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: FUNGAL INFECTION, DECLINE AND PERSISTENCE IN THE ONLY OBLIGATE TROGLODYTIC NEOTROPICAL SALAMANDER
Review round: 1
Reviewer: 1

Output:
Basic reporting: Olivares-Miranda et al. explored whether the chytrid fungus Batrachochytrium dendrobatidis (Bd) could be implicated in declines of Chiropterotriton magnipes, the only obligate troglodytic Neotropical salamander. To this aim, the authors used molecular techniques to detect Bd in both extant and historical (preserved) specimens, conducted field surveys, and attempted to identify the present Bd lineage(s) through genotyping. The authors use clear and unambiguous, professional English throughout. The introduction does a great job in summarizing knowledge on emergence and spread of Bd in Latin America, clearly identifies knowledge gaps, and introduces the case study in a way that emphasises its relevance within the context of amphibian disease decline research. Overall, the manuscript is well-structured, self-contained, and includes necessary info on which ethical body approved the research, and the institute that issued field permits.

I suggest that the authors move the sentence at lines 69-72 ('Declines occurred - Vredenburg et al 2019') upwards, to line 64 directly after 'Catenazzi et al. 2011).'. This way, it is immediately clear why there are Bd records in Costa Rica that predate Bd epizootics, and why Bd was only described in 1999 (lines 64-69). I then suggest to to remove lines 72-79, as the information in these lines is largely repeated in paragraph 80-95. Part of the information in lines 72-79 (for instance, the interesting record from Bolivia) can be integrated into the next paragraph (e.g. around lines 88-93).

Lines 263-268: This section lacks necessary information. If I understand well from Table 3, four magnipes (not two) from two populations tested positive for Bd, is this correct? Also, from which population was Bd genotyped? I was unable to find this information in the text or tables. The sentence ‘to another sample collected from Chiapas’ (line 265) implies that the genotyped sample originated from an Ixalotriton or Nyctanolis population (although I do understand from Table 3 that this isn’t the case). Please rewrite this paragraph, and move sentence 266-267 to the discussion.

Table 1: The use of ‘sampling size’ in the caption title, ‘sampling results’ in the caption, and ‘Number of C. magnipes detected’ in the table itself is confusing. I assume that the latter is correct; i.e., the number displayed in the last column is the amount of magnipes that you observed, but not all could be captured for sampling, right? Please clarify and change the caption.

Table 3: Please add more descriptive information in the caption; for instance, do I understand well that the first ‘N’ column refers to the number of swabs tested for Bd, while the second refers the number of swabs tested for Bsal? Could you explain why these numbers occasionally differ?

Figure 1 is relevant and well-described, although seems to be of low resolution – but this might be a result of automatic downsizing while setting up the review pdf. If this is not the case, please provide a higher resolution version.

The data deposition statement contains information and external links to the multilocus sequence data used for Bd genotyping and data for chytridiomycosis qPCR assays (which are working, all data is available). The deposition information however seems to be missing from the manuscript – please add.
Please note that the data for chytridiomycosis qPCR assays still contains high-resolution locality data for all sampled populations.
Experimental design: In their study, the authors attempt to answer if (arrival of) Bd was implicated in declines of C. magnipes. This is both an important and timely question, especially in the light of recent discussions on the strength and availability of (retrospective) evidence linking chytridiomycosis to amphibian declines, in which the authors partook. The current study adds much-needed information on local presence and estimated prevalence of Bd across time, and is therefore an important contribution to the field.

The employed methods are state-of-the-art, and either follow recently published protocols or are sufficiently described to allow replication. I particularly liked to see that all qPCR analyses were conducted in duplicate or triplicate, and included both positive and negative controls.
Validity of the findings: As mentioned by the authors, the information presented in the manuscript points to a role of Bd in driving salamander declines, but does not provide unambiguous evidence, in part due to low Bd prevalence during declines, limited sample sizes in some time periods, and failure to genotype Bd from historical material. The authors weigh their findings accordingly in the discussion, and do not overstate their results. Larger samples sizes, especially from contemporary times, would have allowed more accurate estimates of infection intensity and prevalence – but I’m aware that these are difficult to obtain due to low abundance of many salamanders in Mesoamerica nowadays. While taking these unavoidable limitations into account, the authors draw sound conclusions, which (as I mentioned before) provide valuable information on local Bd presence and estimated prevalence across time.
Additional comments: Line 19 Batrachochytium > Batrachochytrium
Line 80: It would be good to specify that this concerns Bd-GPL.
Line 101: remove 'most of which belong the genus Chiropterotriton'
Line 148 Bd not in italics
Line 174 Bd not in italics
Lines 175-176: Add a few words to make clear that Ixalotriton and Nyctanolis do not only live in cave environments – it is currently confusing that these are introduced as cave salamanders, while the introduction states that C. magnipes is the only Mexican cave salamander.
Line 187 Bsal not in italics
Lines 189-190: Please add the number of positive and negative controls
Line 205 Bd not in italics
Line 207 (Byrne et al. 2017) > Byrne et al. (2017).
Line 230 Bd and Bsal not in italics
Line 231 calculate > calculated
Line 233 analysis > analyses
Line 243 > remove ‘in’
Line 244 Bd not in italics
Line 245 Bd not in italics
Line 253-255 replace with ‘We detected Bd on other amphibians at three of the six sites where these were found (Table 3), of with 25% (8/32) tested positive’.
Line 256 El Coni or Durango (latter was used earlier in the text)?
Line 259 Bd not in italics
Line 260 Table 1 > Table 3; Table 1 does not contain Bd presence of prevalence data
Line 277 Bd not in italics
Line 281 Bd not in italics
Line 290 Bd not in italics
Line 295 Table 1 > Table 3; Table 1 does not contain Bd presence of prevalence data
Line 296-298 El Coni or Durango? Please check throughout the manuscript.
Line 300 Craugastor decorates > decoratus
Line 307, 308 Bd not in italics


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: FUNGAL INFECTION, DECLINE AND PERSISTENCE IN THE ONLY OBLIGATE TROGLODYTIC NEOTROPICAL SALAMANDER
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment, please see general comments to authors
Validity of the findings: For specific comments, please see general comments to authors.
Additional comments: The authors present results of a study of a rare Mexican cave salamander, focusing on the potential involvement of chytrid fungus (further: Bd) in the species’ decline. Overall, I enjoyed reading this manuscript, which presents novel and relevant (be it mainly for a single species) information. The relative paucity of information presented is due to the rarity of the species; the entire group of neotropical plethodontids has been largely neglected by science (apart from some very active scientists including David Wake and some of the authors eg Sean Rovito) and every bit of new information is valuable from a conservation perspective. I do have some concerns, which I feel should be fairly easy to address and, although these are relatively minor, I would encourage the authors to include these in their revised version.
1)	line 76: this is one of my main remarks throughout the manuscript: a major limitation of most studies that include museum specimen of amphibians to be examined for the presence of Bd, is that they are based on swab-sampling specimens kept in jars, which often contain multiple specimen (sometimes multiple species). Although rinsing animals before sampling will remove some contamination, cross-contamination from other specimen in the same jar (and even at the time of collection: between jars) should never be excluded. This would require additional techniques such as histology or (preferably) immunohistochemistry. The claim of finding a Bd positive specimen in 1863 should be considered in the light of potential contamination. I would like to see this nuance added in the introduction. For the results of this paper: it would be appropriate to taken this into account as well. This will not have any major impact on the relevance of the paper, or its conclusions. I recommend adding information on number of specimen per jar examined and the species present, and a brief comment in the discussion with regard to estimating prevalence based on mere swab sampling museum specimen. I agree with the authors that the sampling method renders estimating infection loads rather unreliable but I would still recommend providing GE counts for the positive samples: it is important to mention this ao to estimate the probability of contamination.
2)	My second major remark is that it is unfortunate that sampling of the museum animals was restricted to collecting swabs. If possible, efforts should be made to try to perform histopathology on the animals that tested positive. This would provide very valuable information with regard to 1 pathological effects on the skin (eg any signs of pathology such as hyperplasia and/or hyperkeratosis) and 2 independent confirmation of actual infection (not contamination of the animals).
3)	A third somewhat major issue is the possibility of repeated samplings of the same animals in the two caves: were these all different animals and, if so, how was this confirmed? Given the low density, possibly (?) small home range of the animals, this may be an issue and would affect any estimate of eg prevalence.
4)	I fully understand few data are available to be more objective regarding the species’ decline. This uncertainty, however, should be reflected in statements throughout the text (eg Line 108: “greatly reduced abundance”, this implies data to be present).
5)	The authors should comment on Bd detectability in formalin fixed specimen. Certainly low infection loads in formalin fixed specimen may be prone to result in false negatives. I agree with the authors that recent Bd incursion (late 60’s) is the most plausible explanation, but their data (small sample size, long term formalin fixed animals) do not allow robust conclusions with regard to excluding a different scenario: long term endemism at low prevalence and low infection loads before 69, with subsequent increase (endemic hypothesis) cannot be excluded based on their data. This may seem rather unlikely but at least needs mentioning in the discussion.
6)	The authors should comment on detectability of Bd in relation to the time the sample has been stored in formalin. If no information is available, this should be mentioned and discussed (mentioning implications for conclusions).
7)	I would strongly advise against including the other (non syntopic) Mexican cave salamanders (Ixalotriton and the stunning Nyctanolis): sample size is too small to allow any sound conclusions and it does not really add anything significant to the manuscript.
8)	line 180: what is meant by: “all samples were processed immediately before release”?
9)	In the results section, please mention the number of samples obtained (not only for the C. magnipes).
10)	The authors demonstrate Bd presence on living animals, at a fair prevalence of 29% and infection loads that are low to relatively high. I have several suggestions here:
a.	please provide information on life stage / sex of the salamanders sampled. Life stage dependent infection and disease dynamics of Bd have been demonstrated (eg it may be possible that Bd exerts negative effects mainly on juveniles, which would impair recruitment)
b.	Stating that infection loads are low should be revised. At least one sample showed a GE load of 2618. While this is indeed not a load one would associate with lethal infections, I would recommend some caution here: the authors have no isolate and the number of GE is a calculation. The actual ITS copy number is important to make any statement with regard to absolute number on the swab.
c.	please discuss the possibility that infected animals are quickly eliminated from the population (as an explanation for the relatively low prevalence).
11)	Table 2: please add locality information here.
12)	Please refrain from any conclusion based on very small sample sizes (eg line 287-289, line 298-299)
13)	Please be careful with any conclusions regarding the species absence in the caves examined. The information provided in Table 1 shows that the majority of caves was visited only once (locality 6 is mentioned twice). Looking at both localities were animals were found (7, 13), numbers are low and even 0 on two occasions.
14)	A bit in line with the previous remarks: please comment on potential connectivity between the different cave systems and discuss in light of Bd epidemiology. I have no personal experience with these species, but I do have with many palearctic species with a (largely) subterraneous ecology. Caves do provide access to for example carstic limestone underground, but the vast majority of these systems is inaccessible for humans (except for the larger cave systems). Would it be correct to state that the species may have a vastly more broad distribution range than only those few caves? Please briefly discuss.
15)	Table 1: please add information per cave: terra typica, availability of historical data (C magnipes presence), newly searched caves.
16)	Table 3: I would recommend to limit to those localities, relevant for C magnipes.


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: SITE SELECTION BY GEESE IN A SUBURBAN LANDSCAPE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript needs many more references, for example, the discussion is over 1000 words long and only contains one reference. Please look into the current literature in high-impact journals for examples.
The manuscript needs to be much more focused and more rigorously supported by references. As it is, large parts (e.g. most of the introduction and discussion) are highly speculative.
Results section: Contains sections that belong into the other sections, e.g. lines 276 – 279 belong in Material & Methods, 289 – 293 are speculative and sound more like a discussion.
The results need a lot more proof. E.g. if you state something is “significant”, give at least the p-value. Don’t expect the reader to go to the supplementary tables to check every result.
Figures and tables: Axes are often unclear – what are you showing? Captions are missing! Large parts of the body of the text can probably moves into figure/table captions.
References: you need to support each statement you make. If you give references, please don’t dump them all together at the end of a long sentence (e.g. lines 105-106), but put each reference right after the statement it belongs too. Make it easy for the reader!
Discussion: Needs a lot more structure. Please start by summarizing your main findings briefly in the first paragraph. Then start each paragraph with a finding, which you then discuss. Go from the most important to the less important results, and keep it short and concise.
Experimental design: Looks good. Good field data.
Validity of the findings: Interesting results, but need to be made a lot clearer. They sound too speculative. You currently give no hard data with p-values, numbers of geese, etc in the results. You have so much good data from so much fieldwork, I am sure you can greatly improve this!
Additional comments: I think the manuscript could benefit from proofreading by a native speaker.
It may benefit from being rewritten into a short communication format, as the findings don’t justify such a huge body of text.


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: SITE SELECTION BY GEESE IN A SUBURBAN LANDSCAPE
Review round: 1
Reviewer: 2

Output:
Basic reporting: The study reports on goose distribution by counts in a park in Belgium considering very rough measures of landscape (Woodland, distance to water). Edge effects are investigated using dropping length measures. Although some sections are well written, there are considerable problems with this paper:

1. Please give this manuscript to a native speaker to correct the English. There are many mistakes. I.e. Instead of “geese” often “goose” would be more appropriate.

2. In a lot of sections, literature references are missing and one cannot distinguish between published information and opinion of the authors.

3. The article structure is only in parts professional. A table is missing in the main section of the paper with the results of the models. Raw data are shared and supplemental figures (however, the latter a not explained).

4. The introduction provides good background and information, but some of it is irrelevant for the study of site selection, it should be shortened by at least 50 %.  Relevant prior literature is not always appropriately referenced. A hypothesis is not formulated as is practice in scientific research? What are the predictions?

5. The order of things studies should be the same in intro, meth, res and dis. It is otherwise really confusing.

6. The discussion is unacceptable. References are entirely missing. I would not accept such a discussion even in a student report. It needs to be rewritten, in a more comprehensive manner including references. There are plenty relevant papers. It should put the authors results into relation to other studies. It should only discuss things based on the initial hypotheses and results and free of personal opinion.

7. Figures are relevant to the content of the article, of sufficient resolution, and appropriately described and labelled.

8. As far as I can see all appropriate raw data have been made available in accordance with our Data Sharing policy.

9. Not at all self-contained with relevant results to hypotheses.

10. A table with the summary of the models should be presented in the main section of the paper, not only as supplement.
Experimental design: It is stated that research fills an identified knowledge gap, but this is not true globally as papers have been overlooked that exist on the subject. However, as sites vary, it would still be relevant to conduct another study on the subject.

Rigorous counts performed but questions remain as to collection of dropping data (see comments in pdf). Areas not randomly chosen, only areas included that are “liked” by the geese), whereby the observer influences data collection subjectively. The technical standard is rather easy: Counting. The research has been conducted in conformity with the prevailing ethical standards in the field. Not all methods have not been described with sufficient detail & information to replicate (also see comments in pdf).
In the count models no consideration is given to seasonal effects, i.e. during moult behaviour of geese changes and may not be the same as in the rest of the season.
Validity of the findings: It is interesting to see the detailed distribution maps of the geese, edge effects are different in different habitats, so the idea is valid although there are other studies which are more refined. It is however disappointing, that habitat is described in such a poor manner.
The data on which the conclusions are based are available.
The conclusions are not all connected to the original question investigated. Speculation is not always identified as such.
Additional comments: Although the question at hand is a relevant one, you fail to provide some basic information, references and the structure of the paper is not coherent. In the introduction you set out with a very global view, but then you only describe goose distribution in one park in relation to a few parameters. You fail to report the behaviour the geese were showing during the count (feeding, resting, walking) and just assume that geese on pastures use them for feeding, which is not true). The manuscript needs shortening. This is not too difficult when leaving out sections that are not relevant to site selection. The method is rather crude and does not consider habitat choice by individuals. Some methods do not follow standards used in the field (random selection of plots, stratifying according to personal observation, which could be seen as critical).


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: SITE SELECTION BY GEESE IN A SUBURBAN LANDSCAPE
Review round: 1
Reviewer: 3

Output:
Basic reporting: Thank you for reporting your results on the overlooked relationship between geese abundance and landscape, in an urban area.

While I welcome your paper and I believe it brings an important output, I have two main comments:

1. You have a strong focus on islands and tree barriers in the first sections on the paper, but you somehow loose this in the Discussion. Although you mention something about the edges of the islands and its accessibility, nothing is written on the dimensions of the islands, vegetation, type of soil and substrate. For the tree barriers, again I believe some more emphasis should be delivered. Which tree species would bring  more benefit for reducing geese numbers. At which height from the ground should the canopy start? Which density do you recommend? Or these factors have no importance at all?

2. When counting the geese in the garden, did you also take into account human presence? You mention the counts were done on Monday and Friday. I guess Monday is not the busiest day in the garden, but I expect Friday you have quite a lot of visitors. It is possible that the admission / entry office keeps a record on the number of visitors. If related to the number of geese, you think there might be a correlation?

Finally, throughout the article the English is sometimes tricky. Several times I've got myself lost in long sentences, where the verb was sometimes missing. I've corrected some of these mistakes, but please take a thorough inspection of the whole text. And I absolutely do not understand why "Egyptian" and "Canada geese" start with capital, but "greylag" and "barnacle geese" do not have capital. You use this system in the entire manuscript and after a few sentences I stopped correcting it.

Please check the annotated manuscript for further comments and details.
Experimental design: Please refer to the 'basic reporting' section and the annotated manuscript. All my comments, questions and suggestions are there.
Validity of the findings: Please refer to the 'basic reporting' section and the annotated manuscript. All my comments, questions and suggestions are there.
Additional comments: Overall, I found your manuscript as an interesting piece of research and I would be happy to see it published as soon as possible.
Please address my comments and I look forward to approve the second version.

With best regards,
Liviu Parau


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: SITE SELECTION BY GEESE IN A SUBURBAN LANDSCAPE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript has been much improved. Some parts are however still lacking references (please see my comments below) and some parts are confusing.
Experimental design: Good experimental design. Results part could be clearer to make the main results stand out. Discussion could be clearer especially in terms of pinpointing main findings and connecting them back to the aims.
Validity of the findings: no comment
Additional comments: The manuscript has been much improved from the previous version and the study is very interesting. I however still have some comments, mainly around lack of clarity and references:

Introduction
Lines 79 – 84 provide reference
84 – 86 does not lead anywhere – omit
98 which features?
117 considered by whom?

Methods
Line 143 change to ‘Canada geese are’
130 – 149 you change keep switching between the terms ‘Garden’ and ‘park’, which I find confusing. If you’re talking about the same area, please keep the terminology consistent.
178 – 179 Please connect this sentence better with the previous one, e.g. ‘Three landscape parameters were examined for their importance for geese in site selection: the size of the survey area, the distance from the site to the nearest lake and the presence of physical barriers preventing direct flight to the nearest lake.’
183 change to ‘….be addressed in statistical models. These are…’
204 – 206 reference missing, and please define the term ‘edge effect’.

Results
256 – 259 is not a result. Please move or omit.
269 – 274 Define terms ‘homoscedasticity’ and ‘heteroscedastic’ in Methods. Make sure that you don’t mix methodology with results.
Figure 1 and 3 As I already pointed out in the first round of revisions, please explain the numbering/labels in your figures more thoroughly. Readers which are not too familiar with maps like the ones you are using will not be able to follow.
Figure 4 Please move the statistics (p-values etc) from the caption to the results text. It makes it easier for the reader to follow the story you’re telling.
In general, as mentioned in my earlier review, please improve clarity. What are your main findings?

Discussion
310 – 314 As I pointed out during the first revision, please give a brief but precise summary of your main results at the start of the Discussion. You mentioned a complicated relationship. Tell the reader why? What are you basing that on? You state that ‘geese are clearly actively selecting’ particular landscapes. Tell us instead what brings you to this conclusion? E.g. ‘In this study, we found that a) geese avoided woodland areas, b)…………etc etc. At the moment, you are losing the reader in the results section and don’t give them a chance to get back on track in the discussion.
316 – 322 Please provide references. E.g. line 319 which potential causes? Line 320 why do you expect this effect to diminish?


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: SITE SELECTION BY GEESE IN A SUBURBAN LANDSCAPE
Review round: 2
Reviewer: 2

Output:
Basic reporting: See general comments.
Experimental design: See general comments.
Validity of the findings: See general comments.
Additional comments: As in my first review, I mention again that the English should be improved. Long, unstructured phrases make the reading difficult. Many Oxford commas are missing.

Furthermore, throughout the text, you are inconsistent with abbreviations. For example, between lines 390 and 411, all scientific names are given in full, except for Branta. However, sometimes you used “B.” and sometimes “Branta”.

Another example, at line 410: you write: “A. anser can be seen to range more widely than other geese”. I changed this to “A. anser can be seen to have a wider range than any other geese”.
Line 419: “Lakes with islands house more Canada, greylag and barnacle geese in the summer”. Changed to “Lakes with islands attract more Canada, greylag and barnacle geese in the summer”
Line 495: “the negative influence of barriers was barely significant”. Changed to “hardly significant”.

Finally, I strongly believe that this is a very important knowledge piece and should be published. Personally, I never regarded landscape structure as having such a decisive influence on urban and suburban geese abundance. But after reading your work, I will definitely pay more attention to park architecture.

Thank you for your efforts in collecting, analyzing and publishing the data!


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: SITE SELECTION BY GEESE IN A SUBURBAN LANDSCAPE
Review round: 3
Reviewer: 1

Output:
Basic reporting: The language and literature have been improved from the first version. Raw data are shared, with the exception of raw p-values (for example, p-values are shared in categories like <0.5, instead of actual numbers (e.g.'0.03') given). The results are relevant to the aims given.
Experimental design: As mentioned before, the authors have tackled a topic which is relevant to many urban areas and have put a lot of work into collecting field data and analysing the resulting data.
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: DICHOCARPUM HAGIANGENSE—A NEW SPECIES AND AN UPDATED CHECKLIST OF RANUNCULACEAE IN VIETNAM
Review round: 1
Reviewer: 1

Output:
Basic reporting: Comments to the Author
This manuscript is dedicated to describe a new species, Dichocarpum hagiangensis, and to update the checklist of Ranunculaceae in Vietnam.
When reviewing the manuscript, several questions and suggestions arose, so here they are.
 1. The authors only provide morphological evidence for the new species. Based on Table 1, most of morphological characters are quantitative and are overlapped among those three species. I strongly recommend adding molecular evidence. Xiang et al. (2017) have presented a phylogenetic analysis for Dichocarpum based on four DNA regions. It is therefore very easy to do this. The same four markers for this new species can be sequenced, at least ITS, trnH-psbA, and matK should be generated since they are usually used as DNA barcoding sequences. I believe molecular data can provide more robust support for your new species if it is indeed a good species.
2. L65: change “and” to “or”).
3. L145: change “ca” to “ca.”.
4. L204: change “follows” to “followed”(language, “by”).
5. The reference should be arranged alphabetically, please notice “Liesner R. 1995.”
6. L406: change “-” to “–”.
Experimental design: 'no comment'
Validity of the findings: 'no comment'
Additional comments: No additional comments


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

Input:
Title: DICHOCARPUM HAGIANGENSE—A NEW SPECIES AND AN UPDATED CHECKLIST OF RANUNCULACEAE IN VIETNAM
Review round: 1
Reviewer: 2

Output:
Basic reporting: See the main comments in the text of the review.
In general, everything is fine, but serious changes are required!
Experimental design: See the main comments in the text of the review.
In general, everything is fine, but serious changes are required!
Validity of the findings: See the main comments in the text of the review.
In general, everything is fine, but serious changes are required!
Additional comments: Reviewing Manuscript 45699v1

Dichocarpum hagiangensis - a new species and an updated checklist of Ranunculaceae in Vietnam

The research of the biodiversity and revealing the new species is the actual and significant problem, and the investigations, aimed on resolving of this problem, are to be warmly welcomed.
The paper is a classical description of a new taxon based on morphological characters. The new species is gorgeous and does seem to be different from the closely related ones mentioned in the manuscript.

The paper could be more interesting and notice by more readers if the more general information in the introduction and conclusion be given, e.g.: newest work about Dichocarpum, number of species in the genus in World, Asia, another regions, a key or at least a checklist of all the all species (with new morphological characters), distribution map of a new species and all species that are relatives of a new species (!) or distribution map new species and all species Dichocarpum from Vietnam. It will be much more informative and useful for many other scientists.
These are general comments!

The main comments which need to be corrected by the authors include:

1. Diagnosis should be changed:
According morphological characters new species belong to Sect. Dichocarpum, subsect. Dalzielia. Dichocarpum hagiangensis is morphologically most similar to D. trifoliata, but differs in flowers diameter (2-2.3 vs 0.7 cm), longer sepals (10.5-11.5 vs 3.5 mm), number,  tooth shape of basal leaves and rhizome diameter (more 0.5 vs 0.4 cm) and dichasial inflorence. However, D. hagiangensis differs from D. basilare in having the 3-5-foliolate leaves and retuse central leaflet apex. And compare with D. carinatum please (because in Xiang et al. 2016 all related species have been included to the one clade)!!!!!

2. Change the terms in table and in text. All leaves is compound. Change “leaf” to “basal leaf” and delete “compound leaves”, change “flower number” to flowers number and add stem leaves parameters. Because new species have stem leaves and bract too. It is also necessary to add the characteristics of stem leaves in the description of the taxon.

3. Make a distribution map of all species of the genus in Vietnam! Use your data, literature data and herbarium funds.
For example (Material and methods): Maps of records will be made with SimpleMappr (http://www.simplemappr.net).

It is necessary to do all the calculations and add information to the sections materials and methods and results.

4. IUCN conservation assessments can only be made with the evidence available at the time of study so it is ingenuous to say that more information may lead to a better assessment in future. It is possible to calculate the EOO and AOO, and to make a full assessment. This should be done. Naturally, more information may come to hand in future but there’s no need to wait before making an assessment.

For example: Conservation analysis was performed using criteria from the International Union for the Conservation of Nature (IUCN 2019). The Extent of Occurrence (EOO) and Area of Occupancy (AOO) of each species were estimated using GeoCat (Bachman et al. 2011).

Literature: Bachman S, Moat J, Hill A, de la Torre J, Scott B (2011) Supporting Red List threat assessments with GeoCAT: Geospatial conservation assessment tool. ZooKeys 150: 117–126. https://doi.org/10.3897/zookeys.150.2109

It is necessary to do all the calculations and add information to the sections materials and methods and results.

5. It is necessary to add a scanned sample of a herbarium of a standard sample with a barcode to the text of the article.

6. If you have not done a DNA analysis of your samples and have not compared with other species, then you need to discuss the position of the species relative to other species. First of all, it will find out the kinship by morphology, then on the basis of known data on DNA analysis, it is necessary to conduct a discussion on the differences and similarities with other types of close kinship. It is imperative to make references to molecular studies and to phylogenetic trees.

In spite of this major changes are needed! Make all changes to the text, according to my comments.
Finally, I would like to ask you to pay close attention to the formatting guidelines of PeerJ. I have noticed that several parts of the text do not meet those requirements. After analysing MS, I am pleased to inform that my decision is to accept your submission, but with the need of Major Revision.


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

Input:
Title: DICHOCARPUM HAGIANGENSE—A NEW SPECIES AND AN UPDATED CHECKLIST OF RANUNCULACEAE IN VIETNAM
Review round: 3
Reviewer: 1

Output:
Basic reporting: All corrections were made according to the recommendations of the reviewers, the manuscript was significantly revised. I recommend to accept.
Experimental design: ok
Validity of the findings: ok
Additional comments: No additional comments


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

Input:
Title: THE REUSE OF PUBLIC DATASETS IN THE LIFE SCIENCES: POTENTIAL RISKS AND REWARDS
Review round: 1
Reviewer: 1

Output:
Basic reporting: I believe this review is of broad interest. Although the scope is for life sciences, I believe there is wide applicability. Many of the concepts raised by the authors could be applied to other disciplines.
Reviews on open data have been published recently, but this manuscript stands apart for its discussion on some of the challenges and limitations they describe. I do not know of any review of this topic for life sciences so it definitely has a different audience. I believe this article to be timely and relevant.
The authors have a great command of the literature. They provide sufficient background although organization is a bit difficult. The introduction I found did not accurately set up the goals of the synthesis. I believe the first two paragraphs could be summarized more succinctly than currently written. The main point of these paragraphs is that big data is expanding due to technologies and initiatives. Revise to be more direct. Then I believe it would make sense to move lines 131-143 into the introduction set up for the reader the benefits of potential data reuse. That better ties in with your current paragraph three 56-64 that identifies there can be risks or negative impacts. Your final paragraph in the introduction then lays out the objectives.
Experimental design: The authors review is extensive and covers a broad number of articles. I believe the authors conducted a systematic review to have an unbiased approach in their writing, although the purpose of the systematic search was unclear. I would appreciate if the authors could provide some description of how their search to help generate the review.
The manuscript would benefit from begin structured around the end of their introduction. It is unclear in the main objectives of the synthesis is to address the three points on lines 67-69 or the “highlights” of challenges/limitations on lines 73-74. Explicitly stating the objectives of the introduction would assist, and then the rest of the review can be structured around that. Ensure the rest of the MS parallels these objectives.
Validity of the findings: I think the benefits section could be expanded on. In your figure 4 you highlight the benefits outweigh the costs, but your “challenges and limitations” section is considerably longer than your “benefits” section. I’m not imply these sections need to be equal, but I did feel the benefits section fell short on selling all the truly beneficial things associated with data re-use. For example, the prevent information loss section could be split to include a short discussion on novel analyses (e.g. meta-analysis, systematic reviews) that have incredible value in the life sciences. Perhaps even discussing the reuse of data from exploratory/preliminary experiments to reduce duplicate labour. This information is present in some forms throughout your MS, (e.g. lines 152-153) but I believe each could be expanded on.
I really enjoy the conclusions set up by the authors including figures 4-5.
Additional comments: Some specific comments
It would be good to end the abstract with big-picture statement, what does this paper do to advance this field
Line 56 – Don’t lead the paragraph with “However”. Needs a proper topic sentence.There are other instances throughout the MS where the authors start a new paragraph that is essentially a continuation of the previous. Please correct these.
Line 98 – I don’t understand this qualifier. Yes, your data exploration is only using life sciences, that was expected based on the title and abstract.
Line 106 – Some other examples to consider: code, statistics, and plots.
Line 117 – Define primary vs derived.
Line 218 - I am not sure what is meant by denormalization. It should be defined
Lines 268-270 - Combine these paragraphs
Line 88-89. This line is very vague for explaining how the information was obtained from the studies. Please expand. Similarly lines 90-91, what is the definition of a successful data reuse.
I believe table 1 could be moved to an appendix since it simply a series of examples.
Figure 1: I don’t understand the possible -> habitat gradient in figure 1.


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

Input:
Title: THE REUSE OF PUBLIC DATASETS IN THE LIFE SCIENCES: POTENTIAL RISKS AND REWARDS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This review paper suggests that the volume and velocity of data in the life sciences creates opportunities and challenges for data reuse to enable novel analyses and improve reproducibility and accountability.  In essence, the authors seem to be making a case for increased data reuse. As a conservation scientist I am not able to comment on the discipline-specific challenges of the genomics/bioinformatics data on which these authors focus, but as a proponent of open science whose work focuses on synthesis of diverse datasets generated by others, the general challenges around open science and open data discussed in this paper are very familiar to me.  Unfortunately, I feel the organization of this paper makes it difficult to extract a coherent message or action that the reader, regardless of scientific discipline, can put into practice.

The stated intent of the study is to highlight the potential of data reuse (line 21, lines 24-25), with a secondary goal of motivating action on the part of the reader: “These benefits for individuals and the scientific community as a whole make a strong case for the obligation to reuse data whenever that is appropriate.” (lines 142-143)  Considering the paper as a call to action, rather than simply a passive collection of loosely connected facts, it becomes important to keep a well-defined audience in mind so that the persuasive argument can be targeted toward the needs and incentives of the reader.

Here, a well-defined audience might be considered along two axes: targeted scope of discipline (general life sciences to specific communities within the life sciences), and the role of the target audience within the discipline.  Re: scope of discipline: Is this intended for a general life sciences audience (as inclusion of phenology and ecology examples suggests), or a bioinformatics audience (as suggested by the bulk of the examples drawn from genomics sequencing literature, lines 126-128, as well as the subjects of Figures 2 and 3)?
• In attempting to address both these audiences, the conclusions drawn seem at once too vague to be useful to a bioinformatics practitioner and too domain-specific to be of use to a general audience.
• Other domains of life sciences have previously explored the space of “big data” in depth, (e.g. ecology, see Hampton et al. 2013: https://esajournals.onlinelibrary.wiley.com/doi/full/10.1890/120103) and should be acknowledged, especially if trying to appeal to a broader life science audience.
• The title suggests a general life sciences audience but the content focuses far more toward reuse of genetic sequence data.  Assuming this is the target audience, I’d suggest a title change to reflect this focus.

Re: role of the target audience: Is this intended for data users/re-users/consumers, data producers, database managers, or policymakers? Any one of these audiences would be a reasonable target, but in attempting to address all at once, the discussion becomes unfocused.
• The recommendations and incentives for data reuse to each of these audiences would be quite different.  For example, in choosing whether to reuse data, a researcher (data consumer) will consider only the benefits with respect to her particular research agenda, and would have no concern for benefits to a database manager elsewhere.  See Lowndes et al. 2017 (https://www.nature.com/articles/s41559-017-0160, full disclosure I am a co-author) as an example of a piece narrowly focused on the needs and challenges of the data consumer, with concrete recommendations for actions the reader can implement.
• In the end, the decision to reuse or not reuse rests in the hands of the data consumer.  The benefits to other stakeholders only accrues if the reuse of data actually occurs, therefore the considerations of other audiences should perhaps be focused on lowering the barriers and increasing the incentive/utility of reuse to the end user.
• The authors touch on several issues that would be of concern to the potential data consumer/reuser, including the need for high quality metadata (lines 261-274), clear and reproducible experimental design and methods (lines 209-210), and access to funding to incentivize/enable such reuse (line 313).
Experimental design: The outlined publication survey methodology seems like a reasonable approach to examine the scope of data reuse in public databases.  However, the methods as written do not describe the process in enough detail to understand the study design or provide any means of replication.
• The authors state that in performing their keyword search, “the publication year and type of journal were unrestricted” (line 84).  Since the noted keywords relate only to data, and not to discipline, the authors must have some other means of restricting the results to life sciences, if not even more narrowly, perhaps through additional keywords or a subset of type of journal.
• The authors state: “From these sources the common benefits, potential, limitations, challenges and risks of data reuse we extrapolated” (lines 88-89). Please provide reasonable description of the methods by which the returned journal articles were qualitatively or quantitatively analyzed to identify benefits, potential, limitations, challenges, and risks.  It would be helpful to highlight/summarize the results of such an analysis in the text or in supporting materials.

In providing examples of “successful data reuse” drawn from different life sciences fields, it would be very helpful for the authors to clarify both their definition of “reuse” as well as their metric of “success” – which may influence and in turn be influenced by the intended audience.
• It may be that the issues of reuse that concern the authors are specific to the sequence-oriented life science community (for example, in conservation ecology, much of the research focuses on synthesis of existing datasets), which would significantly narrow the potential impact of this paper.
• Does “successful reuse” indicate publication of a study that incorporates data generated elsewhere (as seems to be the case from the examples given), or is there some way to quantify the degree to which reuse materially improves the utility of the study?  Are there examples of “unsuccessful” data reuse that can highlight the challenges?
Validity of the findings: The authors lay out several potentially important challenges and benefits from data reuse, but the conclusions are not clearly supported by their evidence and reasoning as presented; what seems to be a central piece of their analysis, the publication survey, is not described or summarized in sufficient detail to support their defined list of risks, benefits, and potential of data reuse.  Much of the paper (including Tables 1 and 2) seems to focus on the problems, warnings, and pitfalls of data reuse, rather than providing a convincing argument in favor.  In conjunction with some of the organization and definition of terms and audience noted above, the authors will be better able to connect the goals of the analysis, as set out in the introduction, to their conclusion, with a clear and explicit chain of evidence-based reasoning.

Some specifics:

Table 1 seems to focus on the specific limitations of each reuse case example, which may be idiosyncratic - not be immediately applicable to other studies even within the same field.
• How were the “limitations/risks” in this table determined?  E.g. were these identified by the authors of these studies that reused the data, or by followup studies analyzing or criticizing the reuse publication, or identified by the authors of this paper? Many of the limitations/risks fail to cite references.
• It would be particularly valuable to identify trends, patterns, and generalizable lessons from these examples that would be more widely applicable and useful to the targeted audience.

Table 2: the criteria column tracks well with the manuscript.
• As for table 1, were the “questions to consider” and “suggestions/suitable controls” determined from the literature?  Few of the suggestions and none of the questions cite a reference.
• If these are the opinions of the authors, that should be made clear in the body of the manuscript or the caption of the table.

Figure 1: the text first referencing Figure 1 (line 31) does not clearly track the flow of the diagram – it seems like only boxes 1 through 3 are referenced here; it may be that the other steps are infused throughout the remainder of the paper, but this expectation could be explicitly signposted here to help the reader track the logical flow of the argument.  Perhaps this figure could form a framework for a more clear outline of the piece.  (Note also the caption seems incomplete).

Figure 3 seems extraneous – the main takeaway is a qualitative observation of exponential growth, which is described well within the text.  In addition, when the authors argue that “the increasing size of scientific data is a challenge for the databases regarding e.g. storage space and data management” (lines 172-173), I think it would be helpful to cite evidence that this exponential growth of data is outpacing the (likely) exponential growth of affordable access to storage and processing power.
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: THE REUSE OF PUBLIC DATASETS IN THE LIFE SCIENCES: POTENTIAL RISKS AND REWARDS
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This is my second time reviewing the paper by Sielemann et al. I commend the authors on all the revisions they undertook to improve the clarity and reading of the manuscript. I believe these revisions have made for a considerably stronger manuscript and enjoyed reading it. Thank you for addressing all my comments.

I have only a few small outstanding issues:
-Try and reduce your usage of "it". Sometimes it comes across what "it" you are referring to. Just restate the subject of the sentence again
- There are a couple cases where you are using double parentheses. In these cases you can simply separate the citation from the example statement using a semi colon. (e.g. line 306)
- Table 1 is very dense. Can you separate it a bit more. Perhaps adding the citations to a third column
- I don't really understand the usage of these colours in Figure 1. Could this instead be grey and white? with the boxes outlined rather than shaded in. I believe it will improve the aesthetic.


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

Input:
Title: THE REUSE OF PUBLIC DATASETS IN THE LIFE SCIENCES: POTENTIAL RISKS AND REWARDS
Review round: 2
Reviewer: 2

Output:
Basic reporting: This review paper outlines the needs, benefits, and challenges of data reuse in the biological sciences, with examples drawn from a range of biological applications. The considerable effort put in by the authors to clarify and organize the paper have strengthened the manuscript considerably.
The language is generally clear though there are a few typos and odd turns of phrase to be addressed (listed below).  The intro and background have been clarified to provide context to the goals of the literature review.  Literature is thoroughly and appropriately cited throughout.  The structure conforms to PeerJ standards, and the authors use helpful subheadings throughout to communicate the structure of the piece.  The review fits within the scope of the journal, and while focused on particular disciplines the general takeaways are generalizable to other disciplines.  The field may have been reviewed recently, but in a quickly evolving topic like big data and open science, it seems like there is good reason for this review.  Finally, the introduction has been reworked to better communicate the authors’ goals, particularly with the “purpose of the review” subsection.

Some specific suggestions:
Lines 75-77: “Additionally, a survey of 100 datasets associated with ecological and evolutionary research showed that 56% databases were incomplete and 64% were archived in a way that partially or entirely prevented reuse” – this is great, but you may also want to check out this reference that I think is very relevant to the point you are making in this paragraph:
• Couture, J. L., Blake, R. E., McDonald, G., & Ward, C. L. (2018). A funder-imposed data publication requirement seldom inspired data sharing. PLOS ONE, 13(7), e0199789. https://doi.org/10.1371/journal.pone.0199789

I noticed a few typos and awkward phrases that the authors may want to address:

Lines 41-43: “Obligations and benefits lead to established sharing behaviour and more datasets become available which can then be reused in turn”: This reads as a run-on sentence.  Perhaps something like “Obligations and benefits lead to established sharing behavior, which leads to more datasets becoming available, which can then be reused in turn”

Lines 44-46: “Data sharing is already common in several disciplines, including
genomics, neuroscience, geoscience and astronomy and an increasing number of studies reuse shared data”: This reads as a run-on sentence.  Perhaps a comma after “astronomy” might help.

Line 112: “life scientist”: Should be “life scientists”?

Line 120: “risks and potential solutions range cross different fields”: Should be “range across different fields”?

Line 160: “like e.g. ‘coexpression’, ‘pangenomcis’, ‘network analysis’ or ‘metagenomcis’.”: “pangenomics” and “metagenomics”? also drop the “like,” as it is redundant with the “e.g.”

Line 282: “can be partially addresses”: “addressed”?

Lines 299-301: “As discussed above, open access to datasets and studies would accelerate science while being
cost-efficient (Spertus, 2012), however, it is important that the limitations of particular datasets are identified, and the associated risks assessed.”: Semicolon or period before the “however,” rather than a comma.  I think the comma after “identified” can also be dropped.

Lines 390-391: “Re-analysis of publicly available data is one way to tackle the issues of unknown quality and denormalization of data, and integration of databases that arise with reuse”: Maybe “…unknown data quality, denormalization of data, and integration…”?

Line 420: “The trade-off between public access and unknown quality, can be partially resolved”: No need for the comma.

Line 458: “data-focused journals, like e.g. GigaScience”: Drop “like” – it is redundant with “e.g.”

Lines 496-497: “The above-mentioned ‘Parasite awards’ use this tongue-in-cheek name after it was introduced to dismay such practices”: Not sure what this means – “to dismay such practices” – perhaps a different verb was intended?

Line 510: “Both, data providers and creators of databases, deserve recognition for their work”: Neither comma is needed.

Lines 553-555: “Additional enforcement could be spot-checking of provided metadata by funding agencies (Bhandary et al., 2018) which are providing the money for the data generation and have an interest in the release of high quality data sets”: I can see what the authors are intending but the sentence is very awkward.

Line 557: “Only combination of obligation and encouragement”: “Only a combination…”?

Line 591: “They aim illustrate the types of considerations”: “They illustrate the types…”?

Line 598: “It has previously been demonstrated that posteori analysis”: “… a posteriori analysis”?

Line 619-620: “illustrates the high potential of data reuse, thus demonstrating its value”: Seems somewhat redundant - I think this could be shortened to “illustrates the high potential value of data reuse.”
Experimental design: I appreciate the additional information the authors provided about their methods for the literature survey.  While the survey methodology may not be comprehensive or unbiased, the authors are transparent about their selection criteria so it should not be a concern.

For the examples listed in Table 1, I still note that many of the ideas listed under limitations and risks are not cited, which is not a deal breaker but I think weakens the authors’ point here.  I understand that many of these are drawn from the researchers’ experience in the field, but some assertions are quite vague or speculative.  I would urge the authors to find a citable source for each of these noted risks to strengthen their assertions; even if the ideas are drawn from the researchers’ experience, certainly they have been documented elsewhere in an academic manner.  For example, one risk noted multiple times is, “Batch effects might be possible if large sample groups come from the same source” – there seem to be many publications and textbooks with information on batch effects, e.g. https://www.researchgate.net/profile/Qian_Liu113/publication/304497610_Evaluation_of_Methods_in_Removing_Batch_Effects_on_RNA-seq_Data/links/577175d208ae0b3a3b7d6f96.pdf.

I have the same concern about the suggestions/suitable controls in Table 2.
Validity of the findings: With the extensive reworking by the authors, their argument seems much better developed and supported.  The conclusion is generally supported by the points made in the discussion, and links back to the goals set out in the introduction.

That said, it seems unusual to introduce figures for the first time in the conclusion.  I would introduce Fig. 4 in the discussion section, and use that to tie together all the pieces of the discussion before moving on to the conclusion.  While the conclusion is an appropriate place for “outstanding questions and challenges,” as you outline in Fig. 5, it seems like those questions should really focus on potential research opportunities going forward. I would suggest dropping Fig. 5 (or moving it to the discussion) and instead craft one good concluding question/challenge that could tie together some of these ideas.  One major challenge that is telegraphed within your text would be identifying opportunities to align incentives among data users, data creators, and other stakeholders (e.g., database managers, funding institutions, journals, academic institutions) to better support effective data sharing.
Additional comments: Overall, I appreciate the work the authors have put in to address previous concerns, and find the paper to be greatly improved in its organization and message.


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: ANALYSIS OF DYNAMIC AND WIDESPREAD LNCRNA AND MIRNA EXPRESSION IN FETAL SHEEP SKELETAL MUSCLE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The English language needs to be improved.
Experimental design: The methods section should be clear and detailed enough. For instance, methods of GO analysis, KEGG analysis, interaction network construction, and statistical analysis of qRT-PCR results, etc. More details are needed in this section.
Validity of the findings: no comment
Additional comments: Line 26: sheep is an important……

Line 32: …longissimus dorsi (LD)…, italic longissimus dorsi in manuscript.

Line 43: …targeted by the different miRNAs…

Line 71: …TncRNA???, not clear.

Line 125: …detected using…, and digested by…

Lines 123, 125, 126, 136, 137, etc: Company information should be consistently written.

Line 129-130: “Equal amounts of total RNA from the muscle samples at the different stages (i.e. E60, E90, E120, D0, and D360; n=3) were pooled into one sample”? Is it means one sample for each stage? Why ?? No biological duplication, is that reasonable?

Line 151-152: How to measure and analyze the area and circumference of muscle fibers?? Provide more essential details.

Line 194, line 254: “The expression of them was consistent with the RNA-Seq results”, Table 1 only provides the qRT-PCR results. How to analyze the qRT-PCR expression and sequencing results consistent?

Line 222: Using the RNA interaction software RIsearch…., Software requires references.

Line 330: “…the 4 lncRNAs, linc-MD1, Yam-1, sirt1AS and H19”, provide references.

The discussion could be further strengthen, highlight the findings of this study, and a clear significance of the study given.

You state in the data availability that the dataset were available on NCBI under BioProject PRJNA526287. Usually, BioProject ID does not indicate that RNA-Seq data were uploaded successfully, the data needs to be submitted to the SRA (Sequence Read Archive) database to obtain the corresponding accession number (starting with SRR or SRA) after obtaining the BioProject and BioSample ID. Please provide the SRA accession number in this 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: ANALYSIS OF DYNAMIC AND WIDESPREAD LNCRNA AND MIRNA EXPRESSION IN FETAL SHEEP SKELETAL MUSCLE
Review round: 1
Reviewer: 2

Output:
Basic reporting: The study is interesting but there are main flaws about the method (pooled samples without biological replicates).
Experimental design: The main flaws were “samples at the different stages were pooled into one sample” and “without biological replicates”.
Validity of the findings: No validation experiment about any target gene or ncRNA.
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: ANALYSIS OF DYNAMIC AND WIDESPREAD LNCRNA AND MIRNA EXPRESSION IN FETAL SHEEP SKELETAL MUSCLE
Review round: 1
Reviewer: 3

Output:
Basic reporting: The Materials and Methods were too ambiguous and too simple.
Experimental design: No replicates were used for RNA-seq and miRNA-seq
Validity of the findings: The DE lncRNAs, miRNA and mRNAs should be validated
Additional comments: Yuan et.al, performed RNA-seq and miRNA-seq to perform the lncRNA and miRNA dynamic profiling during skeletal muscle development at 5 stages. Differentially expressed lncRNAs and miRNAs were identified, and regulatory networks were constructed. This work might be useful for understanding sheep muscle development. However, various critical issues should be addressed.
1.	Your most important issue is that apparently no experiment was performed using replicates, making it hard to assess if any of the observed differences are consistent and reproducible. If not possible, at least, some DEGs should be validate by RT-PCT?
2.	The next most important item is that the description of Materials and Methods section was too simple. For examples, what types of sequencing library were constructed? Whether it’s strand-specific or not? how the lncRNAs and miRNAs were identified and analyzed? How the authors identified differentally expressed lncRNAs and miRNAs? What criterions were used? What software the authors were used to predict the targets miRNAs? What the sex of the prenatal sheep? So many important information were missed in this section, make me very difficult to understand the results.
3.	How many samples were used for analyzing the tightness and evenness of muscle fibers in Figure 1B?
4.	What is long miRNAs in the legend of Figure 5


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: ANALYSIS OF DYNAMIC AND WIDESPREAD LNCRNA AND MIRNA EXPRESSION IN FETAL SHEEP SKELETAL MUSCLE
Review round: 2
Reviewer: 1

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


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

Input:
Title: ANALYSIS OF DYNAMIC AND WIDESPREAD LNCRNA AND MIRNA EXPRESSION IN FETAL SHEEP SKELETAL MUSCLE
Review round: 2
Reviewer: 2

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


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

Input:
Title: ANALYSIS OF DYNAMIC AND WIDESPREAD LNCRNA AND MIRNA EXPRESSION IN FETAL SHEEP SKELETAL MUSCLE
Review round: 2
Reviewer: 3

Output:
Basic reporting: The quality of the revised manuscript has been largely improved. However, several questions still need to be improved.
1. The legends of Figures should provide more information. For instance, in fig.1B, the numbers of pigs and the statistical method used for this analysis should be added. In fig.3, we can't see P value of each KEGG pathway.
2. In table 1, the FPKM or TPM values of each genes should also be listed for better comparison.
3. The written English of the manuscript needs improvement. For examples, in conclusion section, both present and past tenses are used. The tenses need to be unified。
Experimental design: There are no biological replicates for the RNA-seq dataset. If the authors could't add new samples, at least, the authors should discuss this shortages of the experimental  design in the Discussion section.
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: ANALYSIS OF DYNAMIC AND WIDESPREAD LNCRNA AND MIRNA EXPRESSION IN FETAL SHEEP SKELETAL MUSCLE
Review round: 3
Reviewer: 1

Output:
Basic reporting: The revised manuscript have greatly improved. I agree to accept this manuscript.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSIS OF THE ERF TRANSCRIPTION FACTOR FAMILY IN PINEAPPLE (ANANAS COMOSUS (L.) MERR.)
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this manuscript, Huang et al. described identification of the 74 ERF transcription factor in pineapple and their expression analysis. The manuscript is reasonably well written. Although the introduction provides sufficient information to understand the background, it fails to highlight importance of this study. The manuscript requires extensive formatting of the citations and references.
- Line 53: Plant growth, development and adaptation do depend on several molecular players and their dynamic interactions. Citing a recent and brief review discussing such aspects a would be helpful to the reader rather than citing a paper with narrow focus such as Rashid et al., 2012.
- Since the authors performed comparative analysis (with rice and Arabidopsis) to find role of segmental duplication in evolution of this gene family, a gentle introduction on lineage specific polyploidization events in monocots would be helpful.
- There are several places with wrong citation formatting. For example
line 120: citation for MUSCLE has been mentioned as (C, 2004). It should be cited as (Edgar RC., 2004). There are several such cases (line 128,140)which makes it difficult to follow the references.
- Similarly, the reference section needs careful formatting. In several places a "%" appears before the journal name. e.g %J Bioinformatics, %J Plant physiology.
- In general, the tables and figures are helpful and  relevant.
- The phylogenetic trees should display support scores such as bootstrap values.
- The taxon labels in Figure-2 should be formatted like Figure-1. Use different colors for different species.

- The paragraph headings in the Result section is basically repeating the headings of respective paragraphs in Method section. This makes the manuscript unattractive to the reader. The paragraph headings should be modified to tell summary of the findings.
Experimental design: - Line 103: "AP2/ERF genome sequences of pineapple" is it genome or peptide sequences? If Pineapple AP2/ERF genes are already known, then why do authors trying to identify them?
- Line 110: Source of "Arabidopsis AP2/ERFs" should be mentioned.
- Line 136: Authors should describe a clear strategy used to identify segmental duplicates.
- Line 144: It is not cleat whether the authors obtained expression values from a previous RNA-seq analysis or downloaded the raw reads to estimate the expression values. If they obtained the previous estimated expression values they should mention if it is raw read counts or the normalized read counts.
- Line 150: "heatmap" should be "heatmaply R package".
Validity of the findings: - Nearly 27% of the genes identified in this study has been reported as DREB genes in a previous study from the same group(10.7717/peerj.9006). Often single-AP2 domain proteins are often grouped into ERF and DREB sub-families (Nakano etal.,Plant Physiology,2006; Licausi etal., New Phytologist, 2013). Provided there exists a report on DREB genes, authors should classify and discuss something in this direction.
- As mentioned in my previous point that a previous study has identified 20 ERFs as AcoDREB genes (AcoDREB1-20), this study again re-identifies them as AcoERF. Authors should address this issue and reconsider the naming.
- They can also check the phylogenetic tree and ensure that six DREB groups are clearly identifiable in Figure 1.
- Line 340: Do pineapple orthologs of AtERF28 (At5g52020) and OsERF027 (OsDREB1F) also show similar expression under stress conditions?
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: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSIS OF THE ERF TRANSCRIPTION FACTOR FAMILY IN PINEAPPLE (ANANAS COMOSUS (L.) MERR.)
Review round: 1
Reviewer: 2

Output:
Basic reporting: Please refer to overall general comments
Experimental design: Please refer to overall general comments
Validity of the findings: Please refer to overall general comments
Additional comments: The manuscript by Huang et al present the repertoire of AP2 family of DNA binding domain in the Pineapple genome. While the authors have attempted to examine their repertoire, the analysis falls incomplete in many ways.
Major issues:
Primarily the AP2 DNA binding domain is not defined properly. The AT-hook motif and the domain’s structure containing three strands and one helix. Where exactly the DNA binding interface is located. (See and follow PMID: 16040597). This Lacuna is reflected in the analysis as described below.
The phylogenetic classification into 12 subclades is not supported by confidence values. What exactly the sequence features of these 12 subclades? Do they vary in the DNA binding interface or where the variation occurs? How this map on to the structure? Does it fall on the strands or the terminal helical region?
For all that matter, first three figures can be combined into 1. Moreover, the conserved motifs as the authors describe in Figure 4, What are those motifs? They mention Figure S1. But how the reader will know which motif is what. At least the motifs have to be described at first place. Where they are located in the structure and what it can infer us? None of these are described in the text.
What exactly the conclusions are? Yes, there are these many genes and so on but how this advance the understanding and how it will be useful for further downstream analysis is perplexing. In all the authors should perform in-depth sequence-structure analysis to consider the manuscript for publication.


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

Input:
Title: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSIS OF THE ERF TRANSCRIPTION FACTOR FAMILY IN PINEAPPLE (ANANAS COMOSUS (L.) MERR.)
Review round: 2
Reviewer: 1

Output:
Basic reporting: Please refer to the general comment section.
Experimental design: Please refer to the general comment section.
Validity of the findings: Please refer to the general comment section.
Additional comments: The authors have answered all of my concerns and have included most of my suggestions in manuscript. The MS can be accepted for publication.


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

Input:
Title: NO MOW MAY LAWNS HAVE HIGHER POLLINATOR RICHNESS AND ABUNDANCES: AN ENGAGED COMMUNITY PROVIDES FLORAL RESOURCES FOR POLLINATORS
Review round: 1
Reviewer: 1

Output:
Basic reporting: I suggest a number of additional references to consider. I also recommend some slight tweaks to Table 2 and Figure 1.
Experimental design: Research question well defined though framed as objectives. The authors could rephrase as hypotheses if that is the standard for PeerJ. The authors could be more explicit about how they fill research gaps.

I had concerns with the study design, namely the comparison of mowed parks with no mow lawns. See below. Some of the method section requires revising and more clarity. I also am concerned about the lack of independence amongst sites.
Validity of the findings: For the most part, the findings are solid. However, the discussion does get a bit too speculative, particularly because of the small sample size and the comparisons of two different land use types. I suggest the authors address the limitations of their study (which doesn't take away from the novelty).
Additional comments: The manuscript titled “No Mow May lawns have higher pollinator richness and abundances: An engaged community of citizen scientists protecting pollinators and their floral resources” tests how bees respond to a city-wide program aimed at providing pollinator habitat. The study also included a survey to assess perceptions of biodiversity in yards. Providing the scientific evidence to support programs that aim to enhance habitat are important and can highlight the strengths as well as areas of improvement for these types of initiatives. I think this is an important study and has implications for conservation. My main concerns revolve around the site selection, i.e., comparing No Mow yards with mowed parks since these are two different types of green spaces, managed with different objectives, and different sizes and configurations, all of which can influence bees. I think having a lot more caution when discussing the results, in combination with highlighting the study limitations could help ensure the interpretations don’t go beyond the study. I also was not clear about the role of the ‘citizen scientist’, and although they helped collect data, I don’t think this was a citizen science project. If I’m mistaken, then the method section requires more detail. And I think the manuscript could be a bit more explicit about what research gaps the study fills. Nonetheless, I enjoyed reading the manuscript, was excited about the results, and see several future research opportunities based on this study system.

Specific comments (with full citations at the end):

Title
I don’t think the strongest aspect of the study is the role of the citizen scientists, and I suggest changing the title that better reflects how households embraced a city-wide program to provide pollinator habitat. I don’t think the study assesses whether these lawns ‘protect’ pollinators.
Abstract
L16: I’m more familiar with the term ‘citizen science’, or to be more inclusive, ‘community science’. I suggest using one of these more familiar terms.
L19: switch ‘where’ to ‘when’ since there are lots of floral resources in urban areas, though most likely not as abundant early in the season.
Introduction
L 46-51: I appreciate the inclusion of the different types of urban green spaces. However, I would argue that all these spaces are managed but to a different degree. What is meant by ‘functional urban spaces’? Are these for people as well? And I’m not sure the purpose of calling out Apis mellifera. Native bees also provide key ecosystem services (as well as several other flora and fauna). I think this last sentence can be broader. That will lead into the next paragraph.
L59: I’m not sure the need for ‘pollinator’ when describing wild bees.
L66: Remove ‘the’ before ‘late April’.
L63-71: I think this paragraph can be more general to urban bee studies, and not mention Wisconsin. For example, several studies have published bee lists (e.g., Fetridge et al. 2008, Lerman and Milam 2016). I suggest providing a broader overview of urban bee studies, with a focus on those conducted in yards, different management practices, and how floral abundance influences bee patterns. Additional studies to review: Baldock et al. 2015 and 2019, Frankie et al. 2005, Lowenstein et al. 2015, and Pardee and Philpot 2014.
L72-80: I like how this paragraph describes the No Mow May program. I think this paragraph can be strengthened by briefly describing other programs and management practices that promote pollinator habitat (e.g. Xerces society million pollinator garden project, mow less frequently, the Minnesota Bee Lawn program) to demonstrate other efforts for managing for pollinators in built up areas.
L80: This should reference Lerman et al. 2018, not Lerman and Milam 2016.
L81-83: I think the description of No Mow May would work better in the previous paragraph that describes the program.
L85-87: This is a bit awkward. Were the comparisons made in yards of those participating in the No Mow Initiative? If so, could rephrase to: We compared bee richness and abundance in lawns participating in the No Mow May initiative with lawns regularly mowed. Also, although I can appreciate the challenges of accessing private properties (and public parks) for conducting research, I’m concerned that the study does not compare No Mow yards with ‘Mow yards’. See comments in the Materials and Methods section.
Materials and Methods
L95-106: I like the inclusion of the background of the program. However, I think this first paragraph can be broader to provide more context on study area (i.e., Appleton), that includes information about population size, climate, etc. You can also include information about number of bees recorded if you agree with my suggestion to remove that information from the introduction. Then you can describe the No Mow program, and how many sites you sampled. The next paragraph gets into the details of the data collection. The subheading could be ‘study area’, similar to many other method section first paragraphs.
L109-111: move to above paragraph so this section is all about what data you collected. And who are the 8 citizen scientists? Are these people who volunteered their lawns for the initiative? A subset of the sites? I’m not sure the purpose of mentioning the citizen scientists and what they did for the study.
L108-137: Separate these paragraphs so the first describes the bee sampling and the second describes the floral sampling. I suggest this order since I think the main objective is to test whether bees respond to the different treatments. If they do, then you predict it is because of the floral resources. This order makes more logical sense (to me). They get a bit mixed in the first paragraph (e.g., for L119, is the 45 minutes regarding the sweepnet sampling or was the floral sampling timed?)
L111-113: It is unclear exactly how you measured the floral richness. Did you measure percent cover for each species within the 1-square meter sample? Or is it a percentage of all the flowers in the 1-square meter compared to the area without flowers or with bare soil? And does the mean represent the percent floral cover, percent lawn cover and percent bare lawn of these five 1-meter samples?
L115-123: I’m concerned about independence of your samples. 100 meters might be suitable for small-bodied bees but not for Bombus spp, which can forage / travel 2km+. I suggest accounting for spatial autocorrelation to test whether the 3 sites within each park (and I’m assuming there were three 100-m plots within each of the 5 parks…) were independent. Also, to truly get at the effects of No Mow May, I think would require sampling private yards participating and private yards not participating. Comparing yards with parks invites additional variation into the study design (e.g., different motivations for management, different configurations of green space / fragmentation). Thus, observed differences between parks and yards might be due to other factors besides participating in the initiative. Please justify the study design and why it was not possible to either only sample parks (did some participate in the No Mow May program?) or yards, or, sample no mow in parks and yards, and compare with mowed parks and yards.
L124-137: Can you provide some references to support your methodology? Also, which keys were used?
L136-137: see comment above about 100 meters between sites.
L140-142: Was the survey administered to all households participating in No Mow May or only to the 20 yards? Oh, I see on L192 you provide these details. This is part of the methods and should be moved to the survey section.
L139-148: Including the survey really strengthens this study since it provides more context about who participates in these programs as well as highlights opportunities for improvement. I suggest rephrasing the questions to better reflect the questions. As written, they imply (to me) a dichotomous answer though the way the questions were drafted provides a lot more information. This could be rephrased as something like: we asked participants about perceptions of pollinators and flowers in their yards. Alternatively, you can list the questions and responses verbatim from the survey. I like the phrasing of the mowing habits. Also, check out Ramer et al. 2019 and Ramer and Nelson 2020.
L151: I’m not sure what ‘plots’ refers to in this context.

Results
L164: I think this subheading is misleading given the sample sizes. I think ‘Bee diversity’ is more appropriate.
L169: I’m not sure the formatting rules for PeerJ, but other journals will not write out the exact p-value but rather state: p<0.0001, p<0.001, and p<0.01, depending on how significant.
L174-180: I suggest starting with how many flower species identified, which were the most abundant (similar to the bee results). Then report the stats. And I would describe the patterns in terms of the no mow lawns, again, similar to the bee results (i.e., no mow lawns had XX% more flowers…).
L182: Is there a more affirmative word to use rather than ‘suggest’? And can you provide some stats for these statements?
L188-196: I’m not sure much of this paragraph is ‘results’, but rather provides more context for the study system and how you conducted your sampling. For example, didn’t you need to calculate the no mow area prior to sampling bees? I think L194-196 is very interesting and perhaps more suitable for the Discussion. However, 22-40 acres doesn’t mean much to me without any sort of context. How many acres of mowed lawns are there in Appleton?
L198-209: This paragraph would benefit from a different subheading as the use of ‘citizen’ is confusing. Are these the citizen scientists? Or households participating in the No Mow May program? I suggest the latter. If you agree, then please change throughout. If the questions are written out in the methods (as per my comment above), then no need to repeat. Rather, I suggest simplifying and present the results.

Discussion
I think you can strengthen your Discussion sections by starting with the main findings of your study (much of the second paragraph), and how they relate to other studies. This is the big picture paragraph. Then for subsequent paragraphs, get into more details as to why you saw your results, and their significance.
L239-246: I’m not sure the point of this paragraph and how it relates to the study. Yes, bees are important, and cities can support bees. Can you relate to a specific finding? Otherwise, I suggest deleting.
L247-252: I suggest a more cautious approach when describing (human) community responses to the No Mow program. According to Google, there are 74,526 people in Appleton (I suggest finding the figure from the US Census…). Yes, it is impressive that 400+ people registered for the program, and it is likely this number will increase in future as more people become aware of the program and the program gains broader acceptance. However, for this study, you did not assess the effectiveness of the promotion of the program. Only 600 people follow the facebook page (also impressive!), and so the educational opportunities are limited to a small subset of people. There is a lot of potential and I suggest highlighting that and how the program can build upon the enthusiasm and the ecological results.
L265-268: I think this is a liberal definition of ‘citizen scientist’. Are the no mowers really scientists or are they participating in conservation? I’ve collected data in hundreds of yards across the country yet I wouldn’t refer to the householders who granted me permission to collect data as citizen scientists. I have also managed a citizen science project where in addition to 100+ households granting me access to their yards, they also follow a protocol to monitor wildlife and submit data. Both roles are vital for understanding how wildlife responds to different urban green space management, and my distinction recognizes different levels of engagement. And what data did the 8 citizen scientists collect? Again, unless you are asking specific questions to these 8 citizen scientists about their experiences (and I caution against this due to small sample sizes), it is unclear how their participation enhanced their understanding of conservation, etc. Plus, the survey only sampled those who participated in the No Mow program, and did not conduct a pre-survey. Thus, we don’t know whether their perceptions differ from mowers, and whether their perceptions were formed because of their participation in the program.
L274-277: Can you be more specific? Are there plans to present results to the city planners?
L281-294: Please provide some citations to back up these statements. Also, I suggest a more cautious approach given the small sample size and the comparisons between yards and parks. The limitations of the study should be discussed as per my comment in the method section. Could the results observed be explained because parks don’t have as many planted flowers? What about the yards next to the No Mow lawns? Did they have pollinator gardens or other flowers that might have attracted more bees to the area?
L307-309: I suggest citing Larson et al. 2016
L309-312: I think this is an interesting conclusion and I recommend considering how aesthetics plays into the outreach and awareness. One suggestion is to have future research assess the aesthetic perceptions of the No Mow lawns compared with the mowed lawns. See Ramer et al. 2019.
Table 1: Why only include the most common plant species?
Table 2: I suggest having two ‘Count’ columns: 1 for yards and 1 for parks.
Figure 1: I like that you included all the No Mow sites. However, I think it a little distracting from the bee richness results. I suggest the sites where you didn’t collect bees have a smaller dot. And I presume the green polygons are parks? If so, then it looks like some parks had No Mow??

Suggested additional references to include:
Baldock, K. C. R., M. A. Goddard, D. M. Hicks, W. E. Kunin, N. Mitschunas, H. Morse, L. M. Osgathorpe, S. G. Potts, K. M. Robertson, A. V. Scott, P. P. A. Staniczenko, G. N. Stone, I. P. Vaughan, and J. Memmott. 2019. A systems approach reveals urban pollinator hotspots and conservation opportunities. Nature Ecology & Evolution 3:363.
Fetridge, E. D., J. S. Ascher, and G. A. Langellotto. 2008. The bee fauna of residential gardens in a suburb of New York City (hymenoptera: apoidea). Annals of the Entomological Society of America 101:1067–1077.
Frankie, G. W., R. W. Thorp, M. Schindler, J. Hernandez, B. Ertter, and M. Rizzardi. 2005. Ecological patterns of bees and their host ornamental flowers in two northern California cities. Journal of the Kansas Entomological Society:227–246.
Larson, K. L., K. C. Nelson, S. R. Samples, S. J. Hall, N. Bettez, J. Cavender-Bares, P. M. Groffman, M. Grove, J. B. Heffernan, S. E. Hobbie, J. Learned, J. L. Morse, C. Neill, L. A. Ogden, J. O’Neil-Dunne, D. E. Pataki, C. Polsky, R. R. Chowdhury, M. Steele, and T. L. E. Trammell. 2016. Ecosystem services in managing residential landscapes: priorities, value dimensions, and cross-regional patterns. Urban Ecosystems 19:95–113.
Lowenstein, D. M., K. C. Matteson, and E. S. Minor. 2015. Diversity of wild bees supports pollination services in an urbanized landscape. Oecologia:1–11.
Ramer, H., and K. C. Nelson. 2020. Applying ‘action situation’ concepts to public land managers’ perceptions of flowering bee lawns in urban parks. Urban Forestry & Urban Greening 53:126711.
Ramer, H., K. C. Nelson, M. Spivak, E. Watkins, J. Wolfin, and M. Pulscher. 2019. Exploring park visitor perceptions of ‘flowering bee lawns’ in neighborhood parks in Minneapolis, MN, US. Landscape and Urban Planning 189:117–128.