KJ659670 came from UK, not Spain. Add percentages to  the bootstrap support values.
Table 1 caption. Dolichoplana striata Moseley, 1877 and Kontikia andersoni Jones, 1981.
Table 1. von Graff 1899;Winsor, 1991 #4083}. Probably the reference manager created some problems here.
Table 2. Why for some countries is only stated the first occurrence and in others also the work of first occurrence of the species and “this work”? Is the year of these two records the same?
Table 2. It might be useful isolate the record of Corsica from mainland France, since the first one represents an Island without a geographic continuity with mainland France and maybe this date might provide some insights (or not!) about the time of spreading of this particular invasive species.
Table 3. The specimen JL067 was received as a cocoon(s?). Do these sequence came from a single specimen isolated from the cocoon content?
Table 3. What does the “Code” column mean? Is it a political definition of the territories? If so, explaining it might help non-French readers to understand it better.
Table 5. p-distance and Maximum Composite Likelihood)


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

Input:
Title: GENETIC RECOMBINATION AND DIVERSITY OF SAPOVIRUS IN PEDIATRIC PATIENTS WITH ACUTE GASTROENTERITIS IN THAILAND, 2010–2018
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article by Kumthip and collaborators describes the prevalence of human sapovirus among children in Thailand for a period of 9 years. The importance of sapovirus is becoming increasingly recognize as a cause of viral AGE in people of all ages, therefore reports on its prevalence and genetic diversity are necessary. In that sense this manuscript is well timed. I found however that some aspects of the study hasn't been properly described or analyzed in the manuscript as it is in its current form. I will give some more detailed comments in the next sections.
Experimental design: The authors should include a definition of what acute gastroenteritis was considered in this study and also specify the age range of the individuals included in it.
in the end  of the introduction I am missing a sentence in which the authors clearly defined which knowledge gap this study is filling.
In the sequence analysis and genotype identification paragraph ( lines 97 to 107), in particular in line 101the authors mentioned the use of one primer for sequencing, but I assume they used both ( forward and reverse), if so, please modify, otherwise please justify why not because sequencing techniques can have errors and by aligning and curating both sequences these errors can be fixed, if their sequences are based in only one read their accuracy can be compromised.
There is a recently released typing tool for calicivirus, which include sapovirus (https://norovirus.ng.philab.cdc.gov), I would suggest the authors to also try and type their sequences using it.
I noticed the authors didn't specify the type of phylogenetic tree and the model used, but they did mention it in the tree figure legends, please also do so in the material and methods section.
In the results the presence of confections is mentioned, and also in one of the tables, I would suggest the authors to consider adding this testing to the material and methods section.
Validity of the findings: I am missing some information regarding the location of the five hospitals, and if that locations can give a good overview of the sapovirus distribution in the whole country, or only of some particular regions. On that same idea, did the authors observed any particular genotypes in a particular location? or any seasonal trends? maybe include some information on this in the results and /or discussion sections.
In line 227 the  authors suggest that sapovirus classification should be based on both genes: capsid as well as polymerase, but they do not give any justification for that statement, I would mentioned that this is the direction that norovirus classification is going, and since sapovirus is a very similar pathogen in many aspects, it only makes sense to do the same for sapovirus, maybe include a reference as well (J Gen Virol. 2019 Oct;100(10):1393-1406. doi: 10.1099/jgv.0.001318).
Also, in lines 229 and 230 the authors said that the results "revealed the significance of the novel recombinant virus", that is just an empty statement if they have a possible hypothesis on the importance of recombinants, or biological implications, please elaborate that idea.
Additional comments: In line 62 the authors mentioned 17 genotypes, and the additional GII.8, but currently GII.8 is a well accepted genotype, and they can confidently said that sapovirus is divided in 18 genotypes. Furthermore, an additional GII genotype ( provisionally named as GII.NA) has been already proposed (Near-Complete Human Sapovirus Genome Sequences from Kenya. 2019. Diez-Valcarce M, Montmayeur A, Tatusov R, Vinjé J.)
In table 3 I suggest the authors show the patients age in only one unit, probably month, for clarity.Also in that legend specify the highlighted samples are the ones in which recombinant sapovirus were found.


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

Input:
Title: GENETIC RECOMBINATION AND DIVERSITY OF SAPOVIRUS IN PEDIATRIC PATIENTS WITH ACUTE GASTROENTERITIS IN THAILAND, 2010–2018
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manscript describes a study on the prevalence and diversity of sapoviruses in pediatric patients in Thailand. In addition, evidences for existence of recombinant strains are presented.
The manuscript is well written using unambigous scientific language.
Some recent references on prevalences of sapoviruses in human patients from different geographic areas are missed, some of them indicxating higher prevalences than those usual reported. For instance: Bucardo et al. 2014 doi:10.1371/journal.pone.0098201; Varela et al., 2019 doi:10.3390/v11020144; Thongprachumet al. 2015, doi:10.1093/infdis/jit254; Biscaroet al. 2018,  Infect. Genet. Evol. 2018, 60, 35–41, among others. A review of the recent literature is encouraged, since it would improve the discussion section.
Experimental design: The experimental design is correct and the research is within the scope of the journal. The objectives are well defined and the methods described with sufficient detail.
Validity of the findings: Conclusions are well based on the results obtained and linked to the original objectives.
Additional comments: In general, the manuscript is well written, the experimental design is correct and the results and conclusion can be of interest for the potential readers of the jurnal. A review of recent literature is encouraged, which can improve the 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: EARLY-LIFE INTESTINAL MICROBIOME IN TRACHEMYS SCRIPTA ELEGANS ANALYZED USING 16S RRNA SEQUENCING
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors assessed the intestinal microbiome of red-eared slider hatchlings (fed on commercial particle food) was systematically analyzed at four different growth stages (0d,10d, 20d, 30d) by 16S rRNA sequencing approach, and discovered that the gut microbial diversity was different at different development stage, and The diversity and richness of the intestinal microbiomes were lowest at 0-day, and increased with turtle growth except for the period at the start of feeding.
Experimental design: Some conclusion is more convincing the authors can compare the intestinal microbiome of red-eared slider samples from manual environment with that from natural environment.
Validity of the findings: that's ok
Additional comments: Early-life intestinal microbiome in Trachemys scripta elegans analyzed using 16S rRNA sequencing
By Peng et al.

Review:

The authors assessed the intestinal microbiome of red-eared slider hatchlings (fed on commercial particle food) was systematically analyzed at four different growth stages (0d,10d, 20d, 30d) by 16S rRNA sequencing approach, and discovered that the gut microbial diversity was different at different development stage, and The diversity and richness of the intestinal microbiomes were lowest at 0-day, and increased with turtle growth except for the period at the start of feeding. I have some concerns as listed below. I suggest the authors to carefully revise their manuscript before further process.
 Major concerns:
1.	The sample size is small and I found there are different among the 3 samples from each stage from PCoA plots in figure 1 and Taxonomic compositions in figure 2, I don’t know the authors how to resolve the problems ? Moreover, why you take samples from only the 4 development stage (0,10,20,30 days after hatch)?
2.	As we known, Sequence quality can affect the results, in the MS, I have not found the content about the sequence results, specially about sequencing depth.
3.	The authors also sequenced the Water samples in the pool in which the turtles were living, why not compare the results with the samples at 0day? If the intestinal microbiome at 0 day is related with the water?

Other concerns:
1. Some conclusion is more convincing the authors can compare the intestinal microbiome of red-eared slider samples from manual environment with that from natural environment.


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: EARLY-LIFE INTESTINAL MICROBIOME IN TRACHEMYS SCRIPTA ELEGANS ANALYZED USING 16S RRNA SEQUENCING
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper report the analysis of the intestinal microbiota in hatchling Trachemys scripta ranging from 0 to 30 days of life.
The manuscript is overall clear and the English is good.
Provided literature and background are sufficient to understand the subject, still some personal background knowledge is needed, as for all the papers.
The work is well organized and provided raw datas are enough to understand the experimental design and results.
Results are significant and self-contained, but some generalizations made by the authors in the discussion and conclusions sections need to be revised.
Here a list of suggested revisions and some comments. The list is organized by lines (top to bottom):
Lines 25-26: The abundance of Clostridium also showed the highest value in 10-day turtles and then decreased over time.
Based on table S3 information, looks like only at 20-days you detected a decrease in Clostrium concentration.
Clostridium	11.95	24.98	8.23	17.50	0.15

INTRODUCTION:
Line 40: improving host performance
I suggest removing this sentence or to explain the meaning of “improving performance”.
Line 40: reducing environmental pollution
As stated by different papers in the recent literature, microbiome is involved in different biochemical process ending in bioactivation of drug and pollutant compounds. Furthermore, the bacterial population concentration is itself influenced by the presence of pollutant and chemicals, generally speaking. For all these reasons I would recommend to remove this sentence.
Here listed some examples:
Jin Y, Wu S, Zeng Z, Fu Z. Effects of environmental pollutants on gut microbiota. Environ Pollut. 2017 Mar;222:1-9. doi: 10.1016/j.envpol.2016.11.045. Epub 2017 Jan 11.

Yvonne Vallès and  M. Pilar Francino. Air Pollution, Early Life Microbiome, and Development. Curr Environ Health Rep. 2018; 5(4): 512–521.

Yuanxiang Jin, Sisheng Wu, Zhaoyang Zeng, Zhengwei Fu. Effects of environmental pollutants on gut microbiota. Environmental Pollution. Volume 222, March 2017, Pages 1-9.
Lines 44-45: colonization resistance
I would suggest authors to include this paper in the reference list.
Ducarmon QR, Zwittink RD, Hornung BVH, van Schaik W, Young VB Kuijper EJ. Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection. Microbiol Mol Biol Rev. 2019 Jun 5;83(3). pii: e00007-19. doi: 10.1128/MMBR.00007-19. Print 2019 Aug 21.

Line 48: between host health, immunity and disease resistance.
Please consider placing a comma (,), before the and.

Line 59: …invasive environment (Ma et al. 2013; Zhao et al. 2013)Several of these advantages…
I am not sure what authors mean with “invasive environment”, can you please substantiate the term? Additionally, place a full stop (.) and a space, after citation brackets.
Line 70: (absorbed into the abdominal cavity)
Replace abdominal cavity, with celomatic cavity.
Lines 70-71: In captive animals the diet is primarily commercial particle food that has high levels of protein.
Place a reference, please.
Lines 71-72: By selecting for bacteria associated with this change of nutrition access, the host is thought to derive a benefit in the form of increased absorption efficiency.
Place a reference, please. Furthermore, I am not sure how commercial diets could have had an influence on the biological success of Trachemys spp.
Line 73: The present study analyzes (for the first time) the changes in the intestinal bacterial community…
Please, consider replacing brackets with comma (,).
Line 80: Newly hatched red-eared sliders were randomly selected from the Hongwang turtle farm …
It would be thoughtful of you to tell readers how much time after hatching the turtles were collected. If it is immediately after hatching, please say so. Additionally, please clearly state the number of animals included in the study.
Lines: 82-84: The external yolk sac of newly hatched turtles was typically almost fully assimilated by day 10 after hatching and so a standard diet (turtle food, Inch-Gold, China) was first fed after day.
I suppose that yolk sac resorption timing was an observation you made; in this case, consider writing the exact number of days in the result section and here just place a generic “after yolk sac assimilation”. Additionally, “fully assimilated” might be misleading because after closure of the umbilical fontanel, this structure is still present in the celomic cavity (as you stated in the introduction). So, I suggest replacing the sentence with:
After complete closure of the plastron umbilical fontanel, the animals were feeded with standard diet (turtle food, Inch-Gold, China).
Line 84: physiological indexes
Can you please specify what do you mean with this term?
Lines 99-100: The reads archived by high-throughput sequencing were filtered to remove reads containing ambiguous nucleotides and the reads of the primers, and the clean reads were used for further data analysis.
The extensive repletion of the word “reads” makes the sentence unclear. Since I agree that “reads” is the proper terminology, I suggest splitting the sentence.
The reads archived by high-throughput sequencing were filtered to remove both those containing ambiguous nucleotides and primers sequences. The clean reads were used for further data analysis.
Line 106: with SILVA(Quast et al. 2013),
Place a space before the bracket.
Line 125: cultured
Please, replace cultured with raised.
Line 128: body weight, body height, carapace length and width
The procedure you used to perform these measurements must be included in the materials and methods section.
Line 141: difference
Is this different?
Line 138: richness
I am sorry, with richness you mean the overall concertation of bacteria or the number of bacterial populations, or both? Please, consider to rephrase the sentence in a cleared way.
Lines 139-140: highest intestinal abundance after growing for 10 and 20 days
The overall concentration was higher at 10 or 20 days? If was equal, please, state it.
Line 157: was 181.97, 299.80, 2.47, 2.50.
Place an and in front of 2.50.
Lines 180-181: The abundance of Clostridium was also highest in 10-day turtles but decreased somewhat as turtles transitioned to eating commercial food.
I suggest removing this sentence, because as is it is not informative and not even, somewhat, correct.
Line 183: The specific OTU numbers of 0-day, 10-day, 20-day, and 30-day turtles were 1299, 2845, 2509 and
Place a comma (,) before the and.
Lines 185-186: These core OTUs were belonged to three families, the Peptostreptococcaceae, Lachnospiraceae and Clostridiaceae with relative abundances of 23%, 9% and 68%, respectively.
It would be nice to have bacteria listed in order of increasing relative abundance.
Line 192: Bacteroidia and Erysipelotrichi
Consider placing a comma (,) before the and.
Lines 197-199: In summary, these different taxa could be used as distinguishing biomarkers. The red-eared slider revealed 20 such microbial biomarkers that showed significant differences in abundance at different growth stages.
I have a doubt about this sentence. You substantiated that environmental water microbiota dose not seems to affect intestinal microbiota, but what about food and other environmental conditions, such as temperature and season? What about diseased animals? Can you be 100% sure that these bacterial population can be used as a generalized biomarker?
Line 244: produce antineoplastic properties
I am sorry, do you mean that produce antineoplastic substances, or that has anti-neoplastic properties?
Line 260: Thus, the intestinal bacteria of these phyla were rarely affected by environment.
I would use caution saying something like that. Your experimental conditions were standardized, and you might have had no chance of observing environmental effects on the intestinal microbiota.
Line 260-262: So, it could be deduced that the intestinal microbiomes of red-eared slider were mainly regulated by itself, which would endow the turtles with the ability to readily adapt into different environments, different foods and seasonal changes.
You might be right, but you cannot prove it. Please, rephrase the sentence in a more dubitative way.
Lines 271-272: It could lead to adjustments to the microbiome populations, whereas in the captive environment, almost no changes in commercial food might stabilize the bacterial populations more quickly.
This sentence underling that environment can affect intestinal microbiota, and this is quiet in disagreement with what have been wrote above.

Table S1: 20-dayd.
Replaced with 20-day. Please apply the change to all the other tables.
Figure1: Please, consider to maker the legend more readable. Remove TSE and just put Day 0, Day 10,… What does TSEe mean? Which type of grouping represent? It is the water?
Figure 4b: Can you please consider to put all the letters in black and bolted?
Figure 5: In the figure legend, state the meaning of the “star” placed near to some of the bacteria names.
Table S6: Change “Number of sequence” to Sequence number, if I correctly understood what you mean.
Experimental design: This work is well designed and structured but, as many other in the filed, has a major limit, that is lost of variety. I wish to point out, that if you take 12 animals, from the same breeding center, you keep them together (even if in small groups), with the same diet, very limited environmental variables, and a single measure for each animals, generalizations and comparison with wildlife condition must be expressed very carefully.
Some information is missing in the material and methods, such as how you performed euthanasia and how did you take turtles measurements.
Additional suggestion are reported in the "basic reporting" part.
Validity of the findings: The work is innovative and provide some clue on the ecological success of Trachemys spp.
Data are provided and statistical and bioinformatics analysis look correct.
Conclusions and discussion need minor revision in the view to reduce inferences on the finding applied to less controlled conditions.
Additional comments: It would be nice to expand your research by adding wild caught animals and increasing variability. Additionally, you might think to perform cloacal swabs instead of killing the animals; this will allow you to repeated analysis on the same animal. In this way you may take some hatchling Trachemys and "follow" their microbiota evolution over a longer period of time.


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: EARLY-LIFE INTESTINAL MICROBIOME IN TRACHEMYS SCRIPTA ELEGANS ANALYZED USING 16S RRNA SEQUENCING
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is generally clear and well-written, although there are several instances in the manuscript that could benefit from more clear explanation and specific details. For example, it is not clear when the water samples were collected (i.e., at which time point). Also, the Methods suggest that feeding began after the 10-day time point, but in the discussion of the results it less clear whether turtles sampled at 10 days had access to food prior to euthanasia or not (see attached pdf for more specific comments). Good background material is provided, but there is very little information about what is currently known about the gut microbiome in other turtle species. Such information would be helpful for providing comprehensive context and relevance of the current study. The manuscript is structured appropriately.
Experimental design: Study conforms to the aims and scope of the journal and the research question is well defined – it is a descriptive survey of the gut microbiome in developing red-eared slider turtles. I see no obvious issues with the study design, but the limited scoped does restrict the types of conclusions that can be drawn. Methods are generally good, but there are some important pieces that should be explained in more detail, such as whether the alpha-diversity measures used for analyses were produced by Mothur or Qiime (see attached pdf for more specific comments).
Validity of the findings: Data are provided. The results of this study are interesting because they provide baseline information about the gut microbiome in this species and because they document microbiome changes over early turtle development. However, the relatively small sample size and comparative nature of this study do not allow for the types of strong conclusions that the authors propose in the Discussion section regarding adaptability and nutritional efficiency. A general suggestion to the authors would be to use figures to illustrate changes in relative abundance of selected bacterial taxa exhibiting significant variation with age, including appropriate statistical results. Presenting these data in figure form as opposed to in-text would help the reader to better interpret the nature and relevance of these changes. I have included specific comments on which speculations in the Discussion could benefit from clarification and better support from the literature (see attached pdf for more specific comments).
Additional comments: Please see attached pdf for both general and specific comments on this 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: EARLY-LIFE INTESTINAL MICROBIOME IN TRACHEMYS SCRIPTA ELEGANS ANALYZED USING 16S RRNA SEQUENCING
Review round: 2
Reviewer: 1

Output:
Basic reporting: Line 87: ability to exploit new food supplies in a new environment
Consider to rephrase in something like: “… ability to adapt to different environment by exploit new food sources/supplies”

Lines 89-100: The community of the gut microbiome varies at different growth stages (Burgos et al. 2018; Dulski et al. 2018; Huang et al. 2014).
Can you find some references from other turtles/tortoises? All the reported references are from fishes.

Lines 100-105: Although there have been some studies on the gastrointestinal microbiome of sea turtles (Ahasan et al. 2017; Price et al. 2017), as far as is known, there is a lack of studies relation to gut microbiome of Trachemys scripta elegans
There is a project on the intestinal metagenome in Trachemys. See the link below.
https://www.ncbi.nlm.nih.gov/bioproject/481331

Lines 116-117: The newly hatched turtle was still placed in incubator with vermiculite, until its exogenous yolk sac was assimilated almost at day 5-10 after hatched
And in account to wat stated in the rebuttal:
Lines: 82-84: The external yolk sac of newly hatched turtles was typically almost fully assimilated by day 10 after hatching and so a standard diet (turtle food, Inch-Gold, China) was first fed after day.
I suppose that yolk sac resorption timing was an observation you made; in this case, consider writing the exact number of days in the result section and here just place a generic “after yolk sac assimilation”. Additionally, “fully assimilated” might be misleading because after closure of the umbilical fontanel, this structure is still present in the celomic cavity (as you stated in the introduction). So, I suggest replacing the sentence with:
After complete closure of the plastron umbilical fontanel, the animals were feeded with standard diet (turtle food, Inch-Gold, China).
Answer: This sentence has been corrected. It is difficult to give the exact number of days of yolk sac assimilated, because the days of yolk sac assimilated are different for different individuals (most of them are 10 days or so).
Please, rephrase the sentence because it is not clear and probably some words are missing. I would suggest to you not to use the word “exogenous”, and replace it with “extra celomic”. You can consider something: “Newly hatched turtles were kept in the incubator up to 5-10 days post hatching, when vast majority of the yolk was absorbed”. When did you consider the hatchlings ready to come out the incubator? Which was the size of the yolk sac (the mean value)? In the rebuttal you state that most of the animals requires 10 days or so to absorb the yolk-sac, so why you state that the incubation range time is 5-10 days? Five days of difference is a huge amount of time.

Line 118: Then, these turtles of 10-day were mixed farmed
This is not completely true, since you sacrificed 3 animals at day 0, meaning that only 9 animals underwent commercial feeding.

Line 120: after feeding, growth indexes
Do you mean after hatching?

Line 122: and anesthetized at -20℃ crymoanesthesia for 0.5-1 h
Do you mean cryoanesthesia? Please, also consider to place the timing in minutes (30-60 minutes).
I am wondering if you can consider this anaesthesia only. It is likely to me that an animal place at -20C for an hour it is likely to have permanent neural damage, especially in heliothermic species as reptiles. How did you kill the animal before removing the intestinal tract?

Lines 327-328: So, it can be inferred that the intestinal microbiomes of red-eared slider may be regulated by itself,
What about replacing “regulated by itself” with self-regulating

Lines 338-340: In our study, the living water environment can not affect the gut microbiome of red-eared slider under the standard condition.
Sorry, can not or do not?

Lines 340-342: According to other paper about the effects of food on people and other animal (Chen et al. 2014; Zha et al. 2018), so we infer that other factors such as food may affect the gut microbiome of it.
 Please, consider to rephrase the sentence in something like: “Based on the literature available in humans and other animal species (Chen et al. 2014; Zha et al. 2018), it is possible that multiple exogenous factor, including food/feed, influcences the intestinal microbiota community”.

Lines 343-345: In the family and below level, total 10 biomarker was discovered in the 0-day, 10-day, 20-day and 30-day samples. The biomarker was obviously different for the different age groups, so it inferred that gut biomarker might help to predict age of this turtle.
Biomarkers? (in both the sentences).

Line 349: highest at 10-day because of its first offer with food and the change of living environment.
Based on this sentence, I understand that environmental change (i.e. Moving from the incubator to the water) has influenced the microbiota and this is not in agreement with what you stated above. Please, consider to rephrase the sentence.
Experimental design: This work is well designed and structured but, as many other in the filed, has a major limit, that is lost of variety. I wish to point out, that if you take 12 animals, from the same breeding center, you keep them together (even if in small groups), with the same diet, very limited environmental variables, and a single measure for each animals, generalizations and comparison with wildlife condition must be expressed very carefully.
Some information is missing in the material and methods, such as how you performed euthanasia and how did you take turtles measurements.
Validity of the findings: The work is innovative and provide some clue on the ecological success of Trachemys spp. Data are provided and statistical and bioinformatics analysis look correct.
Conclusions and discussion need minor revision in the view to reduce inferences on the finding applied to less controlled conditions.
Additional comments: Thank you for the answer. In my opinion would be of more interest having the follow-up from a single subject at different timepoints, compared to having multiple subjects. For example, having a single subject and see how microbiota change secondary to stress and more importantly how long dose it takes to return to normality (if ever) would be a more useful information (for example for a veterinarian). I do not know how much material you need for the microbiome, but you can also consider to perform intestinal FNA (Fine needle aspirates) to collect fecal material.


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: EARLY-LIFE INTESTINAL MICROBIOME IN TRACHEMYS SCRIPTA ELEGANS ANALYZED USING 16S RRNA SEQUENCING
Review round: 3
Reviewer: 1

Output:
Basic reporting: The authors assessed the intestinal microbiome of red-eared slider hatchlings (fed on commercial particle food) at four different growth stages (0d,10d, 20d, 30d) by 16S rRNA sequencing approach, and discovered that the gut microbial diversity was different at different development stage.
Experimental design: It's ok.
Validity of the findings: Need to supply the Rarefaction curves for all samples.
Additional comments: The authors just answer my reviews in their rebuttla letter, and some I don't agree. Even you sequenced 16S rRNA, you still can check if most of the diversity presented in your samples according to Rarefaction curves, and   you still not compare your results with the ones from the environment.


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: EARLY-LIFE INTESTINAL MICROBIOME IN TRACHEMYS SCRIPTA ELEGANS ANALYZED USING 16S RRNA SEQUENCING
Review round: 3
Reviewer: 2

Output:
Basic reporting: The paper is now ready to be published, in my opinion.
Experimental design: The experimental design is correct
Validity of the findings: The paper presents scientifically valid findings.
Additional comments: I would like to thank the authors for your collaboration in reviewing 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: POSTHARVEST BIOCHEMICAL CHARACTERISTICS AND ULTRASTRUCTURE OF COPRINUS COMATUS
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this paper, the change of color, SOD, CAT and POD activities, chitinase, β-1,3-glucanase, Cx and PG activities and the ultrastructure of Coprinus comatus was analyzed. The research does have some significance to understand why C. comatus is difficult to keep fresh. However, the paper should be major revised before being published.

Major comments

This paper shown the postharvest change of C. comatus, but did not give any suggestion about how to extend the storage life of C. comatus. Author declared that, by inhibiting the activity of PPO, the color quality of C. comatus can be effectively improved. This should be proved by experiment. At last, the author should change the storage condition to decease the postharvest change of C. comatus. Meanwhile, in the discussion, possible technologies to extend the storage life of C. comatus should be discussed.

Writing is very poor. The ms should be revised carefully and checked by native speakers in scientific American or British English. A lot of discussion was in the results part of ms. The results should be describe more clear.

In the ultrastructure changes, the organelles, nucleus, mitochondria et al., should be marked in the Fig., and the thickness of cell wall should be measured and counted.

Line 149. P value for statistics is incorrect. Normally, p < 0.05 means significant differences. The method for calculating the p value should be described in method. The significant differences also should be marked in the figures.

Minor comments

C.comatus should be C. comatus.

Line 50. C. comatus should in Italics

Line 68-70. Lim et al. (Lim et al., 2009) should be Lim et al. (2019). Other references also need to be revised according the requirements of the journal.

Figure 5. “umol/L” should be “mol/L” in symbol typeface.

Fig. 2 was not cited in the ms. Fig. 1 and Fig. 2 could be merged.

Every abbreviation should be shown first with its full form. Such as “FW”, “MDA” and so on in the ms.

Line 231, et al. bisporus mushroom is not the Latin scientific name, and should be agaricus bisporus.
Experimental design: The detail of method should be provided even it is reported by other paper.
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: POSTHARVEST BIOCHEMICAL CHARACTERISTICS AND ULTRASTRUCTURE OF COPRINUS COMATUS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript is described about "Postharvest biochemical characteristics and ultrastructure of Coprinus comatus". It is good manuscript for the readers of PeerJ.
I have some recommendations about this manuscript.

1. You should quote a little more papers in the section of "Discussion".
Line 274-277 :  Are these activities of  SOD, CAT, POD higher or lower than another mushrooms.

Line 287-289: Do the activities of chitinase, Cx, PG, beta-1,3 glucanase increase during postharvest storage in other mushrooms.

2. About the localization of chitinase, Cx, PG, beta-1,3-glucanase
You didn't discuss about the localization of chitinase, Cx, PG, beta-1,3-glucanase (autolysis enzymes). You should discuss about it.
Experimental design: It is ok about experimental design.
Validity of the findings: This manuscript is good findings about postharvest biochemical characterization and ultrastructure of C. comatus.
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: POSTHARVEST BIOCHEMICAL CHARACTERISTICS AND ULTRASTRUCTURE OF COPRINUS COMATUS
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This manuscript reported postharvest biochemical characteristics and ultrastructure of Coprinus comatus and showed some interesting results, however there are some mistakes in the scientific names of the mushroom strain in this manuscript and some concepts of chemical components and structures of fungal cell walls. Therefore, the supplemented data and major revision are needed for further review.

1. Line 70-77. By study of a autolysis mutant of C. cinerea fruiting bodies explored that β-1,3-glucanases plays a major role in the autolysis of Coprinopsis fruiting bodies (J. Agric. Food Chem. 2015, 63, 9609−9614). Authors should cite this recent progress.

2. Line 92. Was the C. comatus strain used in this study really characterized as a C. comatus stain by morphological identification and molecular identification? I felt that the fruiting bodies shown in the manuscript were very different from common C. comatus fruiting bodies.

3. Line 100-104. color difference meter, producer? What do L, a, b, E, and


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: POSTHARVEST BIOCHEMICAL CHARACTERISTICS AND ULTRASTRUCTURE OF COPRINUS COMATUS
Review round: 1
Reviewer: 4

Output:
Basic reporting: The article shows some novel informations about the Coprinus comatus mushroom activity during storage. The English is professional, just some minor modifications might improve the text quality (for example: row: 36-38; 153-158).
The cited references are correct, and contain all the necessary articles. The charts and figures and clear, professional. I couldn't see the raw data, but the output of those can be adequate.
Experimental design: The authors worked with traditional methods and used common techniques for the research. However the used methodology are clear and might be some evidence, the description of those is completly missing. The materials and methods chapter are citing the references, but the way of measurement is missing (line: 106, 108, 110-113, 115-120, 123-126). In my point of view, the proper description of the used methodology (and not the reference's description) is highly improves the acceptance of the results. The instruments, chemicals and details about measurements are needed.
Validity of the findings: The output of the results are claer, and confirmed by the measurements. The conclusions are supported by the charts and are well stated.
Additional comments: - The cultivation technology of the mushrooms have a high influence onto the shelf life and storage. The irrigation during the crop, the compost (is it a compost or a fermented subtrate, sterilised/pasteurised) and the environmental conditions (CO2, RH%, temperature) are having influence into the mushrooms picked. Therefore, some technical data about crop management would improve the text and helps to understand the chemical changes during storage.
- The Fig. 1 shows the Coprinus mushrooms. They are young and looks no light during cultivation were used. Does it have any influence onto the mushroom's quality? The proper identification of the mushroom was done by classical methods?
- In the text a phrase 'Bisporus mushroom' (line: 68, 231) is mentioned but not clear what does it mean. Is it refer to Agaricus bisporus?
- A list of abbreviations would nice to have (PPO, MDA, etc) and the full name would great to write into the title of the figures (Fig. 5,6, 7)


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: POSTHARVEST BIOCHEMICAL CHARACTERISTICS AND ULTRASTRUCTURE OF COPRINUS COMATUS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The revised manuscript still has some issues need to be modified further for publication in the journal.

1. Authors indicate that the C. comatus strain used in this study is a domesticated cultivar of C. comatus77 which looks different from the wild. Authors should give the reference for the strain in which the shape of fruiting bodies was shown and readers can know its difference from common C. comatus fruiting bodies. Otherwise, authors need to give identification data.

2. The revised manuscript still lacks the information of the company for production of color difference meter.

3. Authors have deleted the description of mushroom cell walls containing cellulose and pectin in the revised manuscript. However, the answers to comments are not good.
It is a scientific knowledge that fungal cell walls do not contain cellulose and pectin as components unless new experimental evidences are presented in the future.
As described by Zhen (2011), cellulose in tissues was digested and washed out with H2SO4, the difference of weights between the acid-treated tissue and the non-treated tissue represented the cellulose. Apparently, here the method for analysis of plant cell walls was incorrectly used for analysis of fungal cell walls. In plant cell walls, cellulose is insoluble whereas hemicellulose is soluble. So cellulose could be hydrolyzed with and washed out with H2SO4 to determine the cellulose content in the plant cell walls. However, in fungal cell walls such as basidiomycete cell walls, insoluble components are chitin and beta-1,6-branched beta-1,3-glucans. So, Zhen (2011)'s document did not provide a convinced evidence for existing of cellulose in mushroom cell walls. So far, no definitely report proves that basidiomycetes cell walls contain cellulose except some reports from Chinese scholars. In fact, fungal cell walls contain some beta-1,3/1,4-glucans which is different from cellulose (J Biol Chem, 2000, 275(36): 27594–27607; Molecular Microbiology, 2007, 66(2): 279–290). However, cellulases did not hydrolyze it (FEBS Letters, 52(2): 202–207).
According the methods for analysis of pectin content described by Shen et al (2013),  so-called pectin was extracted from mushroom fruiting bodies with boiled water or boiled acid solution. Again, here the method for analysis of plant cell walls was incorrectly used for analysis of fungal cell walls. No scientist characterized a component as a pectin in fungal cell walls so far. We can image that some components could be extracted from mushroom in Shen's experiment but they were not pectin. So, we could not get conclusion that fungal cell walls contain pectin component only according to the non-specific extraction and quantitative analysis of pectin in fungal cell walls.

4. References format are chaos and must be modified carefully.


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: NICHE DIFFERENTIATION IN THE RHIZOSPHERE AND ENDOSPHERE FUNGAL MICROBIOME OF WILD PARIS POLYPHYLLA SM.
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors used sound statistics to support their work. The background is sufficient enough for the readers to understand the concept of why this work was performed. But I have some reservations. Probably reference list should include some more. The figure legends need to be fixed. There are certain ambiguous statements that needs to be corrected.
Experimental design: The question was well defined. But had it been the authors had some phytochemical data that would have made this work interesting. Experimental methods and statistical procedures were done rigorously.
Validity of the findings: The authors need to expand more on their results in their discussions.  The data should have been supported by some phytochemical data so as to enrich.
Additional comments: It was interesting to go through this manuscript. The experiment was performed with rigorous statistical procedures and bioinformatic analysis. But I have certain reservations.
1.The authors should reflect more in the discussion.
2. Introduction can be expanded a bit.
3. I would suggest the authors to write the identified bacteria with a word 'ÓTU' besides the name. As it is an identified Operational Taxonomic Unit (OTU) .
4. Where ever the scientific name of the plant or the name of bacterial OTU (whether it is genus or species) was written, it should be written in the standard format (e.g. italics) for example in the line 26 and 27
5. The samples name or list in the figures should be same, as in some cases it is written as Rhsoil, Soil, Rhizosphere soil.

Line 26 Remove the extra dot after 'Sm'.
Line 50 Space should be added after 'genotype'
Line 84 Correct the formation of sentence
Line 86: This sentence is confusing when you compare it with line 84. At one place you are saying that you have collected the samples separately and another place you were saying complete plants. Rephrase it.
Line 92: Rephrase this sentence 'the root soil was shaken
Line 106: I could not understand, what the authors want to say regarding these two phrases?
1.  'the deviation of DNA extraction
2.  'Extracted of DNA with unified operate'.
Line 115: What is meant by '3 parts', Were the authors referring to three replicates ?
Line 135: Did you remove the sequences less than 300bp or the terminal primer sequences or the adapters as it is confusing?
Line 160: In the line 152, it says that using Primer deletion software you have removed the sequences that are less than 300 bp. Then how could it be that you used 272 bp (Max) and 172 (min) were used for the analysis. Can you please clarify it?
Line 201: Hardly 40% of the variation is being explained. So how can you say that it is significant. You need to have some kind of data that supports this data statistically and as well as significantly.
Line 207: when you have already classified at Phyla and Species level. Why was Species analysis was carried out to identify phyla?
Line 224: It should be leaves of leaf.
Line 231: Re-write the sentence as it is confusing
Line 290: Are you sure? because Bodenhausen et al 2013 work was about bacterial communities using 16S region primers  (V5-V7 region). But you are talking about the fungi. In general, plant chloroplast always gets amplified during bacterial DNA amplifications.
Line 309: What is it meant by 'OTU levels were different'. Were you referring to the relative abundance?
Line 310: Rewrite the sentence.
Line 313 to 316: Please rewrite the sentence as it is confusing.
Line 333: Many articles have also published this information such as Bulgarelli et al 2012, Lundberg et al 2012 with respect to bacteria and  Nallanchakravarthula et al 2014 with respect to fungi.  It is better to add those references also.
Line 346: instead of fungal write it as 'fungi' or do you want to add another word after 'fungi'?


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: NICHE DIFFERENTIATION IN THE RHIZOSPHERE AND ENDOSPHERE FUNGAL MICROBIOME OF WILD PARIS POLYPHYLLA SM.
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper describes the fungal community of Paris polyphylla Sm. tissues. Although the authors found interesting results regarding fungal diversity and composition, the paper is merely descriptive and authors should consider further studies to test their hypothesis. Also, English needs substantial improvement and the text needs a revision since there are several typing mistakes.
Experimental design: No comment.
Validity of the findings: The authors should consider how they present their results, such as:
- Why use Chao1, Shannon, and Simpson to describe alpha-diversity if you are not discussing trends that are shown in them?
- Fig 5 should show all the replicates to demonstrate that the communities are consistent in each microbial assessment.
Additional comments: No comment.


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

Input:
Title: NICHE DIFFERENTIATION IN THE RHIZOSPHERE AND ENDOSPHERE FUNGAL MICROBIOME OF WILD PARIS POLYPHYLLA SM.
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I appreciate the authors for accepting the suggestions of the reviewers and improved the manuscript. I hope the authors will do the future experiments keeping in mind the suggestions made the reviewers.


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: NICHE DIFFERENTIATION IN THE RHIZOSPHERE AND ENDOSPHERE FUNGAL MICROBIOME OF WILD PARIS POLYPHYLLA SM.
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript "Niche Differentiation in the Rhizosphere and Endosphere Fungal Microbiome of Wild Paris polyphylla Sm." describes the fungal community of Paris polyphylla Sm. in different altitudes.
Experimental design: Why the authors sampled the community at different altitudes? Why is this important to this medicinal plant? And regarding the differents found in the fungal community at different altitudes, what is the consequence to the plant?
And they have generated huge data regarding the fungal community in different parts of the plant. Do they have a relation with its medicinal potential? The authors should discuss more about this.
Validity of the findings: The description of the fungal community of Paris polyphylla Sm. However, I think that the manuscript is merely descriptive and needs major improvements regarding its hypothesis and the discussion of the findings.
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: ASSOCIATION OF THE CACNA2D2 GENE WITH SCHIZOPHRENIA IN CHINESE HAN POPULATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Fu et al. performed an association analysis between 3 SNPs in CACNA2D2 and schizophrenia. The results showed that CACNA2D2 polymorphisms may influence the susceptibility to schizophrenia in female in Han Chinese population of Northeast China. However, there are a couple of fundamental issues that require further attention:
1.	The authors should explain why do you choose the rs3806706, rs45536634 and rs12496815 as research objects. Have you checked these 3 SNPs in large scale GWASs (Li Z et al. 2017 Nat Genet, PGC 2014 Nature, Pardiñas et al. 2018 Nat Genet or others)?
2.	In Statistical Analysis section, please describe which population was used to test the LD of these 3 SNPs.
3.	You can also get the detailed information about this gene in SZDB2.0(www.szdb.org).
4.	As shown in figure 1, the 3 SNPs were in linkage disequilibrium, especially between the rs45536634 and rs12496815. Why do you choose SPNs in LD?
5.	Some typing errors should be corrected.


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: ASSOCIATION OF THE CACNA2D2 GENE WITH SCHIZOPHRENIA IN CHINESE HAN POPULATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this study, the authors performed a case-control study on the associations between SNPs in CACNA2D2 and Schizophrenia in Chinese Han population, they demonstrated the SNP rs45536634 showed significant association with schizophrenia and the haplotype AG consisting of rs45536634 and rs12496815 showed higher risk of schizophrenia.The article written clear. Relevant prior literatures were appropriately referenced.
Experimental design: 1. Only three SNPs (rs3806706, rs45536634 and rs12496815) in CACNA2D2 were selected in this study, the authors should describe the reasons for selecting these SNPs, why the SNPs in exons and introns of CACNA2D2 were not selected, and whether the authors consider choosing the tag SNPs.
2. A total of 761 schizophrenia patients and 775 healthy controls were enrolled in this study. The authors should perform and describe the power calculation for each SNP according to the MAF of SNP and the sample size. If the statistical power is not enough, I suggest that the authors supplement the sample size.
Validity of the findings: The authors used the MALDI-TOF-MS method for SNP genotyping. This method is notoriously error prone and the authors should mention the accuracy of this method in their hands (repeated measurements, verification of SNPs by other methods).
Additional comments: The D’ value for establishing the haplotypes should be described in the Methods.


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: ASSOCIATION OF THE CACNA2D2 GENE WITH SCHIZOPHRENIA IN CHINESE HAN POPULATION
Review round: 1
Reviewer: 3

Output:
Basic reporting: In this paper, Qiong Yu et al. studied the association between the Voltage-gated calcium channel CACNA2D2 and schizophrenia. By analyzing single-nucleotide polymorphisms (SNP) and haplotypes of CACNA2D2 in schizophrenia patients and healthy controls, they found one of these SNPs (rs45536634) significant associated with female schizophrenia patients. Furthermore, they claimed that people with haplotype AG consisting of rs45536634 and rs12496815 increased the risk of schizophrenia. The manuscript is poor-written, the experimental design is not so professional and the significance of this study is limited.

1.	This manuscript is poorly written, with a multitude of English and grammatical errors. Using title as example “Polymorphism of CACNA2D2 and Association with Schizophrenia in a Han Chinese Population”. It should be “Association of the CACNA2D2 gene with schizophrenia in Chinese Han population”. Peer review is not a proof-reading service, and the authors should ensure that the manuscript has been passed through a professional grammatical proof reader if their own ability isn't sufficient to spot these errors.
Experimental design: 2.	The rationale for investigating the association of the CACNA2D2 gene with schizophrenia is not clear. 3p21 is not a schizophrenia risk area and CACNA2D2 is never mentioned in any GWAS of schizophrenia.

3.	As the authors have already realized, the sample size of this study was not sufficient. Especially the positive association was only assessed from half of all the participants (female), which increased the concern that the association between of CACNA2D2 and schizophrenia susceptibility may be biased.
Validity of the findings: 4.	This study only analyzed three SNPs of CACNA2D2, which is insufficient and biased. Thus, the evidence that supports their conclusions are not so strong.
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: ASSOCIATION OF THE CACNA2D2 GENE WITH SCHIZOPHRENIA IN CHINESE HAN POPULATION
Review round: 1
Reviewer: 4

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This paper presents the results of a genetic association study that aimed to identify the association between SNPs of CACNA2D2 gene and schizophrenia by a case-control study. In order to better improve the quality of the article, some issues should be solved. My detailed comments are as follows:

Title:
-There are some syntax errors in the title. Please correct them.

Abstract:
-Please add the purpose of the study in the “background” section.
-Please check the content of the abstract in the submission system. Some descriptions were omitted.

Introduction:
-Authors mentioned that showed SNPs of CACNA1C were strongly significant associated with schizophrenia and have been confirmed in different races. However, I suggest that authors should use more new literatures. For example,
1. Gassó P, Sánchez-Gistau V, Mas S, et al. Association of CACNA1C and SYNE1 in offspring of patients with psychiatric disorders[J]. Psychiatry research, 2016, 245: 427-435.
2. Zhang S Y, Hu Q, Tang T, et al. Role of CACNA1C gene polymorphisms and protein expressions in the pathogenesis of schizophrenia: a case-control study in a Chinese population[J]. Neurological Sciences, 2017, 38(8): 1393-1403.
3. Zhu X, Li R, Kang G, et al. CACNA1C Polymorphism (rs2283291) Is Associated with Schizophrenia in Chinese Males: A Case-Control Study[J]. Disease markers, 2019, 2019.
-Authors should add related research hypothesizes

Methods：
-Authors select three SNPs (rs3806706, rs45536634 and rs12496815) located in CACNA2D2 gene. I am very curious why the author chose 3 SNPs in so many SNPs of CACNA2D2 gene? Please explain the reason in detail.

Results:
-I think that authors should provide more demographic characteristics, such as education status, marital status and ect.  in the result section.
-I suggest that authors should analyze genetic model and power test to avoid the false negative results.

Discussion:
-Line 178.  “Yang Guang et.al showed that…” This is a wrong expression. Please correct it.

Conclusion:
-Authors did not describe any conclusion in the last end of the article

Reference:
-Line 279-281. Please re-check the format of this reference.

Table and Figure
-In Table 5, authors should list all possible haplotypes.


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: ASSOCIATION OF THE CACNA2D2 GENE WITH SCHIZOPHRENIA IN CHINESE HAN POPULATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: In this Major revision version, the authors revised the manuscript according to the suggestion of 4 reviewers. However, I didn't think this manuscript meets the requirements for publication in PeerJ. There are still many grammatical mistakes in the manuscript.
Experimental design: 1. Almost all the reviewers raised the question "why did the authors select the three SNPs (rs3806706, rs45536634 and rs12496815) in CACNA2D2?". But I'm not covinced by the authors' response and the answer was not included in any part of the manuscript.
2. I'm also not satisfied with the answer "Why did you choose SNPs in LD?". It is a common sense to check LD of different SNPs before conducting experiments. Detecting SNPs in LD (rs45536634 and rs12496815) means you only get genotype information of one SNP.
3. Did you check the MAF of these 3 SNPs in different populations (CEU, CHS, YRI)?
Validity of the findings: no comment
Additional comments: Please correct the references "Consortium 2013" and "Consortium 2014" in Line 79 and Line 242.


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: ASSOCIATION OF THE CACNA2D2 GENE WITH SCHIZOPHRENIA IN CHINESE HAN POPULATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have addressed all of my concerns.
Experimental design: The authors have addressed all of my concerns.
Validity of the findings: The authors have addressed all of my concerns.
Additional comments: The authors have addressed all of my concerns.


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: ASSOCIATION OF THE CACNA2D2 GENE WITH SCHIZOPHRENIA IN CHINESE HAN POPULATION
Review round: 2
Reviewer: 3

Output:
Basic reporting: Now, the authors adequately responded to the reviewer's concerns, and the manuscript is acceptable for publication.
Experimental design: N/A
Validity of the findings: N/A
Additional comments: N/A


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: ASSOCIATION OF THE CACNA2D2 GENE WITH SCHIZOPHRENIA IN CHINESE HAN POPULATION
Review round: 2
Reviewer: 4

Output:
Basic reporting: None
Experimental design: None
Validity of the findings: None
Additional comments: The authors have made good responses to the comments of this reviewer.


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: ASSOCIATION OF THE CACNA2D2 GENE WITH SCHIZOPHRENIA IN CHINESE HAN POPULATION
Review round: 3
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The recently published East Asian GWAS of schizophrenia particularly highlighted a new-found locus - CACNA2D2. The authors can check whether the top association (rs374528934) was in LD with rs45536634. In all, the authors have adressed all my concerns.


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: PRIORITIZING RIPARIAN CORRIDORS FOR ECOSYSTEM RESTORATION IN URBANIZING WATERSHEDS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Riparian restoration is an important subject for the importance it has in the ecosystem integrity preservation and the maintenance of ecosystem services. The manuscript is well written and deals with a methodology to identify sites in need of riparian restoration. It is not a very novel subject as there are many papers already dealing with it, but still in need of further research. One possible limitation is being done at watershed level and not at corridor level, at least in this manuscript. Also, it is not clear the relative expression of human pressures, notably the cited urbanization, at a proper special scale. Results and Methods have mixed parts, Discussion and Methods have mixed parts, and they should be separated. In fact, there is no discussion if you take out the methods and results in it.

My first concern is about the so-called urbanization and the other human alterations affecting the corridors. You do not provide information on the urbanization degree of the area. Please provide a map/quantification/table of the degree of urbanization and other land use in your watersheds and in the corridors that you sorted from the watersheds.
We have no details of the watersheds enough to understand if they are very different.
Experimental design: Background and others. You do not need to say (for purposes of anonymity, citation will be added later). Just do not cite.
A spatially explicit methodology probably should not be called a model. Maybe you would consider to change the name, e.g. to methodology, frame, assessment system or strategy?
Literature review is good, including relevant papers. However, you should avoid grey references when it is not needed or else indicate the site where it can be found, e.g. Atkinson et al 2007. Also some references are incomplete, e.g. Feld et al 2018.
You present the results of PCA without having describe it in the methods and give details.
You present the results of LRA without having describe it in the methods and give details. The description in lines 290-293 are obvious to the model, you do not need to put them here, but you need to describe statistical details, notably transformation of variables, and the independent variable, also the spatial scale used.
Figure 1 is already published and this should be avoided, you can just cite it. The Figure you mention in line 146 can use the present Figure 2.
Figure 3 is too simple, it does not add to the subject in study itself and you do not need it, erase it. Figures 4 is totally inadequate in my view. Instead of bars you should use points/dots. You can make a combined Figure using Figures 4 and 5. Figure 5 shows poorly the results using bars and is highly related to the previous. Similar considerations for Figure 6, it can be included in a single Figure, with different dot types.
You should combine Tables 1,2,3 and 4 in a single Table.
The Discussion includes methods (first paragraph), it simply cannot be done like this. Put the simulations on the methods, show the results, and then discuss here.
Validity of the findings: Basically you make a 20 m buffer, and overlay it with Land Use (it is not a vegetation parameter but a land use parameter, you should change it), erodibility and slope (uphill and not river). So you are mixing human pressures with geophysical characteristics, to deploy a gradient of change. This means that the results will be driven in principle by human uses, in other words, the more human pressure, the more restoration. But can some of these patterns be related to other aspects, such as geological constrains, river slope or others? This can be seen if you make a regression between WQCM-P and R values, and if they are negatively related. Have you done so? If this is the case, why not use the opposite of WQCM-P, including the FEMA, and be developing a WQCM-R?
In fact, the floodplain in particular should be restored, and I do not agree in taking out the 100-year floodplain from the restoration assessment. You should present the possibility of using WQCM-inverse for the restoration identification, and discuss it together with your present proposal, notably when the simulations of different restorations are done.
If the regression model is so good (lines 295-298) why do we need the WQMC-R model an use the regression equations instead? Can you address this in the discussion?
Additional comments: No additional comments


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

Input:
Title: PRIORITIZING RIPARIAN CORRIDORS FOR ECOSYSTEM RESTORATION IN URBANIZING WATERSHEDS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper uses a GIS modeling approach to identify areas that are importance for conservation to protect water quality. The writing is clear and the workflow is sufficient for the intentions of the project.

As is, this manuscript describes the modeling methods, but does not sufficiently emphasize the "so what" for the analysis region. What do the results mean? The authors show them, but do not provide much discussion of what the results mean on the ground for managers and the public. It appears that figures one and three show how areas in need of restoration are those that were highly degraded and therefore not conservation priorities in the past. This should be more clearly emphasized in a local context rather than the broader discussion used in the introduction and conclusions.

As is, the framing is clearly based on water quality, but the tool is for riparian restoration priority. Riparian areas may protect water quality, but this is not their only value. Please reframe the introduction more regionally toward the services relevant in northern Texas. Please see the work of Fremier et al on using riparian corridors as conservation corridors: https://www.sciencedirect.com/science/article/abs/pii/S0006320715002529
Experimental design: The research is clear in its workflow and rationale, and falls within the scope of the journal. It is a novel application of a modeling framework to inform watershed management and water quality. However, the methods make trade-offs between established alternative data and methods, and this should be mentioned. Don't just say what you did in the materials and methods, but why, and in some case why other methods weren't selected.

There should be a clear rationale for why a 20-meter buffer was used instead of a threshold tied to the active floodplain. For example, there are several tools that use the 100-year floodplain and then proceed with GIS analyses based on the valley bottom width or a similar high magnitude flood extent. While I don't expect the authors to reproduce their analyses at this extent, they should write a paragraph acknowledging the trade-off they make between studies that perform similar watershed analyses based on valley bottoms. Anytime an arbitrary threshold is picked for a large landscape, this should be justified based on the fluvial geomorphic and hydraulic context it provides to a riparian zone. For example, in some canyons or gorges, the 100-year floodplain might be narrower than 20-meters, while in larger wadeable streams and rivers' unconfined valley bottoms, it may be much larger.

Macfarlane 2015
http://www.sciencedirect.com/science/article/pii/S0169555X15302166
Macfarlane et al. 2016 http://www.sciencedirect.com/science/article/pii/S0301479716308489
O'Brien 2019 https://onlinelibrary.wiley.com/doi/abs/10.1002/esp.4615
Gilbert 2016: https://www.sciencedirect.com/science/article/pii/S0098300416301935
Nagel et al 2014: https://www.fs.fed.us/rm/boise/AWAE/projects/valley_confinement.shtml

Several of these studies can/should be acknowledged as examples of landscape scale riparian planning tools.

Given that a 30-meter DEM was used for the topography, it seems like the buffer width may be small for many landscapes, so once again acknowledge this and justify your approach in the methods. Does this coarse resolution slope data work well in the topography of north Texas, which is flatter than mountainous watersheds with more relief.

Why was NHD used instead of NHD+ or NHD+HR? This is a fair thing to do, but should be mentioned. https://www.usgs.gov/core-science-systems/ngp/national-hydrography

Why was vegetation based on eight classes derived from classified LANDSAT imagery instead of just using the LANDFIRE product provided by USGS/USFS? The existing vegetation height and existing vegetation type parameters may be quite useful here:

https://www.landfire.gov/
Validity of the findings: The findings appear to be correct although the presentation would be more useful if specific conservation priorities were discussed in the context of the study area.
Additional comments: The WQCM-R model is basically the inverse of their earlier WQCM model, which begs the question, why not just assume areas of low conservation priority are degraded and likely need restored? You should really discuss how the models complement one another or whether one model run provides both results by deductive logic. Also - use the continuous and categorical priority values for the figures, not just the categorical values. Add a scale bar and north arrow to any map, labeling nearby geographic landmarks.