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: CRYSTALLIZATION AND STRUCTURE ANALYSIS OF THE CORE MOTIF OF THE PKS13 ACYLTRANSFERASE DOMAIN FROM MYCOBACTERIUM TUBERCULOSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have answered all questions adequately. The manuscript can be accepted.
Experimental design: -
Validity of the findings: -
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: CRYSTALLIZATION AND STRUCTURE ANALYSIS OF THE CORE MOTIF OF THE PKS13 ACYLTRANSFERASE DOMAIN FROM MYCOBACTERIUM TUBERCULOSIS
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: 1-	Basic reporting
The authors have made some significant changes to the paper, including new figures, references. Unfortunately, this work does not provide significant new information considering that (i) no functional data have been provided and (ii) the intact full-length AT domain X-ray structure has previously been described in great details by Bergeret and colleagues.

Some important facts…
1-	Writing problems throughout: there are myriad writing problems including diction (word use, lack of prepositions and plurals, etc) and grammatical inaccuracies.... It would make sense to have a professional or at least a native English speaking scientist review the manuscript and correct these errors. There are just too many.
2-	Line 34 “Phosphopantetheinyl (P-pant) transferase (PPtT), encoded by the sfp gene…” should read Phosphopantetheinyl transferase (PPTase)
3-	Line 59 “The sfp gene from Bacillus subtilis str.168 (Chalut et al., 2006), which encodes the 4 -phosphopantetheinyl (P-pant) transferase PptT…” sfp and pptT are two different genes.
4-	Table 1 - Sfp (PptT). Same as above.


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

Input:
Title: A SURVEY OF THE VIEWS AND CAPABILITIES OF COMMUNITY PHARMACISTS IN WESTERN AUSTRALIA REGARDING THE RESCHEDULING OF SELECTED ORAL ANTIBIOTICS IN A FRAMEWORK OF PHARMACIST PRESCRIBING
Review round: 1
Reviewer: 1

Output:
Basic reporting: Thank you for the opportunity to review the manuscript titled “Exploring the views and capabilities of community pharmacists in Western Australia regarding the rescheduling of selected oral antibiotics in a framework of pharmacist prescribing”.

The researchers investigated the factors for appropriateness and the level of support for re-scheduling selected antibiotics to enable community pharmacist prescribing of oral antibiotics for a selected range of infections.

Discrepancies between the manuscript and the survey questionnaire raised a level of concern regarding the care taken over the conduct of the study and subsequent data analysis (additional comments below state where these discrepancies occur).  Two of these discrepancies seem to be errors in the presentation of the survey question (Section B2) and case vignettes (Case 1 and Case 3) which may have affected participant responses.  Light editing is required for clarity of some passages.

Abstract:
1.	The denominator used (i.e. 630) refers to the number of responses (not respondents).  Should be reported as percentage of responses (as each respondent provided 7 sets of responses for Section C).

Introduction:
2.	Line 49-51: “There has been a movement towards the re-classification of selected prescription-only medicines to be made available from community pharmacies as S2 or S3.”  Please cite reference/s for this statement.
3.	Line 51-52: “Various level of control can be placed on selected Schedule 3 listings such as prescribing emergency contraception.”  Please describe the levels of control alluded to in this statement for the benefit of international readers.
4.	Line 55: “ … such decisions.” Please clarify.

Case Vignettes:
5.	Page 4, line 101: “…if there was no improvement following 24 hours (otitis media) or 3 days (other vignettes).”  The manuscript does not match the actual case vignette – it was Case 3 Community Acquired Pneumonia with acute respiratory symptoms that had the “After 24 hours of the treatment …” question; other vignettes stated “After 3 days of the treatment …”.  See also item 13 of comments (under Results).

Questionnaire distribution:
6.	Page 4, line 104 – please justify the 40% sample.
7.	Page 4, line 109-110 – please explain how non-responders were identified.  Were the questionnaires or reply paid envelopes printed with a unique code allocated to each community pharmacy?

Sample size distribution:
8.	Page 4, line 115 – 240 pharmacies (each pharmacy may have one or more pharmacists).

Data analysis:
9.	Page 5, line 125 – the manuscript did not match the survey – in Section B of the survey there were nine statements regarding “down-scheduling” of antibiotics. Please clarify.
10.	Page 5, line 124-127 – please explain scoring used for the collapsed 3-point Likert in order to arrive at the classification of “in agreement” and “not in agreement”.  How were neutral responses handled?

Results:
11.	Page 7 and Figure 1 - Please explain why statements (h) and (i) (in Section B1 of the survey) were not reported in Results and in Figure 2.
12.	Page 10, line 215-217 – Discrepancy:  p-value for respondents in the role of consultant pharmacists stated as p=0.0009; whereas Table 3 shows 0.0068. Please clarify.
13.	Page 10, line 226-227 – “In the case of otitis media, respondents were asked to select therapy after 24 hours of no improvement instead of 3 days (as per current guidelines).”  If this is the case, then Case 1 and Case 3 vignettes in the survey were presented incorrectly to respondents (states 3 days for Case 1 and 24 hours for Case 3).  This error may have affected how participants responded.
14.	For the vignettes, were the responses for “Other (please specify regimen)” analysed?  Were these responses appropriate?

Questionnaire:
15.	Section B, Question 2 – responses to statements (from strongly agree to strongly disagree) are not aligned with the question asked (level of comfort in prescribing the listed antibiotics).  There is a chance that respondents may have misread the question as the level of agreement that the listed antibiotics are re-scheduled, rather than their level of comfort in prescribing the listed antibiotics.

References:
16.	Reference 15 and 17 are duplicates.  Please remove one.

Tables and Figures:
17.	Table 2: Formatting change – “Age group” to be in bold.
18.	Figure 3 – not explicitly referred to in the manuscript.
19.	Figure 4 – reconsider title (as one vignette had an interval of 24 hours instead of 3 days) e.g. Respondent follow up actions after an interval of no improvement with initial therapy.
Experimental design: The research question is well defined, relevant and meaningful.  See also comments 5 to 15 provided in Basic Reporting section above.
Validity of the findings: Findings seem to be largely valid.  Errors in the presentation of the survey question (Section B2) and case vignettes (Case 1 and Case 3) may have affected participant responses.  Authors should clarify and propose how they could reasonably address this issue.
Additional comments: Congratulations on completing an interesting and useful study.


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

Input:
Title: A SURVEY OF THE VIEWS AND CAPABILITIES OF COMMUNITY PHARMACISTS IN WESTERN AUSTRALIA REGARDING THE RESCHEDULING OF SELECTED ORAL ANTIBIOTICS IN A FRAMEWORK OF PHARMACIST PRESCRIBING
Review round: 1
Reviewer: 2

Output:
Basic reporting: Thank you for the opportunity to review this manuscript. The clinical decision making capability of pharmacists is an important area, particularly with the increasing scope of pharmacist practice. Should the editor choose to accept this manuscript for publication, the following comments should be addressed:

General: Overall this is a well written manuscript with few grammatical errors. Please clarify the author order as it differs from title page to abstract. Font changes occur, please review as it my do due to the pdf generation process. Please ensure all intext citations are consistently placed in reference to punctuation with reference to journal guidelines.

Title: Please add ‘survey’

Abstract: ‘Pharmacist’ not ‘pharmacy’ in results. Please add n values for all percentages. Provide the numbers compared with all p values.

Introduction:
Lines 33-6: Please reference statement.
Lines 38-41: Please reference statement.
Lines 49-51: Please reference statement.
Lines 51-52: Please clarify and reference ‘Various level of control can be placed
on selected Schedule 3 listings such as prescribing emergency contraception’.

References: Please review pagination consistency of citations. Reference 5 only reference with DOI. Reference 30 title is the only reference with an abbreviated title.
Experimental design: Methods:
Line 74: Mixed methods as defined by Creswell is the use of qualitative and quantitative methods to measure the same phenomenon. Looking at the attached questionnaire, the case vignettes have structured responses. As such, have two quantitative methods been employed in this instance? Further, are questions in Section B relating to attitudes and case vignettes in Section C which test knowledge the same phenomenon? These two issues would suggest multiple methods design rather than mixed methods. Please review.
Lines 79-82: who developed the questionnaire?
Line 98: were only ATG endorsed regimens provided? If not, how many options were endorsed of the total? Were all non-endorsed regimens classed as inappropriate? If so, who decided? How were ‘other regimens’ assessed?
Line 99: who graded the complexity? What criteria were used?
Line 104: why was 40% chosen as a sample? OK mentioned below. Please consider merging these sections so the power calculation is provided with the sample size.
Line 124: add possessive apostrophe to ‘respondents’.
Line 126-7: please clarify why “The overall response was classified as “in agreement” if the
mean score was less than (or equal to) 2, and classified as “not in agreement” otherwise.”
Line 129: change ‘best’ to optimal.
Line 134-5: Were all immediate referrals included in the GEE analysis? If so, please provide the research question being addressed as referral may be required or not required. Some vignettes could be self-limiting e.g. otitis media as opposed to pyelonephritis.
Validity of the findings: Results:
Line 152: Please add specify Australian dollars ‘AUD’.
Line 155: Why state approximately 50% support of down-scheduling antibiotics, yet Table 1 suggests more and the following statement in the abstract is made; “There was more than 60% respondent support for expanded prescribing (rescheduling) of commonly prescribed antibiotics.”
Line 157: Table 1: Please provide the question regarding support of downscheduling that is used for the cross tabulations in this table. Is it Selected oral antibiotics should be down scheduled from Schedule 4 to Schedule 3.? If so, why are the proportions in agreement for male (56.5%) and female (54.6%) both lower than the proportion reported in Figure 1? Why were multiple 2 x 2 Chi-squares and Fisher Exact tests used on nominal data with more than 1 degree of freedom i.e. position held, setting. Were Chi-square tests used for ordinal data?
Line 159-62: Please justify grouping these items with a collective average. I suspect there are multiple factors here. Was exploratory factor analysis performed? (see below).
Line 163: Figure 1: of interest is the large minority disagreeing with downscheduling that are not disagreeing with the potential benefits of downscheduling in following questions. This is a discrepancy worth mentioning. Why are only 7 of the 9 questions in this section of the questionnaire presented in this Figure? Please update.
Line 177-218: Please provide values that are being compared when a p value is reported.

Discussion:
Line 254-9: Please do not equate confidence with competence. While there is overlap, they are not the same.
Line 272-9: Please posit why conflicting findings were found regarding experienced pharmacists in different countries e.g. educational differences.
Line 286-90: Please consider the lack of observation or real-time deployment of case vignettes in this study. Would a case vignette questionnaire in which resources may be referred to and completion occurring at a time point of potentially low interruptions and work stress similar to real-life practice? Arguably these findings would be representative of optimal performance (sans training) rather than real-life performance.

Conclusion:
Well written.
Additional comments: No additional comments


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

Input:
Title: A SURVEY OF THE VIEWS AND CAPABILITIES OF COMMUNITY PHARMACISTS IN WESTERN AUSTRALIA REGARDING THE RESCHEDULING OF SELECTED ORAL ANTIBIOTICS IN A FRAMEWORK OF PHARMACIST PRESCRIBING
Review round: 1
Reviewer: 3

Output:
Basic reporting: The paper is easy to read with excellent English and an interesting topic.
The introduction would benefit from further work to provide context, ensure references support the statements made and provide balance. Line 28 and 29 is not supported by reference 3, and reference 2 is about secondary care – this needs to be clear in the introduction given it is a different context to this study which is about primary care, and also particularly given the perhaps excessively general statement attributed to it in line 32.
It is important to include references to community pharmacy research with respect to supply of antimicrobials by pharmacists, for example:
Booth JL, Mullen AB, Thomson DAM, et al. Antibiotic treatment of urinary tract infection by community pharmacists: a cross-sectional study. Br J Gen Pract. 2013;63:e244-e249.
Klepser ME, Adams AJ, Klepser DG. Antimicrobial stewardship in outpatient settings: leveraging innovative physician-pharmacist collaborations to reduce antibiotic resistance. Health security. 2015;13(3):166-173.
Gauld NJ, Zeng ISL, Ikram RB, et al. Antibiotic treatment of women with uncomplicated cystitis before and after allowing pharmacist-supply of trimethoprim. Int J Clin Pharm. 2017;39:165-172.
There may be others too, e.g. supplies of oseltamivir in the US I think, and New Zealand. While not being antibiotics they may be relevant.
Another relevant paper that I believe would be beneficial to include in the introduction is:
Reeves DS, Finch RG, Bax RP, et al. Self-medication of antibacterials without prescription (also called 'over-the-counter' use). A report of a Working Party of the British Society for Antimicrobial Chemotherapy. J Antimicrob Chemother. Aug 1999;44(2):163-177.
While old, this is a very well-considered paper that covers many of the key issues that still remain.
The paper would be more balanced and informative if there was a discussion of the downsides also of pharmacists providing these medicines, for example potential for overuse, both in the introduction and the discussion. Antibiotic resistance is a key concern internationally and in Australia, and there is a possibility of increased use of antibiotics under this scenario.  Concerns about overuse of antibiotics are important with pharmacy availability. While not oral antibiotics, increased use is still relevant with chloramphenicol papers published internationally (2 in the UK and another in Australia I think), and the paper on mupirocin as below:
Upton A, Lang S, Heffernan H. Mupirocin and Staphylococcus aureus: A recent paradigm of emerging antibiotic resistance. J Antimicrob Chemother. 2003;51(3):613-617.
I would expect a mention (referenced) at least in the introduction of the rescheduling status of oral antibiotics without prescription e.g. the availability of azithromycin in the UK and trimethoprim in NZ, and possibly that trimethoprim and nitrofurantoin for UTIs in the UK did not progress.
The sentence 47-49 has references that are not particularly pertinent to the mention of S2 and S3 in Australia, are there more appropriate references? Papers by Gilbert et al, or Gauld et al, for example.
While the use of schedule 3 was explained and is well known in Australia, it would be helpful to use terms “pharmacy only” and “pharmacist only” throughout rather than S2 or S3, respectively, to make it easier for an international reader skimming the manuscript to understand quickly. See in particular line 51 for a mention os S2 and S3.  My understanding, which might not be correct, was that there needed to be direct involvement of a pharmacist, with S3 medicines in Australia, if legislation or guidelines allow for supervision instead it would be very helpful to include that reference (line 36-38).
There is quite a difference between an specialist antibiotic pharmacist in hospital and a community pharmacist with no additional training. Would additional training be recommended, as is required for trimethoprim in NZ and is encouraged for azithromycin in the UK? Would there be a requirement or expectation that Australian guidelines would be adhered to?
The tables should include the abbreviations used in full at the bottom of the table.
Expanding line 54 on the potential benefits of such availability would provide context.
The English is excellent throughout and the paper is easy to understand. Check the wording of the sentence line 266-267.
Line 270-271 – I agree with the potential for commercial interests, perhaps larger pharmacies might also have more pharmacists on staff to make it easier to manage longer consultations. Noting this commercial interest though, is there a risk for inappropriate supplies, e.g. immediate treatment in someone with minor symptoms who could take a wait and see approach? Supplies in advance of need for “in case”. Some studies in Australia have shown S3 medicines being sold without pharmacist input – this should be mentioned (referenced) and consideration of how the risk might be mitigated would be useful.
It would be helpful in the discussion to think about how this availability could work in practice, for example, by simple down-scheduling, or by allowing pharmacists to become prescribers of antibiotics if they have completed special training, perhaps in a similar way as for vaccinations in Australia. Bear in mind the codeine example whereby upscheduling is about to occur in Australia after some misuse and abuse, despite the S3 category and resultant patient harm.
There would be benefit in considering further research which is required. In particular, research on actual behaviour in the UK with azithromycin could help to inform the appropriateness of therapy.
Experimental design: The research is original. The aim is well written and meaningful.
Method: The way the vignettes were developed, based on literature and by using the Australian Therapeutic Guidelines appeared to miss expert input specifically into the vignettes e.g. from an infectious diseases specialist or consultant microbiologist and a doctor working in general practice. I think this is an important deficiency. For example, it seems surprising to suggest treating pyelonephritis in pharmacy. This can be a serious illness and at best cystitis would be treated in the pharmacy and pyelonephritis referred to a doctor given that pharmacists are not trained to the same degree as doctors. Either this was done and was overlooked in the method, or it is a limitation that should be mentioned and affects the usefulness of the research in my view.
Another point is that the right antibiotic is important for antibiotic resistance, but so is the correct dosing and the correct duration (e.g. Dryden). It would be helpful to mention in the limitations that this was not measured and is relevant.
The questions asked about their opinions of down-scheduling avoided asking about any negative areas, for example, OTC prescribing of antibiotics could increase the risk of antibiotic resistance. Or OTC prescribing of antibiotics could lead to unrealistic expectations from patients of having antibiotics when they are not appropriate. Having a consultant microbiologist involved would have helped provide more balance. This could be an area to highlight for further research, and I think should be mentioned as a limitation - that the potential downsides were not explored.
Validity of the findings: See notes under experimental design about the development of the vignettes.
Data is fine.
Additional comments: No additional comments


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

Input:
Title: A SURVEY OF THE VIEWS AND CAPABILITIES OF COMMUNITY PHARMACISTS IN WESTERN AUSTRALIA REGARDING THE RESCHEDULING OF SELECTED ORAL ANTIBIOTICS IN A FRAMEWORK OF PHARMACIST PRESCRIBING
Review round: 2
Reviewer: 1

Output:
Basic reporting: No further comments
Experimental design: No further comments
Validity of the findings: Two comments remain, specific to the case vignettes.

1. The deployment of case vignettes via non-supervised survey is a limitation to external validity of actual practice as previously commented. Despite responding that my initial comment related to a referenced statement, please note what the reference 27 (Evans et al, 2015) states "Similarly, in regard to the external validity and generalizability of findings, participants’ behavior in a vignette study is not intended to be interpreted as representative of their behavior in the real world, but rather as strong predictors or proxies for such behavior, given the circumstances approximated by the vignette." Therefore my assertion that the vignettes are representative of optimal performance (sans training) rather than real-life performance stands as the vignettes may be answered in a situation in which resources may be referred to and completion may occur at a time point of low interruptions and work stress. The authors can simply state that the vignettes provide a demonstration of potential performance. My apologies for not making my meaning sufficiently clear in my initial comment.

2. As previously commented and as Reviewer 3 eloquently commented, the content validity and grading criteria of the vignettes themselves may be questioned. Piloting with community pharmacists determines face validity. The content validity is questionable as the process of vignette development by the researchers themselves and piloting with community pharmacists with extensive experience with antibiotics may not be deemed equivalent to content experts such as a panel of specialist infectious diseases physicians. A seperate panel of experts in addition to piloting is a recommendation of Evans et al, 2015 (reference 27). Further, the method of determining the grading has not been provided or validated. The reliability of the grading scale is not known. Again, these issues could simply be expressed as limitations. These limitations do not significantly impair the quality of the overall work but nonetheless should be stated.
Additional comments: Thank you for the extensive revisions. The revised article is an excellent and complex piece of research and should be a significant contribution to the area.


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

Input:
Title: A SURVEY OF THE VIEWS AND CAPABILITIES OF COMMUNITY PHARMACISTS IN WESTERN AUSTRALIA REGARDING THE RESCHEDULING OF SELECTED ORAL ANTIBIOTICS IN A FRAMEWORK OF PHARMACIST PRESCRIBING
Review round: 2
Reviewer: 2

Output:
Basic reporting: The abstract contains abbreviations which are not in full.
Line 142 were not was
Line 274 remove the apostrophe
Experimental design: No comment
Validity of the findings: No comment. Pleased to see the addition of protocols.
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: ULTRASOUND-PROMOTED SYNTHESIS OF 2-ORGANOSELANYL-NAPHTHALENES USING OXONE® IN AQUEOUS MEDIUM AS AN OXIDIZING AGENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is written in a good level of language which makes it clear and understandable.
The introduction section is informative with a reasonable length. The literature is well explained with relevant reference; however, more references are required to support some important information (see the general comments below).
In general, the structure of the manuscript fits to PeerJ standards (considering the suggested corrections and explanations).
The figures are relevant and informative but the need to be uniformed and with a better quality!
The appropriate raw data are available.
Experimental design: The work is original within the area of green methodologies of organic synthesis. The manuscript describes the development of a new methodology for the synthesis of an important class of organic compounds (2-organoselanyl-naphthalenes) using water as solvent as green solvent with a relatively short reaction times!
The experiments are well designed in a good sequence of work steps that showed how to get the optimum conditions of the developed methodology followed by proving the applicability of the method on deferent substrates which were chosen to cover deferent structural properties. The new method is well described with sufficient details, the variety of the substrates and obtained results indicate that the method is reproducible!
Validity of the findings: Positive results are reported, proving the validity of the newly developed method.
Clear raw data are supplied. The choices of the different substrates cover a broad spectrum of molecular structures properties!
The conclusions are well stated and connected to the core of the work and the obtained results.
Additional comments: Lines 46-47: “The reaction of diorganyl diselenides with a halogen source is the most used method to access electrophilic selenium species.”
References are required to support this statement.

Line 49: “alternative methodologies”
Explain some of these methodologies supported by recent refernces.

Lines 48-52: “This point has motivated the development of alternative methodologies to synthesize electrophilic species of selenium and a greener alternative to selanyl halides are the convenient sulfate analogues, formed in situ by the reaction of diaryl diselenides with ammonium (Tiecco et al., 1989) or potassium persulfate (Santi & Tidei, 2014).”
The statement need to be re-written to make it clearer to the reader!

Line: 109: NMR Spectrometer brand to be mentioned.

Line: 110: are the chemical shift values “referenced to the solvent peak of CDCl3” or to TMS?!

Line 115: “(HRMS). The experiments” to be replaced by “(HRMS), the experiments”

Line 130: “dried with MgSO4” to be replaced by “dried over MgSO4”

Line 132: “hexanes” to be replaced by “hexane”

Line 136: [33] should be referring to the reference (Recchi, Back & Zeni, 2017), follow the author guidelines consistently, the same mistake in Lines 143, 150 and 158.

Line 144: The spectrum in the raw data supplied shows that the signal at 7.82-7.80 d rather than m, it could be reported app. d!
The same for 7.73 (Line 159), 7.79-7.77 (Line 181) and 8.07-8.05 ; 7.79-7.77 (Line 194).

Lines 153-154: There is a mismatch with the provided spectrum in the raw data!

Line 212: Is it 0.25 or 0.125 mmol of Oxone?! (Check table 1).

Lines 217-218:” Aiming to improve the yield of 3a, different amounts of starting material 2a
218 and Oxone®, as well as the nature of the solvent, were evaluated (Table 1, entries 3-12).”
Table 1 shows that 0.125 mmol of  2a was used in all cases!
Referring to entries 3-12 is not accurate, because in entry 9 the US amplitude was changed!

Lines 236-237: 0.125 mmol of Oxone; Line 241: 0.25 mmol of Oxone; there is a contradiction even with Table 1 (check entries 1 and 13)!.

Line 249: 3 to be replaced by 3a-i

Line 249: 1 to be replaced by 1a-d

Lines 269-270:  “it was not possible to infer any electronic effect of substituents in the aromatic ring of alkynols 2b and 2c.”
The statement is not clear!

Line 271: Csp, what does it mean?
Line 272: “entry 11” to be replaced by “entry 9”.
Other Points and Questions:
Correct the caption of Table 1.
For the reactions with relatively moderate yields obtained, have the authors tried to improve the yields by giving the reactions longer time to proceed?
In some of the 1H NMR spectra (compounds 3b-d) signal at around 5.1 ppm is observed, any explanation?

In conclusion the manuscript can be considered for publication in PeerJ after minor corrections (considering the points mentioned above).


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

Input:
Title: ULTRASOUND-PROMOTED SYNTHESIS OF 2-ORGANOSELANYL-NAPHTHALENES USING OXONE® IN AQUEOUS MEDIUM AS AN OXIDIZING AGENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is written in good and clear English level.
The article fits the PeerJ standards with some minor mistakes as shown in the general comments for the author.
Experimental design: The experiments are well designed  with good reaction sequence steps.
Validity of the findings: No comment
Additional comments: Need to double check the matching of the manuscript data and table 1 for example:
Line 212: not matching with Entry 1 (Table 1).

Some minor mistakes in references formatting, for example:
Line 344: Year of Publication (not written).
Line: 363: Name of the book (shouldn't be italic).
Line 374: Name of the journal (should be italic).
Line 375: space.
Line 382: No italic.
Lines 390, 422 and 423.

The manuscript may very well be suitable for publication in PeerJ after making sure of previous observations and correcting some minor errors.


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: ULTRASOUND-PROMOTED SYNTHESIS OF 2-ORGANOSELANYL-NAPHTHALENES USING OXONE® IN AQUEOUS MEDIUM AS AN OXIDIZING AGENT
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is very well written with nice finding and I recommend it for publications
Experimental design: no comment
Validity of the findings: no comment
Additional comments: •	Abstract: is seems very well written
•	Introduction: it is seems that the introduction cover the most important papers and the recent one but it is too long, I suggest to reduce it
•	In line 76: you should use “comma” and “and” (2KHSO5, KHSO4 and K2SO4) instead of (2KHSO5.KHSO4.K2SO4) because it is mixture as you said in the same line.
•	Material and method: clear with small comment:
•	Line 108: it is better to replace hydrogen by proton
•	Line 109: you need to write the instruments brand and model
•	Results and discussion: no comments
•	Conclusion: no comments
•	References: no comments
Overall, the manuscript is very well written with nice finding and I recommend it for publications


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: VIROMES OF ONE YEAR OLD INFANTS REVEAL THE IMPACT OF BIRTH MODE ON MICROBIOME DIVERSITY
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comments
Experimental design: The manuscripts question is well defined, relevant and interesting. An important point that is made throughout the manuscript is regarding the "early life virome/microbiome", however, is not well defined anywhere in the manuscript what is considered as "early". The introduction mentions that individuals at 1year of age begin to resemble an adult microbiome, so intuitively it can be thought that an "early" microbiome can be defined as the first weeks of months of age. However, they use samples at 1 year of age to define differences in the "early" microbiome, where many changes due to environmental exposure could have significant effects.

2) Line 174 mentions the presence of crassphage in that early life microbiome. Due to the same argument as before, unless is well defined what "early" represents, and the exact age of the individuals at the sampling where the crassphage was identified, is difficult to make the point about crassPhage being present at an early age.

3) Line 52: cites Reyes et al, 2010 as a reference of the "early virome", however, that manuscript describe the differences in virome between adolescent/adults twins, samples taken within a 3 year period, not at 0-3 years in age. This should be corrected and any reference to those results as representing an early age virome should be revised.

4) The earliest study of the gut virome is: Viral diversity and dynamics in an infant gut by Breitbart et al in 2008. Should be cited.

Regarding the Methods:
5) What was the insert size of the library? If less than 500 the pair end reads could be assembled before a de novo assembly. Why the trimming had a max length of 250 if 300bp were generated? Important data may have been lost.

6) Line 125, why the prediction was only done for those lengths? Sometimes a partial assembly may lead to smaller contigs, but still real, thus, ignoring those may lead to an underestimation of the diversity.

7) Line 141, check the sentence “All statistical analyses R v3.3.0"

8) Line 166: Mentions richness and abundance of TTV and references Fig 1b, but the figure only shows Number of TTVs per sample (richness) so no abundance is shown.

9) No info about assembly statistics is given, number of assembled contig, average length or coverage, etc.

10) No mention of the differences in identity about the crassphage is done either (Fig S3), which is cited in line 176 but no mention of the results shown or discussion about those is done.
Validity of the findings: The only comment here is following the comment on defining an "early virome" and the fact that the samples were originated from ~1 year old individual. Line 170 states that the fact that breast-feeding is not a factor determining the TTV abundance, "strongly supporting transfer during vaginal delivery". I consider that during 1 year of age there could be many other environmental factors that could be relevant for that TTV colonization that need to be ruled out, or stronger evidence for the vaginal delivery transfer is needed to support such statement.
Additional comments: Three minor comments:
Fig S1: A log or square root transformation will be ideal so the outliers don’t take most of the image.

No legend for supplementary figures was found.

Fig S3 is cited before S2.


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: VIROMES OF ONE YEAR OLD INFANTS REVEAL THE IMPACT OF BIRTH MODE ON MICROBIOME DIVERSITY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The basic reporting is satisfactory.
Experimental design: The research is primarily exploratory and hypothesis generating.  The methods are adequately described.
Validity of the findings: The results on colonization with anelloviruses differ from a published paper (Lim et al.).  This deserves more discussion.
Additional comments: The authors present a study of the virome in stool of 20 one year old infants.  They find groups of viruses typically seen in human stool, including Caudovirales, Microviridae, Anelloviridae, and others.  The authors obtain data indicating that TTVs (from the Anelloviridae group) may be enriched in babies with spontaneous vaginal delivery versus cesarean section.  Samples from spontaneous vaginal delivery are also proposed to be more diverse.  The authors thus propose that verticle transmission is important in formation of the virome at one year.

The formation of the virome early in life is an interesting question, and the work is generally technically well done.  The paper would be improved by addressing the following points:

1. Data in this paper differs from that of Lim et al. in suggesting TTVs are inherited vertically.  Lim et al. studied samples taken earlier, and saw TTVs were not present in the first time point for most subjects, but were acquired later.  Unfortunately the authors’ only sample at one year, so the timing of TTV acquisition is unclear, and the main point is in real doubt.  This should be discussed carefully.

2.The authors were not clear about whether they analyzed negative controls (blank virome purifications), and if they did what sequences were in them.  The issue of DNA contamination in low biomass samples is increasingly recognized as a major issue in the field.  Please specify.

3. For the diversity analysis, was this done with database attributions, or over all contigs?  How was possible fragmentation of viral genomes handled?  That is, a large viral genome, partially sequenced, could potentially yield many short contigs—how was this dealt with?


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: VIROMES OF ONE YEAR OLD INFANTS REVEAL THE IMPACT OF BIRTH MODE ON MICROBIOME DIVERSITY
Review round: 1
Reviewer: 3

Output:
Basic reporting: This short paper reports on viromes from feces of 20 children at 1 year, 10 of which were born by caesarean section, 10  by spontaneous vaginal delivery. The sequencing depth is high, apparently many contigs could be assembled from the viromes. There seems to be some differences in the virome composition with the birth mode, which would be interesting. At present however, results need to be strengthened to reach any conclusion.
Experimental design: Two examples were results are not reported fully:
     * Lane 121: “Reads were then assembled with the metaSPAdes assembler”. Results not shown. How many contigs of what length? How many reads are mapped back on these contigs? No abundance table given, no description of the contigs. Some phages of the study are said to infect Bifidobacteria, a genus for which 60 prophages have been described (Lugli et al. Env Microbiol 2016), so details about these should be given.

      * Lane 123: "Raw reads were classified using Kaiju": results not shown.

Concerning the risk of contamination of viral DNA with bacterial material:  suppl. table 2 shows the 16S DNA content of the viromes, which in 3 cases is quite high (above 0.02%). This means that prophages could confound the signal of the temperate phages. Appropriate controls should therefore be added when quantifying viral contigs of known bacterial hosts (such as Bifidobacteria infecting phages), by mapping reads on bacterial DNA of Bifidobacterium.

Presentation of the results needs to be improved: all data are shown as boxplots, but given the small number of data points, all points should be shown instead, together with a bar for the average.

The sequences have been deposited, but have not yet accession numbers.
Validity of the findings: The two main results of this manuscript need to be strengthened:
1. Lanes 160 -166: A difference in abundance is suspected for TTV, a circular single strand DNA virus. Authors are aware of the distortions introduced by genomiphi amplification, but nevertheless consider that “all samples were processed in an identical fashion allowing comparisons between groups”.

This should be proven with repeats, or controls. A qPCR confirmation on the virome samples prior genomiphi amplification would be a good way to confirm this interesting result.

2. Lane 192: “However, DESeq2 did identify 32 contigs differentially abundant by birth mode, including TTV and several contigs bearing high levels of nucleotide homology to Bifidobacteria prophages.”

Results are not shown. Are the differences statistically significant? Which Bifidobacteria prophages were found (technically, they should be named temperate phages rather than prophages.  ?

Lane 196 :”While this study only analysed 20 infants it is sufficiently powered to provide the first evidence that birth mode significantly affects the infant gut virome. Given the differences in viral diversity observed here, we hypothesize birth mode plays a role in shaping the early life gut microbiome and that the virome is an effective biomarker of bacterial diversity at sub-OTU level”

This conclusion is not supported by the data.
Additional comments: Most of the data are not shown, statistical significance is not always given and the conclusions are therefore not supported by the data. So I cannot recommend publication of this manuscript at this premature stage.


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: VIROMES OF ONE YEAR OLD INFANTS REVEAL THE IMPACT OF BIRTH MODE ON MICROBIOME DIVERSITY
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The manuscript has improved from the original version and all my concerns have been adequately addressed. My only concern remaining is the suggestion of causation in the abstract regarding mode of birth and the impact on the virome. Definitely there is a strong correlation and there are clear and statistical differences in the virome depending on the birth mode. However, even though other factors were taken into account, the fact that there is only one time point and is after 1 year of age, I don't think there is enough evidence for concluding causation.


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: VIROMES OF ONE YEAR OLD INFANTS REVEAL THE IMPACT OF BIRTH MODE ON MICROBIOME DIVERSITY
Review round: 2
Reviewer: 2

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


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: VIROMES OF ONE YEAR OLD INFANTS REVEAL THE IMPACT OF BIRTH MODE ON MICROBIOME DIVERSITY
Review round: 2
Reviewer: 3

Output:
Basic reporting: OK
Experimental design: OK
Validity of the findings: OK
Additional comments: Thanks for this new version, where more data are given.
The qPCR data on TTV really add strength to your conclusions.
I have only two points left:
(1)	I really insist that the box plots should be replaced by graphs with dots, with a bar for the median. This is not aesthetics, but shows the real data points.
(2)	A mistake is present in the following new sentence “CrAssphage is thought to predate on bacteria within the genus Bacteroides (Dutilh et al 2014)”. Replace  "genus Bacteroides" by "phylum Bacteroidetes" and add the Yutin et al reference, confirming this possible origin (a very large branch in fact).

Once these two things are corrected, I accept 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: SMALL TROPICAL ISLANDS WITH DENSE HUMAN POPULATION: DIFFERENCES IN WATER QUALITY OF NEAR-SHORE WATERS ARE ASSOCIATED WITH DISTINCT BACTERIAL COMMUNITIES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well written, logically structured, and satisfies the requirements of an academic manuscript. The study and research questions are also self-contained and the results address the hypothesis that is posed within the introduction of the manuscript.
	It is clear that the authors have made an effort to make their data accessible and their analysis reproducible. The raw data sequences are deposited within the European Nucleotides Archive and are available to download. Additionally, the metadata associated with these files is comprehensive and complete. The authors have also submitted well-annotated r-scripts that demonstrate how the amplicon data were processed, how statistical analysis of the data was completed, and how the map of the Spermonde archipelago was generated.

Below is a list of comments and suggestions that I have for the authors regarding basic reporting of the study that was completed.
 1. Are there supplementary tables, figures, or documents? I am not able to see or review them, but they are referred to in the text of the manuscript (i.e. line 228, 239, 307).
2. Lines 228- 229, Line 234- 235: add “The” to the beginning of the sentence.
3. Line 223: remove the word “spectra” from this sentence and change the sentence to “Concentrations of the two different classes of molecules of organic matter, DOC and TEP . . .” or something similar.
4. Line 247: change “on” to “an”.
5. Lines 318- 323: restructure or break this sentence into two sentences for clarity.
6. Lines 323- 325: this statement should be supported with citations and belongs in the discussion section.
7. Lines 406- 407: insert “being” in between taxa and well and insert “using” between to and various.
8. Lines 405- 424: please restructure this discussion of Gammaproteobacteria abundance, Vibrio sp. presence, and pathogens. The content of this paragraph is important and of interest to the community, but the structure of this section is jumbled and harder to interpret than it needs to be. For example, state that Vibrio sp. was detected in samples from both the inhabited and uninhabited islands at similar relative abundances after line 417. Also, make it more apparent that even though Vibrio sp. have been implicated as pathogens in specific circumstances, the presence of Vibrio sp. genes does not necessarily indicate that the Vibrio sp. detected within these specific samples are pathogens. This is touched upon in lines 423-424, but a more obvious statement would serve this discussion.
9. Line 430: change “is” to “are”.
10. Line 435 and 437: change “can” to “may” to emphasize that these explanations are speculative and suggestive, not necessarily evidence-based.

Overall, the high quality figures and tables complement the content of the manuscript, but could be improved with the following suggestions:
1. Fig 2: replace the phrase “distance to island” on the x-axis with “distance from island”. The island is the origin of the x-axis so this phrasing logically makes more sense. Please rephrase this phrase when it is used elsewhere within the text and within other figures or figure captions.
2. Fig 4: label PA, SED, or FL next to each corresponding letter in the figure so the reader does not have to jump from the caption and then back to the figure.
3. Figure 5: Are there supposed to be “uninhabited North” data points included within plot A). These data are noticeably absent. As suggested above, label FL, PA, or SED next to each plot letter.
4. Figure 6: explain how these samples were grouped to generate this plot within the methods or underneath this figure in the caption (i.e. were all of the microbial samples grouped together- like PA collected from both transects at the inhabited island were combined into one category?)
5. Table 1: please condense the title for this table into one sentence and place the rest of the content within the method section. The parameter key should be placed underneath the table.
6. Table 2: see above comments on table title length.
Experimental design: The manuscript clearly outlines the research questions and discusses how the following research fills a knowledge gap, seeking to understand how inhabitation status of these small islands in Indonesia impact water quality parameters and microbial diversity and composition (of three different marine microbial community niches) along a distance gradient from the two islands.
	The methods are described clearly and are reproducible to follow, especially because the authors have provided R scripts detailing the analysis of their data. Even so, please address the below comments.

1. Line 106-111: provide the depths of each sampling point if possible (especially because sediment samples were collected at each of these locations).  Similarly, provide information on the benthic cover and/or the presence of reefs at these specific sampling points, as the presence of reefs can influence water quality and microbial community composition. This is also important because many connections are made between the presence of copiotrophic bacteria and how this functional group of bacteria may impact reef health within this manuscript.
2. Line 123: please provide what are the collection canisters made of and how were they cleaned prior to sample collection? These details should be included in the methods as they can impact the analysis (and can also introduce contamination to the samples).
3. Line 142-143: please clarify if this seawater was also collected in triplicate from the three different 5L canisters at teach transect X distance from each island.
4. Line 143: what is the rationalization between these size cut-offs?
5. Line 146: how were the sediment samples collected? Was it shallow enough for a snorkeler?
6. Line 150: separate “5” from “min” in “5min”.
7. Line 170: change “silvangs” to “SILVAngs”.
8. The sequence range for the PA, SED, and FL microbial community samples ranges from 964 – 49, 329 sequences per sample. While the topic of subsampling is controversial in our field, the differences in sequence number in this study may have  influenced microbial community diversity amongst the samples and could contribute bias. Did the authors see a difference in the number of reads obtained from PA, SED, and FL samples that are correlated with the number of OTUs recovered from these samples? Please provide a comment regarding these potential biases and an argument as to why subsampling or other sequence standardization methods were not completed on the samples in this dataset.
Validity of the findings: 1. Line 314: provide examples of which Gammaproteobacteria genera were depleted at the inhabited island.
2. The chla concentration in the inhabited North transect is initially twice the chla concentration in the inhabited south transect and the chla concentrations in the south transect of the inhabited island hover around ~ 5 ug/L. This is an interesting pattern that could be addressed or discussed.
3. Lines 433- 438: this is an interesting explanation, but needs to be expanded and linked back to the original research questions. Please provide taxonomic affiliations of the other “potentially sulfur-reducing taxa” that were recovered in this study and elaborate on the effects or impacts on high organic matter loading in tropical and shallow marine environments if possible. Have sulfur-reducers been recovered from coral reef sediment adjacent to highly populated areas? How does high organic matter loading tie into water quality of coral reef environments?
4. Lines 458- 465 and generally throughout the discussion- avoid overgeneralizations like using entire classes of bacteria to indicate disease prevalence or degraded marine habitat as a result of anthropogenic inputs and please rephrase these lines to mitigate this. For example, while specific genera within Gammaproteobacteria have been implicated as potential pathogens and/or with having copiotrophic lifestyles, not all OTUs within this class exhibit these behaviors. The reality is much more nuanced. This manuscript does not provide enough evidence to suggest that the Gammaproteobacteria recovered within these samples are pathogens (and this is stated once in line 423). Additionally, Gammaproteobacteria are normally present within the marine environment as well and this should be mentioned within the manuscript to provide a more comprehensive view of marine microbial diversity and composition.
5. Lines 445- 449: please elaborate upon how this region could be used in the future to study the effects of nutrient enrichment? Along these lines, please comment on if and how this study could be improved.
Additional comments: Nice work, overall!
Please remember to submit the supplemental files that are referred to within the manuscript. I am able to download a 'supplemental file' zip drive, but it is just a copy of the R-scripts that are already available.


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: SMALL TROPICAL ISLANDS WITH DENSE HUMAN POPULATION: DIFFERENCES IN WATER QUALITY OF NEAR-SHORE WATERS ARE ASSOCIATED WITH DISTINCT BACTERIAL COMMUNITIES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript was generally well written and structured. I've provided some suggestions on rephrasing sections of the introduction and results (see comments to authors). There are several additional references that should be cited in the introduction, but the authors cited most of the appropriate literature. The objective were clearly stated.
Experimental design: This study provides an important contribution of the field of microbial ecology and highlights the potential role of anthropogenic inputs on altering biogeochemistry and ecosystem function. I do not have any issues with the experimental design. However, I do have a lot of questions about the statistical analyses (see comments to authors). Generally speaking, the authors need to provide more details on their analyses particularly in regards to how they present their mixed models.
Validity of the findings: With further clarification on their statistical approaches and interpretation, their results will be sound. The authors did a nice job of discussing their results in relation to previous research and providing possible explanations for patterns without over speculating the results.
Additional comments: Abstract-
Line 22- Since there have been a number of studies that have established gradients of water quality in Spermonde (e.g.  Plass-Johnson et al. 2016, Polonia et al. 2015), I would rephrase this sentence to say something like “The present study is the first to investigate how bacterial community composition responds to water quality in several coral reef habitats, including the water column…..” Note, “back-reef” should be 2 words not hyphenated.

Line 30- This sentence needs to be reworded. Try something like this: “Bacterial communities in sediments are particle attached communities were significantly different between the two islands with bacterial taxa commonly associated with nutrient and organic matter rich conditions higher at the inhabited island.”

Line 37- I agree that Spermonde is a good model system for this type of question, but I think you can broaden the sentence. I would suggest something like: “Given the growing strain on coastal region, this study suggests that densely populated islands lacking sewage treatment have the ability to alter bacterial communities that may be important for normal coral reef ecosystem function.”

 Introduction:
Line 44- There are definitely other classic studies that should be cited here (e.g. Lapointe et al. 2004 and other work done in Caribbean).
Line 46- this also leads to the proliferation of macroalgae

Line 53- I suggest starting a new paragraph when you discuss Spermonde. I would also suggest starting with a sentence that introduces water quality issues in Indonesia more holistically then segway into Spermonde as a model system.

Line 76. I think this paragraph should be placed after you intro paragraph before you start discussing Spermonde.

Line 91. Please review Lamb et al. 2017 (Seagrass ecosystems reduce exposure to bacterial pathogens of humans, fishes, and invertebrates) and cite here. This study assessed bacterial communities along gradients from shoreline to reef with and without seagrass beds at both of the islands you studied.

Line 101- What do you mean by “potential pathogen vector function” This sentence needs to be reworded.

Methods:
Line 108- what year were these surveys done?

Line 113- Why did you sample at high tide when the strongest land-based signal is typically found at low tide? In fact, you should mention in your discussion that because you only sampled at high tide, the water quality values you mentioned are likely underestimating terrestrial input.

Line 120- Was chla measured in the surface water?

Line 148- Were the samples extracted on Barrang Lompo or shipped somewhere else? How were they handled when shipped (e.g. dry ice, blue ice, etc)?

Line 180 I need further clarification on your GLMMs. The acronym GLMM is typically used in associated with generalized linear mixed models. You state that you ran “general linear mixed models”, which would make sense since you log-transformed your data presumably to meet assumptions of normality. If this is the case then you need to state why you log transformed your data. However, your use of permutation tests suggests that these are generalized linear mixed models, if this is the case what distribution did you fit to your data? With permutation tests, your F statistic is actually a pseudo-F statistic. You need to state more explicitly what your random and fixed effects are. Which package in R did you use to run your models? I’m assuming you ran separate models for each water quality parameter. If so, this needs to be stated here as well.

Line 202- What was your cut off for the VIFs in terms of collinearity? Which parameters were dropped? I would rephrase the last sentence to state that AIC were used to identify the best fit models and adjusted R2 values were used to determine goodness of fit of individual water quality paratmers.

Line 213- This should go at the beginning of the stats section

Results

Overall, the results need to be more concise. With your focus on the effects of water quality on community composition, what is the value of looking at bacterial diversity indices as well. If there is solid justification for including it then I would introduce diversity into your intro as well as state it in the objectives. Otherwise consider cutting it.

Lines 225-238, Table 1 and Figure 2: The GLMM (or LMM if you used linear mixed models) results need to be rewritten to be more concise, and better reflect the statistical analysis and results reported in Table 1. For example, it’s fine to start with significant patterns as a function of island and distance, but then you also need to mention that you found a significant interaction in several variables then go onto discuss underlying reasons for that interaction. I’m also confused why you are talking about transect level patterns when I presume you incorporated transect nested within island as your random effect? On a similar note, if you are treating transect nested within island as a random effect why are you presenting plotting individual transects in Figure 2.If you are truly interested in the between transect differences then you should include that as a fixed effect in the model. However, given that you seem to be most interested in island and distance from island I would suggest treating transect nested as a random effect.

 Line 256- How were your confidence intervals generated (bootstrapping)? Were your “slightly stronger correlations” significant?

Line 277- this should be figure 5

Line 288- this should be fig. 5.

Line 291- I would argue that with a R2 of 0.18 island status has low explanatory power.

Discussion
Overall, the discussion was well written and summarized the results well.

Line 383- you need a transition sentence here. For example, “These differences in bacterial communities’ responses to water quality and proximity to human input may be attributed to individual taxon responses.”


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: SMALL TROPICAL ISLANDS WITH DENSE HUMAN POPULATION: DIFFERENCES IN WATER QUALITY OF NEAR-SHORE WATERS ARE ASSOCIATED WITH DISTINCT BACTERIAL COMMUNITIES
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The reviewers addressed my comments and I have no further suggestions for this manuscript. Nice work!


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 ΦBT1 LARGE SERINE RECOMBINASE CATALYZES DNA INTEGRATION AT PSEUDO-ATTB SITES IN THE GENUS NOCARDIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Generally, the manuscript is well written. The experiments are described clearly and the data presentation is fine. The sequences shown are relevant and sufficient. There are sections where the style of writing could be improved upon. These have been highlighted in the note to authors.
Experimental design: The research objective is clearly defined and the authors have chosen appropriate methods and analyses to address the question. The Methods section provides enough information to understand the work and evaluate the validity of the findings.

However, there are some incomplete information on the materials used. No details were provided on the source of the integrase and the integrating vector.
Validity of the findings: The findings from the work are valid and will be of interest to researchers using integrases for transgenesis and genome engineering studies. Similar analyses have been carried out for related integrases from ΦC31 and TG1, as well as ΦBT1 in Streptomyces. Results presented here will also make a direct contribution to studies on the reaction mechanism and sequence specificity of serine integrases.
Additional comments: In this report, Herisse et al. describe ΦBT1 integrase pseudo-attB sites in Nocardia sp. that recombined with canonical ΦBT1 attP site. The authors identified sequences with varying degrees of identity to published ΦBT1 attB sites, and attempted to explain the factors that influenced the accessibility of the integrase to these DNA sequences.
The findings are valid and would be of interest to researchers using integrases for transgenesis and genome engineering studies. Since, similar analyses have been carried out for related integrases from the phages ΦC31 and TG1, as well as ΦBT1 in Streptomyces, it will add to our understanding of the potential application of serine integrases. In addition, it could make a direct contribution to studies on the reaction mechanism and sequence specificity of serine integrases. I think it has the potential to attain the ‘publishable’ state, but it requires some careful revision.
The main area where improvement is required relates to a more effective use of relevant literature in putting the findings in context. There are some obvious inaccuracies reflecting inadequate familiarity with the relevant literature or weak understanding of the subject area. I have made a few specific comments below, which I believe will make the manuscript better, and more accessible to researchers working in the field.

The following needs to be attended to by the authors:
1.	Line 21-23: The integrases do more than ‘bring attP and attB sites into contact’. Integrases are enzymes that catalyse recombination reactions between attP and attB sites, and this is not limited to ΦBT1 and ΦC31 integrases.
2.	Line 54-55: The recombination directionality factor or RDF is not an enzyme in the strict sense. The integrase catalyses both the forward and reverse reactions, but specifically requires the RDF to activate the reverse reaction. There is no evidence that the RDF catalyses the reaction in the sense of acting as an enzyme.
3.	Line 201:”homology to the canonical 73 bp attB”. What is this based on? Is there a reference to support it?
4.	Line 212-213: “Furthermore, pseudo-attB sites have not been reported for ΦBT1 Int-based vectors”. This is not strictly true. Chen & Woo (Hum. Gene Ther. 2008; 19, 143-151) reported pseudo-attB sites for BT1 integrase in the human genome. The authors could include data from this paper in discussing their findings.
5.	Line 272-275: It is not easily obvious to the reader what this sentence is implying. It will be clearer if the sequence of the attP site is included to help the reder see the 4-6 bp overlap alluded to in this sentence. See also Figure 3 legend. The authors may wish to include this in the supplementary information.
6.	Line 294-295: Which previous studies are being referred to here? Again, including the relevant references will help put this point in context.
7.	The authors have attempted to interpret the frequency of the pseudo sites and the base positions that are important. The data could probably be better explained by taking into considerations some detailed analysis reported in Rutherford et al (Nucleic Acids Res. 2013; 41, 8341-8356.) and Van Duyne & Rutherford (Curr. Opin. Struct. Biol. 2014; 24, 125-131.). In those two papers, the relationship between attB and attP sites were discussed extensively, and some of the principles there could greatly simplify the interpretation of data presented in this manuscript. Interestingly, neither of the two papers was cited here. See Lines 337-339, Lines 393-395, and Line 401-416.
8.	Line 341-343 and Line 371-372: These sentences should be rewritten to make them clearer way. In its present state, it reads in an ambiguous way.
9.	There are several examples where “ΦBT1 integrase” should be used rather than just “ΦBT1”. While “ΦBT1” is the phage, “ΦBT1 integrase” is the recombinase enzyme. See lines 28, 366, 377, 382, etc.. The same applies to ΦC31 and ΦC31 integrase (Line 405). The authors should adopt this nomenclature throughout the manuscript.
10. There are some incomplete information on the materials used. There are no details provided on the integrating vector, pRT801. What is it? Where is its source? In addition, what is the source of the integrases used? Were they obtained from another laboaratory? Or were they made by PCR? Gene synthesis? I could not find the relevant description in the supplementary information as well!


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 ΦBT1 LARGE SERINE RECOMBINASE CATALYZES DNA INTEGRATION AT PSEUDO-ATTB SITES IN THE GENUS NOCARDIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Strong. Please see points A, B, I, and J in the General Comments to the Authors section regarding wording and the reader's ability to interpret the raw data.
Experimental design: No comments other than those made in the in the General Comments to the Authors section.
Validity of the findings: The issue of controls is discussed in in the General Comments to the Authors section. I would like to see an additional figure with annotated sequences of the pseudo attL and attR sites showing the attP half-sites and pseudo attB half-sites.
Additional comments: I very much enjoyed reading this paper - it embodies a great deal of valuable work and has convinced me to revisit the debate as to whether or not pseudo sites for serine integrases exist.

The existence of pseudo sites for serine integrases has been the subject of some debate since they were first reported (1). Serine integrases bind attP and attB sites, bring them together, cleave them generating double strand breaks, the enzyme subunits rotate in relation to each other, and the attP and attB half-sites are ligated to make attL and attR sites. Much of the doubt around the existence of pseudo sites comes from the generation of the double strand breaks. How do we know that the integrase does not dissociate after the DNA is cleaved leaving endogenous DNA repair mechanisms like non-homologous end joining or double strand break repair to take over?

I have not yet found a report with controls sufficient to make me completely believe in the existence of pseudo sites (references [not limited to those] in reviews 2 and 3). Such controls would compare the frequency of integration into pseudo sites with frequency of integration into wild-type attB sites (frequency of integration = number of colonies plated on antibiotic / number of colonies plated on no antibiotic x 100); measure integration frequency in the absence of integrase; or use a strain in which DNA repair mechanisms were knocked out. Although I understand that inclusion of such controls would take considerable effort at this time, if the authors have any such data or data indicative of the frequency of pRT801 integration, I would strongly encourage its inclusion.

The work done to determine the sequence of a pseudo-attB motif in this paper is the most compelling evidence for the existence of pseudo att sites I have seen yet. What’s more, I believe there could be additional compelling evidence in the form of “pseudo attL and attR site” sequences from the multiple integration events observed in various pseudo attB sites. If these are the products of site-specific integration mediated by a serine integrase, the expected pseudo attL sequences would consist of the left arm (half-site) of the pseudo attB site and the right arm of the attP site joining at the central GT dinucleotide; and the pseudo attR sequences would consist of the right arm of the pseudo attB site and the left arm of the attP site joining at the central GT dinucleotide. I understand that this information would be available in the sequencing data provided and that reference to “no deletions or insertions” is made in Line 225, but if this information was presented in a figure, clearly annotating the pseudo attB half-sites and the attP half-sites within the pseudo attL and attR sites, this would provide a strong indication that integration events are not the products of DNA repair mechanisms. I believe this would be very valuable information within the field of site-specific recombination.

In addition to providing the sequences of pseudo attL and pseudo attR sites, please consider the following points:

A.	Line 54: recombination directionality factors (as far as we know) don’t have enzymatic activity; it would be better to refer to them as proteins rather than enzymes.
B.	Line 55 and throughout: Although much literature refers to recombination by serine integrases as “unidirectional” there is some evidence that the reaction can be reversed in the presence of integrase alone (4); “highly directional” may be a safer phrase.
C.	Line 211-212: which reference refers to this likelihood?
D.	Line 298: I’m not convinced frequency of insertion has been measured.
E.	Line 314: positive for the presence of pRT801 or insertion of pRT801 into the genome?
F.	Line 318: The reference to Figure 3 does not make sense here, please reconsider.
G.	Line 351: Out of interest - of the 52 sites with significant homology to the combined Nocardia pseudo-attB motif found using FIMO, how many are in genes that would result in a lethal phenotype if pRT801 was inserted into them? Could it be that integration is happening at all of the 52 sites but 48 result in cell death?
H.	Figure 2A: From reading the main text, should the key say “% identity to minimal attB site”?
I.	After looking at the raw data deposited in SRA, a supplementary table explaining how read names (eg. gnl|SRA|SRR6764005.4.1) correspond to organisms would be helpful.
J.	An accession number for the sequence of pRT801 would also be helpful.

Congratulations on your very interesting findings.

1.	Thyagarajan et al. Site-Specific Genomic Integration in Mammalian Cells Mediated by Phage PhiC31 Integrase (2001) Molecular and Cellular Biology, 21;3926
2.	Fogg et al. New Applications for Phage Integrases (2014) Journal of Molecular Biology, 426; 2703
3.	Merrick et al. Serine Integrases: Advancing Synthetic Biology (2018) ACS Synthetic Biology, 16; 299
4.	Zhang et al. Highly Efficient In Vitro Site-Specific Recombination System Based on Streptomyces Phage PhiBT1 Integrase (2008) Journal of Bacteriology, 190; 6392


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 ΦBT1 LARGE SERINE RECOMBINASE CATALYZES DNA INTEGRATION AT PSEUDO-ATTB SITES IN THE GENUS NOCARDIA
Review round: 1
Reviewer: 3

Output:
Basic reporting: This is a very nicely prepared manuscript. It is written in excellent English; literature is properly cited; and the figures are clear. I see no serious problems in these respects; minor comments below.
Experimental design: This is a straightforward study characterizing the ability of phiBT1 integrase to promote plasmid integration at genomic pseudosites in a range of bacterial species. The experimental work is to a high standard, and is properly described. The results are significant and clear. The work will be a useful contribution to knowledge in this area, and may be relevant especially to those who are investigating the molecular genetics of Nocardia, Streptomyces and other Gram-positive bacterial species.
Validity of the findings: I think the findings are valid and will be useful to others.
Additional comments: Overall I think that this is a clear, well presented article that will be a useful contribution to the literature. I have only a couple of minor points that I think should be addressed before publication.
1. Rarefaction analysis (Line 247, Figure 2C). I am not familiar with this analysis method. Some further details and/or a reference should be provided.
2. Line 345. English needs corrected.
3. Figure 1B. Text is very small - make sure it is all legible in the final version.
4. Figure 3. It might be better if the colour coding in this figure is the same as in Figures 2 and 4 (i.e. red indicates identity, not difference).


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 ΦBT1 LARGE SERINE RECOMBINASE CATALYZES DNA INTEGRATION AT PSEUDO-ATTB SITES IN THE GENUS NOCARDIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: This aspect has now been greatly improved and the issues raised in my initial review have been clarified to a satisfactory degree.
Experimental design: This aspect has now been greatly improved and the issues raised in my initial review have been clarified to a satisfactory degree.
Validity of the findings: This aspect has now been greatly improved and the issues raised in my initial review have been clarified to a satisfactory degree.
Additional comments: This aspect has now been greatly improved and the issues raised in my initial review have been clarified to a satisfactory degree.


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 ΦBT1 LARGE SERINE RECOMBINASE CATALYZES DNA INTEGRATION AT PSEUDO-ATTB SITES IN THE GENUS NOCARDIA
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: Thank you for taking the comments on board as far as possible. I am excited for the publication of this paper.


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: TEMPORALLY-AWARE ALGORITHMS FOR THE CLASSIFICATION OF ANURAN SOUNDS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The title should be changed: "sequential" is a confusing word here, since in bioacoustics "sequence" usually means a sequence of sound events, NOT a sequence of acoustic frames as in this paper. (See for example Kershenbaum et al "Acoustic sequences in non-human animals: a tutorial review and prospectus".)

The intro should make clearer what the goal of classification is: to recognise individuals? to recognise species?

English language could be improved. Specific examples: l26 "Let us indicate that"; l62 l73 "Every frame is featured"; l368 "ROC analysis has also been accomplished". In all these the verbs are odd choices.
Experimental design: I have a concern about method. Some parameters are selected by inspecting the results: e.g. l268 "To determine the value of r, the F1 score is used." The authors do not state if this F1 score is from the training data, the testing data, or held-out validation data. It is unfortunately quite common for some people to use the test data as a guide for parameter selection, but this is bad practice since it leads to over-optimistic estimates of performance, due to "peeking" at the testing data groundtruth: the testing data groundtruth should never be used for any part of the training or tuning process. The authors do not state how their parameters are tuned, only that they are. If the testing data has been used, various of the results reported should be called into question.
   This issue arises on l268, l290, l361
Validity of the findings: Important validity question discussed above re "Experimental design".
Additional comments: This paper is about automatic classification of anuran sound recordings. The authors use a single dataset of anuran recordings, and evaluate various classifiers as well as various types of feature representation, in particular whether to classify individual acoustic frames or entire temporal sequences of them. The results find many methods that don't work very well, and a couple of temporally-aware methods that slightly outperform the baseline.

The paper is broadly OK and falls within a long tradition of papers that evaluate various tweaks of classifiers to find which gives the best results on a particular dataset.

The set of methods analysed is a mixture of very common (stacked frames in sliding windows, HMM) and unusual (recurrent sliding windows, local IQR). A useful outcome of the paper is that some common methods do not perform well for these authors. Note that the two strongest temporal methods perform only slightly better than the baseline "non-sequential" methods via decision-tree. We are given no confidence intervals on the performance (in principle those could be estimated from bootstrap sampling the results) so we do not know if this slight improvement should be considered significant. However, if taken as a case study of a range of methods applied to this dataset, various of the results would be interesting to a reader with an interest in such data.

The discussion section of the paper should really engage more with this issue. Is a small, possibly non-significant boost in score really worth the cost of more complex computation? Note also that the "non-sequential" method offers an extra benefit, of identifying when within each audio recording the call is located.

The paper is limited only to this one dataset, which is not uncommon practice - however it does mean that the generality of its conclusions is an unanswered question. The dataset is 3 classes corresponding to 2 species, and 63 recordings overall, making quite a small dataset to draw conclusions from.

The comparison of crossvalidation testing versus "instance selection" is a strength of the paper.

l72: "C additional parameters are constructed" - what does this mean? Authors must clarify. "Constructed" here is ambiguous.

l78 "The frame features are compared to..." - how are they compared? (The paper later states that it's via various methods. Meaning should be clear at every point)

l106-119: this new feature, the local IQR of feature values, they call "temporal parameters". That is an empty an unhelpful label (even if a previous work used that label). More helpful to the reader would be "local IQR features".

l120: Authors might like to note that "Sliding windows" has also been called "frame stacking" or "shingling" in various other works.

l139 claims that the hidden Markov model "quantizes" every sound frame. This is mistake. It assigns a discrete label to each frame, but it does not "quantize" it - that's a related but different concept. Must fix.

l156: "the r most significant values have been used" - the most significant values of what? What does it mean? How does one judge significance? Must be rewritten.

l182 "maximum likelihood" - under what probability distribution? It seems later that the authors are using Gaussian distributions (with full covariance? I don't know) - this must be stated clearly or else the classification model is unspecified.

l185 "neural networks" - which neural network? There are so many neural network types that it's not really appropriate to say, after testing one specific neural net, in a non-leading edge software framework (matlab), one has tested "neural networks".

l197: "the r most significant features of each frame" - again, what is "significant"? And is the same r as mentioned on l156 or not? Not clear.

l200 "Feature selection procedures are employed" - which ones? Without this info the method section is incomplete. Must fix.

l210 "Accuracy: Overall effectiveness of a classifier" - this is not a definition. How is it calculated? Must rewrite.

l211 "Precision: Class agreement of..." - "class agreement" is not clear how to calculate.

l221 the ROC statistic - this is a rather unusual metric. Much more common is to use the AUC metric. Why is AUC not used? Yes it can be calculated from a single point in ROC space.

l258 this para about method should not be in the results section, it should be in the method section.

Fig 6: add more description in the caption. The reader should be able to understand the figure. What is "best". What is the "mean" over?

l297 the authors claim that a window size of "between 2 and 7" emerges as best. However Fig 9 shows not a very clear picture - it seems there's no consistent pattern emergin. Authors should be more honest about this.

Fig 12: make the HMM points stand out more clearly please. e.g. greay out the others

l350 avoid "p" for a variable name; readers may confuse with probability.

l359 most of this paragraph is method not results - move it to method.

Table 3: please apply bold to the strongest value(s) in each column.

l399 "The sliding window with an underlying decision tree attained the best results" -- not a true statement. Must be fixed. In Table 3, the strongest results came most often from "temporal parameters", sometimes from "sliding window" and sometimes N18.


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: TEMPORALLY-AWARE ALGORITHMS FOR THE CLASSIFICATION OF ANURAN SOUNDS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript aims to test different methods to classify anuran vocalizations. Anurans are a widely threatened group and acoustic monitoring is an important tool to evaluate changes in their populations. Considering the large amounts of information produced by acoustic monitoring, effective classifiers and recognizers of calls are of great importance to manage the information obtained.
As a general commentary, I think that although the techniques seem to be well applied and the manuscript may provide valuable information, the focus on anuran calls and climate change are not well developed in the text. The authors should try to improve the background provided in the introduction. Although traditional sections are provided (i.e., Introduction, Material & Methods, Results, Discussion and Conclusions), the text included in each section was not in fully accordance with the corresponding section. For instance, the scientific names of anurans (not well written) and the length of acoustic recordings appears for the first time in the Results section. In addition, there are formulas in this section. I think that a large amount of text in the Results sections should be moved to Material & Methods. The Discussion and Conclusion sections need more work. Perhaps the authors would benefit by reading the paper from Xie et al 2017 (Ecological Indicators, 82: 13-22). Until these general issues are not taken into account, I cannot provide more specific recommendations.
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: TEMPORALLY-AWARE ALGORITHMS FOR THE CLASSIFICATION OF ANURAN SOUNDS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Much clearer and more completely reported.
Experimental design: Concerns about design have been addressed satsfactorily.
Validity of the findings: Yes.
Additional comments: The authors have successfully addressed my two main concerns from the first review:
(1) the confusing "sequential" language has been clarified, including in the much better title;
(2) the setting of classifier hyper-parameters, via training/validation/testing data splits has been clearly stated as part of the method and is satisfactory.

They have also implemented bootstrap confidence interval calculation as suggested, and have made productive use of this.

The "Discussion" section is not really a discussion, it's really a repetition of the main results. This is a real weakness of the present paper: the authors should DISCUSS the results, i.e. consider their importance, their connection to other knowledge in the field, their implications.
    In my first review I said: "The discussion section of the paper should really engage more with this issue. Is a small, possibly non-significant boost in score really worth the cost of more complex computation? Note also that the 'non-sequential' method offers an extra benefit, of identifying when within each audio recording the call is located." This is now partly addressed in the "Conclusions" section. But it should be in the "Discussion" section, and should be more discursive.
    The authors could merge the Discussion and Conclusions sections into one perhaps. The current Discussion section adds very little; it could be deleted. Ideally more thoughtful discussion would be added.

Minor point: some of the figures duplicate each other. Fig 17 not needed, since Fig 18 presents the same information in a more readable fashion.


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 PITFALLS OF SHORT-RANGE ENDEMISM: HIGH VULNERABILITY TO ECOLOGICAL AND LANDSCAPE TRAPS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article was clear and well-written. I found no grammatical errors.

Mason et al provide sufficient background information for their study in their introduction, although they may consider putting their study in a wider context given that there are many arachnid taxa around the world that are short range endemics.

The authors should consider providing more information about the individual species in their study. Is there available life history information in the species descriptions that are relevant for comparing and contrasting the results shown here?

The Figure and Table were informative and clear. The authors provide summary results for their measurements of temperature and humidity, as wells as prey abundance and diversity, but they should provide additional tables with more information for these. I found the information regarding the prey taxa and size particularly lacking. The authors should provide the raw data for their collection and categorization of prey items in a supplementary table.
Experimental design: Mason et al present novel findings in their study that will be of value to researchers who study short range endemic taxa. Mygalomorphs are logistically a very difficult group to work with for behavioral studies due to their cryptic nature and longevity. General observations of microhabitat specificity have been made for mygalomorphs, but Mason et al present the first statistical tests of spiderling habitat choice for burrow construction. As the authors state, this has important conservation implications given that mygalomorphs are low-vagility taxa, as mygalomorph spiders would have to expend considerable energy to seek a new place to generate a burrow.

Mason et al have conducted a thorough study with only a few exceptions. The sample size Mason et al use is small given that only three species and only one brood from each of these species is studied. However, given the difficulty of collecting mygalomorphs in the wild, especially mygalomorph spiderlings, this is understandable. The statistical analyses for spiderling choice are robust and convincing. However, only a few descriptive statistics are offered for the temperature and humidity tests, and no tests are offered to show if there is a significant difference between microhabitat types. The same is true for their tests of abundance and diversity of prey types in different microhabitats. It is also not clear what categories Mason et al used for size and what exactly they mean by recognizable taxonomic unit, thus making this aspect of their study difficult to replicate.
Validity of the findings: As stated above, the conclusions drawn from the test of spiderling choice are robust and convincing. However, the lack of tests of significant differences for environmental and prey item measurements limits the authors’ ability to draw conclusions about the role of these variables in microhabitat choice. That said, the discussion is well-written, convincing, and addresses the original research question. I found limited, if any, speculation.
Additional comments: The authors should consider providing a picture of each species, if available.

Can the authors comment on whether the same enclosure was used for multiple spiderlings in their tests of microhabitat choice? If this is the case, did the authors attempt to prevent any influencing factors among spiderlings? For example, were observed silk threads removed that could potentially influence (in a positive or negative orientation) where later spiderlings might place their burrow?

The authors should consider commenting on aspect as it relates to veldt grass coverage. Mygalomorph spiders typically prefer shaded slopes. Did the authors observe veldt grass more commonly on south-facing, shaded slopes, which might be particularly detrimental for mygalomorphs?


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 PITFALLS OF SHORT-RANGE ENDEMISM: HIGH VULNERABILITY TO ECOLOGICAL AND LANDSCAPE TRAPS
Review round: 1
Reviewer: 2

Output:
Basic reporting: English is good, writing is clear. Bibliography and structure of the ms are both correct.

To me the issue comes from the gap between the objective of the study, the hypotheses and the results.

This study basically compares the (micro-)habitat preference of adults vs. juveniles of three mygalomorph species. It consists, at best (because methods are differ between stages, making results hardly comparable), in comparing habitat selection among species with different life history. The assessment of the impact of an invasive plant of the mygalomorphs, which could be an alternative story, is even not possible given the data available (see detailed comments below). To sum up, the study cannot be published as such, or at least not regarding the objectives and the logics it has. I’m sorry to be so tough, but it is an extremely descriptive work, poorly replicated, with very few experimental data and lacking many details. I hope the comments can still be helpful for a further submission.
Experimental design: Many details are missing, rendering the study impossible to replicate.

Abstract: Sampling methods, experimental and field works, names of the species / families, number of samples / individuals, location and date of the study need to be added.
L74-77: Did you use field or lab’ work? Did you conduct surveys or experiments?
L105-107: how did you standardize the litter? By volume, weight? Did you dry it before?
L109-110: Where and when did you do the lab’ work?
L129: How did you define the RTUs? Which books / keys did you use?
Validity of the findings: I’m afraid the authors the proper design regarding what you want to assess (e.g. would larger-range species react differently?). The study should be re-written with another objective, i.e. comparing the local distribution of different spider species.

L3-4 (and further in the ms): you studied one single trait, and it is not related to short-range endemism. So again, you cannot make any statement because 1 out of 3 species has juveniles preferring micro-habitats different from the adults.
L73: Are these 3 species phylogenetically or ecologically related? Why testing 3 species? What are your expectations if they have different life history traits?
L151-158: no figure, no replication, no test of significance…
L163: How can you conclude that? Invasive species can actually be positive for few species. You have no clue of any negative effect here (if the potential food estimate would have been replicated, there is very few evidence of food limitation in web-building / sit-and-wait spiders). The whole paragraph is completely hypothetical.
L185-225: out of scope. You should discuss the results instead.
L218-219: Again, you have no evidence of that.
Additional comments: Title: too vague, and does not reflect the content of the ms.
L6 (and further in the ms, e.g. L69): Do you make a difference between male and female mobility?
L13 (and further in the ms): You claim that the veld “can” make uniform landscapes, but does it? Where is actually the “landscape trap” here?
L31: Please explain how an established invasive plant can be seen as a disturbance.
L32-38: Paragraph poorly connected to the others, and not specific enough.
L52 (and further in the ms): do you consider mygalomorphs as species with limited dispersal? Do you test for pre-dispersal behavior in juveniles?
L65: what do you mean by “and other specialist species”?
L82-82: Reads like M&M
L89: I’m not sure I got it: SWA is not a biodiversity hotspot because it lost 90% of “original” habitat, right?
L102-103: Which mass?
Table 1 and in the text: nothing is said about statistics.
L123-144: could have been placed before.
L156 and below: better talk about taxonomic richness.
L173: Right, but you have no indication they did not…


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 PITFALLS OF SHORT-RANGE ENDEMISM: HIGH VULNERABILITY TO ECOLOGICAL AND LANDSCAPE TRAPS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed my concerns.
Experimental design: The authors have addressed my concerns.
Validity of the findings: The authors have addressed my concerns.
Additional comments: The authors have addressed my concerns regarding the previous version of the manuscript. Please note the following minor suggestions:

line 94 (last paragraph of Intro): It is unnecessary to say "microhabitat habitat preference..."

Study Species paragraph: Provide citations, where available, for information about the species, such as the inferred relationship based on genetic data and burrow morphology/behaviour.

line 136 in Microhabitat preference: remove to after Microhabitat variables