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 EXTENT TO WHICH GENETICS AND LEAN GRADE AFFECT FATTY ACID PROFILES AND VOLATILE COMPOUNDS IN ORGANIC PORK
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript entitled "To what extend genetics and lean grade affect fatty acid profiles and volatile compounds in organic pork?" is well written, interesting, and well planned. The outcomes obtained in this study are of great value to the field of Food Science, specially for Meat quality researchers and related professionals. Tables and figures are adequate to indicate the results and the discussion is suitable and contains updated studies. I would like to recommend few improvements.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Dear authors,
The manuscript aimed to evaluate the impact of genetic and lean grade on fatty acid profile and volatile compounds in organic pork. The focus of the study is in agreement with current lines of research that connects consumers demands/desires with high quality scientific evaluation to answer relevant questions for the field. Finally, I would like to suggest some improvements.
Line 24: Please define the meaning of "Pi"
Line 26: higher proportion/content? Please check this sentence
Lines 54-55: Please check the parenthesis in this passage
Line 145: Please indicate the meaning of VC
Line 350: I would like to recommend that this sentence be update to: The estimated concentration of short-chain...
Line 361: Please remove "origin"
Line 363: ecorrelated?
Lines 386-387: Please check this sentence


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 EXTENT TO WHICH GENETICS AND LEAN GRADE AFFECT FATTY ACID PROFILES AND VOLATILE COMPOUNDS IN ORGANIC PORK
Review round: 1
Reviewer: 2

Output:
Basic reporting: The work is interesting inasmuch as nowadays quality products have a great relevance and can influence consumer acceptance.
The aim of this study was to evaluate the potential role of genetic type and lean grade on fatty acid composition and volatile compounds of pork under organic husbandry. I think that the topic of the manuscript is interesting for the journal and contributes to the knowledge of each factor and their interactions to improve nutritional quality of pork meat.
Experimental design: This work has a good scientific quality and is well designed.
Validity of the findings: The work needs to revise some questions to be published. I recommend a minor revision.
Additional comments: Comments to authors (e.g. suggestions of changes to the text.):
Abstract
Line 24: Please define the meaning of "Pi" and “Du”
Introduction
LINE 45. Change “… fatty acids profile …” by “… fatty acid profiles …”.
Material and methods
Line 54-55: Please check the nomenclature and use it throughout the text.
LINE 97. Insert the reference for IMF analysis.
LINE 163. What is the meaning of “spearman??”
Results
LINE 181. Change “… (P > 0.10) …” by “… (P > 0.05) …”
LINE 185. Introduce “of” before “as a consequence …”
LINES 201-224. I think is better to present first the results of the figure 1 and then the results of the Tables 2, 3 and 4.
Discussion
This section should be separated into subsections as those used in results section. This would facilitate the reading of the work.
LINES 359-360. Change this reference because it is related with dry-cured meat products. Please change it for another where the comparison is with a similar product to the one evaluated in the present work.
LINES 369-370. I understand that you mentioned regarding the abundant research has been conducted regarding the VC derived from pork products, and less information is available for meat. However, this reference should be replaced by another more appropriate.
Below, I show you some references that could be useful:
-	Domínguez, R., Gómez, M., Fonseca, S., & Lorenzo, J. M. (2014). Influence of thermal treatment on formation of volatile compounds, cooking loss and lipid oxidation in foal meat. LWT-Food Science and Technology, 58(2), 439-445.
-	Lorenzo, J. M., & Domínguez, R. (2014). Cooking losses, lipid oxidation and formation of volatile compounds in foal meat as affected by cooking procedure. Flavour and fragrance journal, 29(4), 240-248.
Tables
TABLE 1. Check the nomenclature of fatty acids according to “Domínguez et al. (2018). Effect of linseed supplementation and slaughter age on meat quality of grazing cross-bred Galician x Burguete foals. Journal of the Science of Food and Agriculture, 98(1), 266-273” and use it throughout the text.


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

Input:
Title: THE EXTENT TO WHICH GENETICS AND LEAN GRADE AFFECT FATTY ACID PROFILES AND VOLATILE COMPOUNDS IN ORGANIC PORK
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article represents an excellent contribution to understand how the genetics and lean grade affect fatty acid profiles, and volatile compounds of meat of the pigs reared under organic husbandry. The article is well written.
Experimental design: The experimental design is adequate. The methods are described with sufficient detail and information to replicate.
Validity of the findings: The article covers the subject with scientific accuracy. The conclusions are well stated and support the results.
Additional comments: Some detailed comments below:
Line 17 write in full FA when it appears for the first time. See all manuscript for similar issues.
Line 19 Please replace “pig genetic types (Duroc vs. Pietrain crossbreds)” with “pig genetic types- Duroc (Du) and Pietrain (Pi) crossbreds”.
Line 36 Please replace “amount and nature of aroma precursors presents” with “amount and nature of aroma precursors present”
Line 77 Please replace “measured at 3rd-4th last rib” with “measured at 3rd-4th lumbar vertebrae”
Line 108 Please check for uniformity. For example, C18:3 n-6 and in the same line C18:2n-6; C18:3n-3. See all manuscript for similar issues.
Line 114 volatile compounds with volatile compounds (VC)
Line 163 delete ??


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: EFFECTS OF REINDEER GRAZING AND RECOVERY AFTER CESSATION OF GRAZING ON THE GROUND-DWELLING SPIDER ASSEMBLAGE IN FINNISH LAPLAND
Review round: 1
Reviewer: 1

Output:
Basic reporting: Unfortunately the text is not well organized and there are problems with Figs 3 and 9. See my suggestions in General comments. The raw data are sorted by species and trap lines, some data based on individual pitfall traps are also needed.
Experimental design: The specific hypothesis is rather complicated and it needs some clarification. The response variables and sample sizes are not sufficiently well described. See my suggestions in General comments.
Validity of the findings: Parts of the statistical analysis is questionable and should be revised. See my suggestions in General comments.
Additional comments: I think this is an interesting study. Given the circumstances with fenced areas, it is possible to investigate the effects of reindeer grazing. This is a unique situation and I congratulate the authors to have taken the opportunity to explore these data. The authors are basing their conclusions on a large data set and they have accomplished data collection of a number of environmental variables that are pertinent to combine with the grazing effects. However, on the down-side of this study, there is a general weakness in the statistical analyses and the presentation of a massive number of results is making the text rather unstructured. I would also suggest that the authors clarify their "specific hypothesis" (Lines 88-93) as it is rather complicated.

My main criticism is focusing on the analysis of data.
- First, the authors are performing a very large number of tests on their data. A general rule of thumb is to include as much data as possible in each test in order to keep the number of tests at a minimum. There might be problems with the interpretation of p-values in the case of an excessive use of statistical tests. However, there are ways to reduce the number of tests. For instance, start by focusing on species and specimen numbers as response variables. It should be possible to perform ANCOVAs including both experimental treatment and some of the environmental variables. If this is not possible, the authors need to explain why. When the influence of the environment on spiders has been established, then continue with details in the ordination studies.
-Second, it could also be questioned why vegetation height is divided into several taxonomic components. These measurements (e.g. lingonberry, bilberry, etc) are analyzed separately for differences between experimental treatments in one-way ANOVAs. There are no attempts to link vegetation height, other than lichen, to the spiders. On line 246- it is claimed that a number of spider species are affected by "increasing lichen dry mass and height" (referring to Table 5): a large number of linear regressions on separate spider species and families are presented. Vegetation structure per se is since long known to affect spiders both at species and community level (see multiple studies over several decades, starting with e.g. Duffey 1962 Oikos 13; Colebourne 1974 J Anim Ecol 43; Hatley & McMahon 1980 Env Entomol 9, etc). Therefore, the focus on vegetation height of different plant taxa that is analyzed separately in the present manuscript can be questioned. I suggest that a general quantification of vegetation "height" and/or complexity could be useful to examine the effects of vegetation on the spider community.
- Third, the tests that are shown in Figure 9 and Table 4 are not based on independent data. The "total abundance" and "species richness" include the families being tested. From a statistical point of view this is not acceptable.
- Fourth, the exact response variables are not well described. For instance, it is unclear what "Species" and "Specimen" in Table 3 are referring to? What are the sample sizes? 180 pitfall traps? This means that the paragraph "Data analysis" (line 146) needs to be expanded to provide full details about analyses.

The general presentation of hypotheses, data and conclusions needs to be revised. I would suggest that the authors consider dropping some of the tests that are not essential to the "bigger picture" (e.g. "Evenness of Lycosidae and Linyphiidae spiders" (line 382), "Grazing effects on Thomisidae spiders" (line 395)). On line 434 the authors state: "Even though this study was not designed to reveal bioindicators..." – I suggest this part of the study to be omitted. Moreover, as the text is organized in the present version, it is very difficult to follow the line: hypotheses, methods, results, conclusions. Please, revise the manuscript accordingly.

Albeit the data can be regarded as the outcome of an "experiment", I think the authors should point out that the study is based on data from one site in one year. Addition of another site, or another year, would have made a great difference. Therefore, I suggest that the Conclusions (line 464 -) are revised with this reservation in mind.

Specific comments:
- Line 97: Nothing about the vegetation of the study area is presented under "Study area and methods". On line 467 ("Conclusions") it suddenly turns out that the study area is "lichen dominated dry pine forest". This information should be given in the beginning of the paper.
- Line 170: How was the conclusion about no "fence effect" reached?
- Fig 3: The labels on x-axis are not the same as in the figure legend.
- Fig 9: There are no labels on x- or y-axes.
- The data file is entirely sorted by species and trap lines. Data based on individual pitfall traps for species and specimen numbers should also be provided.


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: EFFECTS OF REINDEER GRAZING AND RECOVERY AFTER CESSATION OF GRAZING ON THE GROUND-DWELLING SPIDER ASSEMBLAGE IN FINNISH LAPLAND
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is written in good English. Literature references and background/context are insufficient for publication in their present form (see my general comments to the authors). Figures and tables are informative and well done.
Experimental design: Experimental design is appropriate, research question well defined and relevant, methods described in sufficient detail.
Validity of the findings: Findings are valid. Conclusions or the take-home message does not come out clearly.
Additional comments: Please see a separate attachment for detailed comments and suggestions for improvement.


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

Input:
Title: EFFECTS OF REINDEER GRAZING AND RECOVERY AFTER CESSATION OF GRAZING ON THE GROUND-DWELLING SPIDER ASSEMBLAGE IN FINNISH LAPLAND
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I think the manuscript now is considerably improved.
But I still think the correlation tests between spider families (Table 4) are problematic because data are not independent. This could be solved quite easily by correlation test of e.g. Family 1 vs (All Families minus Fam 1), etc.


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: EFFECTS OF REINDEER GRAZING AND RECOVERY AFTER CESSATION OF GRAZING ON THE GROUND-DWELLING SPIDER ASSEMBLAGE IN FINNISH LAPLAND
Review round: 2
Reviewer: 2

Output:
Basic reporting: Review on manuscript “Effects of reindeer grazing and recovery after cessation of grazing on the ground-dwelling spider assemblage in Finnish Lapland” by Saikkonen et al.

In my opinion, authors did a fairly good job in revising this manuscript. Some issues remain, which I have listed below.

Line 36: Why call grazed area as a “degraded state” here? How does using this term reflect the main finding of the study (= no effect of grazing on spider abundances)? Provide a more thorough justification for using this term or revise it into something more neutral.

Line 47: “This is since…” does not fully reflect the reason why reindeer stay at the same areas throughout the year. The reindeer management system was originally created, because reindeer herds could no longer access the natural summer ranges.

Lines 93-96, and the rest of the paper. While I appreciate seeing some of these newer papers cited in this manuscript, these papers do not fit that well in the context of the paper. As the effects of grazing depend very heavily on the vegetation type as well as the grazing patterns, it would help concentrating on the previous work conducted in boreal systems with a lichen-rich vegetation, similar to the present study. Please, replace the sentence written in 93-96 with a sentence summarizing the effect of reindeer grazing on vegetation, nitrogen and carbon mineralization and soil carbon stocks in lichen-rich ecosystems. By this way, the reader may be able to link the present investigation on spider assemblages with the big picture.

Suggested reading:

Köster, E., K. Köster, M. Aurela, T. Laurila, F. Berninger, A. Lohila, and J. Pumpanen. 2013. Impact of reindeer herding on vegetation biomass and soil carbon content: a case study from Sodankylä, Finland. Boreal Environmental Research 18:35-42.

Köster, K., F. Berninger, E. Köster, and J. Pumpanen. 2015. Influences of reindeer grazing on above- and below-ground biomass and soil carbon dynamics. Arctic, Antarctic and Alpine Research 47:495-503.

Köster, K., E. Köster, L. Kulmala, F. Berninger, and J. Pumpanen. 2016. Are the climatic factors combined with reindeer grazing affecting the soil CO2 emissions in subarctic boreal pine forest? Catena 02838:dx.doi.org/10.1016/j.catena.2016.1006.1011.

Santalahti, M., Sund, H., Sietiö, O.-M., Köster, K., Berninger, F., Laurila, T., Pumpanen, J., Heinonsalo, J. 2018. Reindeer grazing alter soil fungal community structure and litter decomposition related enzyme activities in boreal coniferous forests in Finnish Lapland. Applied Soil Ecology 132:74-82.

Stark, S., Männistö, M.K., Smolander, A. (2010): Multiple effects of reindeer grazing on soil processes in nutrient-poor boreal forests. Soil Biology & Biochemistry 42: 2068-2077.

Susiluoto, S., T. Rasilo, J. Pumpanen, and F. Berninger. 2008. Effects of grazing on the vegetation structure and carbon dioxide exchange of a Fennoscandian fell ecosystem. Arctic, Antarctic and Alpine Research 40:422-431.

Also a good review on the effects on vegetation: Bernes C, Bråthen KA, Forbes BC, Hofgaard A, Moen J, Speed JD. 2015. What are the impacts of reindeer/caribou (Rangifer tarandus L.) on arctic and alpine vegetation? A systematic review protocol. Environmental Evidence 2:6.

Line 814. Having four different grazing treatments is a very novel and interesting feature of the present study and the link with the intermediate disturbance hypothesis puts the study into a very interesting context. Here is one more suggestions for a relevant paper considering the role of slow lichen growth on the recovery of lichen vegetation after disturbance:

Kumpula, J., A. Colpaert, and M. Nieminen. 2000. Condition, potential recovery rate, and productivity of lichen (Cladonia spp.) ranges in the Finnish reindeer management area. Arctic 53:152-160.
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: GEOGRAPHIC CONTEXT AFFECTS THE LANDSCAPE CHANGE AND FRAGMENTATION CAUSED BY WIND ENERGY FACILITIES
Review round: 1
Reviewer: 1

Output:
Basic reporting: Details in attachement
Experimental design: Details in attachement
Validity of the findings: Details in attachement
Additional comments: Details in attachement


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: GEOGRAPHIC CONTEXT AFFECTS THE LANDSCAPE CHANGE AND FRAGMENTATION CAUSED BY WIND ENERGY FACILITIES
Review round: 1
Reviewer: 2

Output:
Basic reporting: This was a very well written paper on an interesting and very timely topic.  The presentation was extremely clear and I have few comments.
Experimental design: The presentation was extremely clear and I have few comments. The assessment of variable importance and parameter estimates for the statistical models is solid and well done.
Validity of the findings: As renewable energy, and wind energy in particular, expands rapidly in response to both calls to reduce CO2 emissions as well as the levelized cost of electricity makes wind one of the cheapest forms of new electricity capacity – it will be critical to proactively consider siting and mitigation of wind energy impacts. Landscape-scale assessments like that described in this manuscript can be used to evaluate impacts needed to guide land-use planning and management decisions.
Additional comments: Comments to the authors of “Geographic context affects the landscape change and fragmentation caused by wind energy facilities” by Jay E Diffendorfer, Monica A Dorning, Louisa A Kramer, Jolene Keen, and Robert V Taylor.

This was a very well written paper on an interesting and very timely topic.  The presentation was extremely clear and I have few comments. The assessment of variable importance and parameter estimates for the statistical models is solid and well done. This is a great example of the interface of landscape-scale assessments and field research in order to evaluate impacts of land-use decisions. I think it would be very interesting for a wide variety of readers and could help land managers see how science can be used to better guide land use decisions. As the authors state their results support the intuitive, but not well-tested, hypothesis that the geographic context in which energy is developed can alter the types and levels of impacts such development has on natural systems. As renewable energy, and wind energy in particular, expands rapidly in response to both calls to reduce CO2 emissions as well as the levelized cost of electricity makes wind one of the cheapest forms of new electricity capacity – it will be critical to proactively consider siting and mitigation of wind energy impacts. Landscape-scale assessments like that described in this manuscript can be used to evaluate impacts needed to guide land-use planning and management decisions.

As I stated I have few technical comments – most of the specific points that I think should be addressed relate to the interpretation and communication of the results.

My biggest concern of the manuscript is that I think it fails to include one of the most significant forms of impact associated with energy development: transmission. In many cases the infrastructure needed to support energy development has a larger impact than the development itself. For example, the US Department of Energy estimates that it will take approximately 5 million hectares to reach 20% electricity production. But it will also take an additional 18,000 kilometers of new transmission lines. The current study examines only the impacts of “onsite” transmission features when it is the “offsite” transmission that has the largest impact. It would be great to discuss how siting new wind installations near previously altered landscapes may further reduce the impacts from new development.

The authors ask the important question is it possible to construct facilities that minimize the levels of habitat loss and fragmentation? Their results do suggest siting facilities in locations with higher levels of existing development can reduce impacts. Several other studies have speculated as to the importance of siting renewable energy on lands already impacted from development in order to reduce impacts given projections of future wind energy development. It would however be good to link the current assessment to these other studies that have estimated this potential – Kiesecker et al. 2011 (US wide), Fargione et al. 2012 (Northern Great Plains), Baruch-Mordo et al. 2018 (Global).

I see a reference to Jones et al. but don’t see a Jones et al. in the literature cited.

I would like to see how the authors think the results of their analysis could be incorporated into application – more specific details here would be good.


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: INFECTIOUS HEMATOPOIETIC NECROSIS VIRUS: ADVANCES IN DIAGNOSIS AND VACCINE DEVELOPMENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall, The article by Yong et al is well written . However, I detected some english misspellings such as the word "salmons". I recommend the authors to check potential misspellings . Sufficient  backgroud is provided and the introduction adequately introduces the subject  The review is of  cross-disciplinary interest since recombinant IHNV  vaccines can be used to control infectious diseases in many different animal species. Diagnosis of salmonid fish was previosuly reviewed in the book "Molecular diagnosis of salmonid fish" edited by Carey Cunningham (Springer-Science) and in the book "Fish Diseases and Disorders" edited by Woo et al., 2011. However, to my knowledge the area of the development of vaccines against IHNV has not been deeply reviewed. This review offers  a complete picture of all the vaccines developed against IHNV. I particularly find figure 1 very interesting.

I have missed some vaccines in this review. For instance Alonso et al, 2003 developed the first  fish specific expression vector containing the interferon regulatory factor 1A (IRF1A) promoter for genetic immunization of fish. The same autors developed a suicidal DNA vaccine for infectious hematopoietic necrosis virus (IHNV) in 2011. Both references should be included in Table 1 and the first one disccused in the mansucript.

In addition the authors shoud specify which vaccines from Table 1 have been patented, which are commertially available and which countries are currently using  vacines to control IHNV infections in fish farms and under which conditions. Killed vaccines and a DNA vaccine have been licensed for commercial use in Atlantic salmon net-pen aquaculture on the west coast of North America where such vaccines can be delivered economically by injection. However, vaccines against IHNV have not yet been licensed in other countries where the application of vaccines to millions of smaller fish will require additional research on novel mass delivery methods. Are IHNV vaccines being used in Chile and Norway?

I believe that the survey methology section should be deleted .

Line 218 should be clarified. Please give more deaeils about the mutant tested by Roberti et al., 1998.

Concluision section should be revised
Experimental design: The article content is within the aims and scope of the journal.
The authors provide a full coverage of the subject. Sources were adequately cited.
I encourage the authors to organize the review in three  subsections: General introduction, Diagnosis of IHNV and Vaccines against IHNV. Line 97 should be include in the clinical diagnosis section.
Validity of the findings: - In the conlusions sections  I believe that the autors should emphize the OIE recommendations for IHNV diagnosis and its definition of a suspected or confimed case. Please check http://www.oie.int/fileadmin/Home/eng/Health_standards/aahm/current/chapitre_ihn.pdf. The  methods included in the conclusions do not agree with the OIE recommendations.

- Line 307 -the authors state that multivalent DNA vaccines have an added advantage over multi-DNA vaccination due to its lower cost of producion, as only one type of plasmid is required to produce multiple immunogenic antigens. However, it has been demonstrated that the size of the plasmid might affect the efficacy of the plasmid transfection into muscle cells. The aurthors should disccuss  this issue, since the size of the plasmid can affect the efficacy of the DNA vaccines.

Line 315- can the authors explain why the admistration route affects the efficay of the DNA vaccines.?

Line 32- Line 394, conclusions. The authors state that rapid and accurate diagosis are important  to preven IHNV outbreaks. If IHNV is detected in a farm, what is the next step. Is this disease noticeable? If IHNV is detected, are all the fish in the fish farm killed? are they separated? Do the authors really belive that IHNV diagnosis helps to prevent the outbreak?. or is diagnosis a control measure instead?

Line 401- Is apex-IHNV being used in smal farms in Canada?

-The thorough disinfection of fertilised eggs, the use of virus-free water supplies for incubation and rearing, and the operation of facilities under established biosecurity
measures are all critical for preventing IHN at a fish production site. Biosecurity measures are important to prevent IHNV outbreaks and should be detailed  in the text.
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: INFECTIOUS HEMATOPOIETIC NECROSIS VIRUS: ADVANCES IN DIAGNOSIS AND VACCINE DEVELOPMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The manuscript is well written, and fully covers main progresses on diagnosis technologies and vaccines development issues of IHNV. However, there are minor concerns should be verified before publishing.

1.	The sentence in Line 44-45 need to cite a reference.
2.	I think the sentence in line 45-47 is describing the general mortality and economic caused by IHNV worldwide. If it is true, please cite a review of IHNV instead of the paper just about IHN outbreak in Iran. Or add more references.
3.	In the section “Diagnosis of IHNV”, references should be cited to support the abnormal behaviors in infection of IHNV. The subtitle “Diagnosis of IHNV” is not appropriate due to the fact that this part is just diagnosis of IHNV by behaviors.
4.	Sentence in line 223-224 is ambiguous and lacks supportive references. Although there are several studies about attenuated vaccine against IHNV, but nothing to do with commercialization.
5.	Reference in line 295 is not correct.
6.	Sentence in line 387-388 “Apart from live attenuated vaccines, Apex-IHN ® is the only licensed DNA vaccine approved in Canada.” The sentence is ambiguous. It seems that there are commercialized live attenuated vaccines against IHNV. But the Apex-IHN is the only one commercialized vaccine against IHNV.


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: INFECTIOUS HEMATOPOIETIC NECROSIS VIRUS: ADVANCES IN DIAGNOSIS AND VACCINE DEVELOPMENT
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The authors have correctly addressed my previous concerns


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

Input:
Title: ASSESSING SUBSPECIES STATUS OF LEOPARDS (PANTHERA PARDUS) OF NORTHERN PAKISTAN USING MITOCHONDRIAL DNA
Review round: 1
Reviewer: 1

Output:
Basic reporting: A good job overall with clear and professional English for the entire manuscript. Except for a few places, that I had references already in my comments, a good job in general with providing backgrounds and context.

Major comments
1.	The introduction can help from background information regarding mtDNA, how it has been used in phylogenetic analyses with proper reference is also going to improve the overall background. Any previous work done with mitochondrial DNA with the cat family/ leopard/ tigers will draw nice relevance to this work as well. (line 83)

2.	Why was subunit 5 of NADPH chosen? The authors do not provide enough rationale for this. For the broader audience, it might be beneficial to provide some introductory background explaining the rationale behind the choice? (line 82-83)

3.	The format of sequencing, which type, platform etc. is not even mentioned once in the methods. Granted the authors refer the approach to two previous works on lines 114-115, the manuscript might improve if information on the type and nature of sequencing is included here with some details. At the very least- what type of platform was used for sequencing and some statistics on that.

4.	The authors mention how this work will impact and contribute “…….to knowledge of species assessment at national and international level and help prioritize the conservation efforts for Pakistan” (Line 88). However, after going through the discussion part, there’s no overall mention of how this work contributes at a global level. The authors do a good job in describing the relevance of the work how it can contribute at the national level mostly in Pakistan, but either remove the international part on the introduction or address that aspect better in the discussion section.

Minor comments

It would be nice to have the Genbank accession number supplemental file referenced somewhere in the manuscript, since they can’t be uploaded to Genbank before July.
No need for switching lines and leaving empty space on line 70

Roberts 1977 missing “et al” ? on line 71-72 ?

Parenthesis needs to be closed for reference; line 80

……Conservation efforts for “leopards in” Pakistan?  (line 88)

No need for period/full stops after sub headings (Materials and methods/ introduction etc. as well as after “sample collection”, “DNA extractions and amplifications” etc.)
Any reference for stating leopard population is considered stable in the northern part of Pakistan? (Lines 92-93)

The authors keep switching between numeric and alphabets to describe numbers like 18 and 15. Consistency is needed- choose any one and preferably stick to that pattern. (Lines 95-97)

When mentioning positive results for DNA isolation, mention at least what kind of purity (O.D 260/280 values may be ?) (lines 104-106), the authors obtained and what made the tests positive that convinced the authors to pursue that at a broader scale by outsourcing to South Korea.

Insert comma after Seoul (Line 105)

When stating PCR as abbreviated for the first time (Line 105), consider writing Polymerase Chain reaction here and then abbreviating as PCR in the following lines through the manuscript. The full form instead comes up later on line 113.

The sentence – “These isolated a sequence………….of the mitochondrial DNA.”  is confusing and can be written probably in a simpler manner. Please consider revising and rewriting the sentence (Lines 111-112)

Remove period (line 122)
Remove period (line 139)
Remove period (line 160)
Remove colon and may be underline? (line 231) Consistency
Remove period (line 239)
Insert “the” before latter (line 194)

“g” missing from Fig on line 201 and 205
Experimental design: A bigger sample size would have been much better, especially if doing phylogenetic analyses and trying to related to global impact for the study as well.
Validity of the findings: No additional comments. The findings seem to relate to the original hypothesis.
Additional comments: General reporting is good, but authors need to take into consideration some major revisions and some minor revisions to make the manuscript better overall.


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: ASSESSING SUBSPECIES STATUS OF LEOPARDS (PANTHERA PARDUS) OF NORTHERN PAKISTAN USING MITOCHONDRIAL DNA
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1. The title needs to be revised because the research methods do not address subspecies status in Pakistan. See Point 1 from "Experimental Design" comments.
2.The Results and Discussion sections are disjointed and would benefit from more continuity between the sentences. This would make it easier to understand for an international audience and follow the logic of the authors.
3. The manuscript would benefit from a broader context for the work. The authors do a good job detailing the scarcity of genetic data on leopards in Pakistan, but need more info to frame why finding subspecies within Pakistan is important. It would also be good to talk about any geographic barriers that would either limit or enhance movement of leopards into and within Pakistan, as this would directly influence isolation and the evolution of potential subspecies/populations.
Experimental design: 1. The research methods don't address the statement of the title. The title suggests the manuscript surveyed the majority of Pakistan and looked at multiple mitochondrial DNA markers to assess genetic diversity of leopards across all of Pakistan. The manuscript had a very limited geographic scope and only looked at one mitochondrial DNA locus to determine if haplotypes within the NADH-5 gene matched leopards from other geographic origins.
2. The manuscript needs to be reframed to address the limited geographic scope of sampling (northern Pakistan) and the use of a single mitochondrial DNA locus. Such instances occur in lines 33-34 (authors present no evidence Pakistani leopards are experiencing a bottleneck), lines 161-162 (not a genomic dataset because only uses mtDNA, and can't say Pakistani populations because only looked at northern Pakistan), lines 180 - 183 (authors may have excluded genetic information from gene regions other than NADH-5, and looking at these areas may uncover more information).
Validity of the findings: 1. The authors should explain why samples were too poor in quality for the haplotype analysis, but not too poor in quality for the phylogenetic analysis (line 149). Missing or incomplete data could have effected the ML trees.
2. The use of a single mitochondrial DNA locus and limited geographic scope limit what the authors can say and they overstate much of their findings as already outlined in this review. The results are still compelling, but the scope of the manuscript's findings must be more properly stated to reflect these shortcomings.
Additional comments: 1. The methods described are sound and the results are valuable, however the main issue is the statements regarding the implications are overblown. Sequencing multiple nuclear markers (such as microsatellites or nuclear genes) in addition to more mitochdronail markers would have been better suited to answering questions of gene flow and bottlenecks. Without this information, the authors are limited to describing how northern Pakistani leopards compare to other leopard samples with respect to the NADH-5 gene. The paper should be reframed as such.


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: UK UNIVERSITIES COMPLIANCE WITH THE CONCORDAT TO SUPPORT RESEARCH INTEGRITY: FINDINGS FROM CROSS-SECTIONAL TIME-SERIES
Review round: 1
Reviewer: 1

Output:
Basic reporting: Thanks for asking me to review this manuscript. I know Liz Wager, the author. For the record, I also listened to the author present the results at a seminar a few weeks ago.

The reporting of change in contact info over time (2012, 14, 18) is clear and useful.

The reporting about annual RI statements is clear and useful.

Per Exp Design, I'd like to see more info about how the web searching/browsing to get the data was done in a consistent way.
Experimental design: Line 97 and 98
"Contact details obtained by searching a university directory, staff information, or a general ‘Contact Us’ page were not counted."

This seems overly harsh to me. I recognise that the study is measuring precise compliance with concordat "guidance" (ie, not "requirements"). I recognise that you're not going to re-do the work. But it seems that there are many ways to "peel an apple," and if a univ decided to make it's RI person identifiable in a way like the 3 you excluded, to me this would be OK as a way to comply in a roundabout way with the concordat.

"Number of clicks"
Number of clicks is not a measure of compliance. I think it's worth noting that this is a measure that's of secondary importance. This is particuarly because user behaviour on the web is a mixed bag, and browsing to get what you need is, presumably, less common than searching to get it. So a Google search for something like "research integrity AND universityname" might get you results for universities in the same number of clicks in each instance (presumably 2 clicks: one to initiate the Google search, and one from Google results to the right page on the university site, no matter how "deep" in the university website the actual information is housed). So I think "number of clicks" is of mild interest, and -- if the author agrees -- would suggest that this is mentioned in Exp Design or somewhere else in the manuscript.

Would like to have seen more info on how the people collecting the information were systematically exploring each website to find the information they were looking for. I think that's an important part of the design that's missing from the manuscript.
Validity of the findings: Per Exp Design comments, browsing to find results is a rather imprecise thing. So a description of how you achieved consistency across the different people who did collected the data, and how each person also maintained a consistent approach between universities, would be valuable. This probably would not impact on the accuracy of the main result (presence or absence of a contact person, of annual RI reports) but would impact on the "number of clicks" result.

That aside, let's not get too distracted: the findings that a large proportion of UK universities do not comply with the concordat suggestions (note: not condordat requirements) despite having signed up, via their parent body UUK, to the concordat is what's important here. From the methods and results, that is a valid finding.

The comments on variability of titles of people seem a bit harsh. A univ can assign who they want (per concordat), and job titles are going to vary no matter what. So I'd not get too judgemental about that. Instead, the important thing is that people with problems can report them, and that they get addressed, and then that we're as transparent as we can be about the whole thing. Of course, you could still say that consistency would be helpful, and so perhaps a more realistic suggestion than implying "all the listed people should have the same job title" might be something like suggesting "all univ websites should use the same language to enable people with problems to find how they report those problems."
Additional comments: The implication seems to be that universities are at fault, and I'm not completely happy with that.

UUK and UKRIO (and others) could be criticised for not supporting the implementation of the concordat as well as they might have. Or perhaps for engaging with universities in the first place about the recommendations in the concordat. You might add a comment along those lines - at the moment it feels a bit like an attack on universities and I don't think that's helpful: other organisations are also involved. Perhaps the new concordat needs to do that "engagement" piece better.

Also: All universities are not the same. Some are research intensive, and RI info is critical for these. (I'm sure we all would argue that if any research is conducted by a univ then that univ needs an RI infrastructure). I'd like to see some recognition that all univs are not research intensive, and "recommendations" or "requirements" in a new concordat need to be sensitives so they can be made to work in both research intensive and less research intensive settings.


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: UK UNIVERSITIES COMPLIANCE WITH THE CONCORDAT TO SUPPORT RESEARCH INTEGRITY: FINDINGS FROM CROSS-SECTIONAL TIME-SERIES
Review round: 1
Reviewer: 2

Output:
Basic reporting: I find the manuscript to be clear, crisp, informative as presented.
Experimental design: The methods are fully described. The methodology is matched to the question, and is well-supported by the available materials. The question is simple, well-defined, relevant, and meaningful. It adds more information to an on-going open question.
Validity of the findings: Conclusions are well stated, linked to question, and limited to supporting results. This is not a sophisticated study. Unfortunately, the situation is such that there is no room for sophistication: the failures by universities are so basic, that continuing to track and publish this information is critical to improving the situation overall.
Additional comments: Thank you for doing this. If institutions are not meeting this bare minimum requirement, how can one have any faith they are fulfilling their other obligations for research integrity. Discouraging, yet important.


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: UK UNIVERSITIES COMPLIANCE WITH THE CONCORDAT TO SUPPORT RESEARCH INTEGRITY: FINDINGS FROM CROSS-SECTIONAL TIME-SERIES
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comments
Experimental design: No comments
Validity of the findings: No comments
Additional comments: Thanks for taking time to address the points I raised, Liz.


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: UK UNIVERSITIES COMPLIANCE WITH THE CONCORDAT TO SUPPORT RESEARCH INTEGRITY: FINDINGS FROM CROSS-SECTIONAL TIME-SERIES
Review round: 2
Reviewer: 2

Output:
Basic reporting: The revised paper is clear, crisp, and to the point. It is well written, and complete. A deceptively simple, elegant study that provides clear results and stands on its own.
Experimental design: Elegantly simple. Demonstrating so clearly that even minimal compliance with the Concordat is still not uniformly achieved is important information. The small 2013 pilot comparison with US and Australian universities is enlightening. Methods straightforward and clearly described.
Validity of the findings: This is an important foundational study. It is cleanly described, well-written, and worthy of publication.
Additional comments: Bravo, Elizabeth. Revisions make this strong paper even better.


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: MONITORING CYANOBACTERIAL TOXINS IN A LARGE RESERVOIR: RELATIONSHIPS WITH WATER QUALITY PARAMETERS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript correlates a good amount of water quality data (cations and anions)  with several cyanotoxins in a reservoir in Texas. The data during a two-year monitoring period was extensive to make a strong case and is publishable. However, it appears that the manuscripts did not go through the polishing and scrutiny by the senior author of this manuscript. There are some irrelevant and distracted discussions needed improvement of graphing and language.  Since the data is in good quality, I think it can be publishable after a major revision of the writing part.
Experimental design: The work is within the Aims and Scope, it reflects one of the challenges in the harmful algal bloom study. In the Introduction, there should have some more literature review decsribing why the algal toxins could be related to the inorganic ions, and are there any similar work/data on this subject, rather than a general discussion of water quality and cyanotoxins unless the main them of this manuscript is changed to the general water quality and algal toxin issue. I believe the data collection parts and the analytical methods are rigorous with essential details.
Validity of the findings: The authors should present some representative figures for the correlation data instead of the tables with only the p-values such as Table 2 and Table 3. The readers will have a better idea of the correlations between toxins and the anions/cations, which is the main novelty and/or knowledge/data gap of this study.

Conclusions/discussions should also be focused on this main theme rather than the distraction of some general water quality discussions.

When presenting the cationic and anionic data from water quality analysis, it is always prudent to double check the validity of the analysis by checking the charge balance between cations and anions by converting mg/L into meq/L (e.g., data in Table 1). if the charge balance is not closed, then it indicates the analysis of certain ions or the errors in analysis.

The section starts Line 198 should include some figures showing the relationships between water quality and toxins. The scatter plots with indicated p-value are more powerful than just the data shown in Table 2 and Table 3.

Table 1 can be better shown with some box plots?

Table 2: The scientific notation is written incorrectly, should be xxE+05. For K+, it is 87? or 0.87?

In the results section explaining the ones with p<0.05 (Table 3), there should have some more elaboration why Cl-, Na+, Ca2+ have a significant positive correlation with space (location), and why NO3-, Na+, and Mg2+ have a seasonal correlation?
Additional comments: 1. From the abstract, it is hard to tell rationales what leads to the main research question regarding the relationship between toxins and common ions. There seems also research question regarding cell count numbers and toxins that confuses the readers.   The results part of the abstract is also weak because there is no clear conclusion of such relationship and an indication of what is the implication of such a relationship.  Rewrite the abstract.
2. Some typos and grammar errors: (1) lIne 26, parenthesis rather than in its superscript. (2) Line 47-48: hard to understand? (3) Line 44: Add "the" prior to United States, (4) LIne 67-69: Should just be N in nay form dissolved in water rather than N2 (ga) which is the atmosphere, (5) Line 110: the (we" and "they (samples) are awkward; (6) Line 117: why "deep" is relevant here for samples stored in a constant temperature freezer; The same is true on Line 162 (deep-freezer); (6) Line 127: water samples rather than water experimental samples; (7) Line 191: remove the dash before the word "detected"; (8) Line 251: add "were" between "month" and "relatively"; (9) "can start" not "can started"' (9) Line 259: which are subsequently enhanecs? (10) Line 27: "were either retard or stimulate": remove "were"; (11) Line 282: add "that" before patasssium (K); (12 "could be support the" to "could support the" (13) Line 289: add "the" prior to Us EPA. Grammar and language errors like these can be easily eliminated if teh senior authors spent time polishing it.
3. A map showing the area of Grayson and various sampling locations in the Supporting Info should be included, in particular, the results section describe the spatial variation. With such information, the results on spatial variation will be hard for the readers to follow.
4. Line 139-183: Spike recovery studies should be placed in the materials and Methods section,
5. The Discussions starting line 219 is pretty weak, most general water quality discussions are ok, but they have deviated from the major theme of this work, i.e., the relationship between toxins and w\ions. Some statements are a common knowledge, and should be removed, such as Line 252-253; line 269
6. The Conclusion part (Line 288-294) has no conclusion regarding the main topic of this 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: MONITORING CYANOBACTERIAL TOXINS IN A LARGE RESERVOIR: RELATIONSHIPS WITH WATER QUALITY PARAMETERS
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1. The English language and the flow of text should be improved to ensure that an international audience can clearly understand your text.
a)  Lines 42-44 " According to Paerl (2008), increasing rate of cyanobacterial hazard algal blooms (cHABs) in aquatic ecosystem have undoubtedly contributed by the loading of nitrogen (N2) and phosphorous (P)."
Here the authors probably mean that the increasing loading of N2 and P have contributed to an increasing rate of cHABs. This sentence needs to be re-written.
b) Lines 49-52 give an introduction to cHABs and should precede Lines 42 so that a reader already has an understanding of the subject before the factors affecting it are described
c) Lines 44-45 describe economic loss due to cHABs. A line describing how they are affecting the economy can help the reader understand the statement.
d) Lines 61 to 68 is a single sentence which describes various factors affecting cyanobacterial growth. This sentence needs to be grammatically corrected or perhaps better if broken into shorter sentences.
e) Line 87 is missing a word " Methanol, acetonitrile, formic acid and water were with LC/MS Optima grade and obtained from Fisher Chemicals (Fair Lawn, NJ, USA)". This sentence should be Methanol, acetonitrile, formic acid and water were analyzed with LC/MS Optima grade and obtained from Fisher Chemicals (Fair Lawn, NJ, USA)
f) Line 125 " Anatoxin-a, microcystin-LR,-LA, and -RR by LC-MS/MS". This should again be something like Anatoxin-a, microcystin-LR,-LA, and -RR analysis by LC-MS/MS
g) Lines 180-184  : These lines also needs grammatical correction. " The recovery of LCS and MSS in algal toxin analysis were fall in the range of 50 to 150 % (US EPA Method 544, 2015) during the study period. Reported results were uncorrected based on recovery. Whereas the observed recovery of anions and cations were fall in the range of 85 to 115 % (US EPA Method 300.1, 1997)."
h) Lines 190 seems to have a typo in reporting BDL of MC and needs to be 0.024 ng/mL instead of 0.0.24 ng/mL
Overall there are numerous grammatical errors throughout the text and it is beyond my scope to point each and every one but I would recommend to do a thorough proof reading and get these corrected during revision.
Experimental design: Lines 122 mention that ELISA tests were performed using method provided by Abraxis Inc. A short summary of the analysis method or at least a reference should be provided.
Validity of the findings: 1. In the discussion section "Inorganic ions load, salinity, lake water level and in fresh water ecosystem" the authors  state that they " quantified traces (~ 1 mg/L) of NO3- throughout the sampling period". I am not exactly sure what the authors are referring to here. Their collected data doesn't support this statement. Are they referring to average concentration levels throughout the year? Please clarify.
2. Furthermore, in the same discussion section the authors discuss salinity as a variable. I do not see any data related to salinity unless the authors are correlating it to conductance. Please clarify.
3. In the "Algaltoxins and water temperature" section the authors are not describing their results clearly. They state " In our study, traces amounts of microcystins presented during summer seasons and the water temperature values from the EPA database for the corresponding month relatively higher than 15 ˚C. It was supported by the following discussion.". It is unclear what their results are from the above statement. Clearly from their Table 2 they found a positive correlation. The authors should describe this more clearly.
4. In the " Turbidity, pH and conductivity" section the authors state " The turbidity in water system were either retard or stimulate the algal growth. It depends on the availability of nutrients in the water system (Wang, 1974). In clear water systems, light can penetrate and favor for algal growth". Are the authors stating that the turbidity depends on availability of nutrients? Please clarify.
Additional comments: “Monitoring algal toxins in a large reservoir: Relationships with inorganic ions”

The authors monitored cyanobacterial toxin concentrations and inorganic ions in monthly water samples from a large reservoir over a 2+ year period.  Seasonal changes in cyanobacterial toxin concentration were observed.

Overall the authors have collected samples and analyzed them adding useful information to the database of the scientific community. The English language can be improved throughout the text for better understanding to the readers.  The conclusions can be more specific even if no correlation or inconclusive results are obtained. I would recommend to accept this publication after necessary revisions by the authors.


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: MONITORING CYANOBACTERIAL TOXINS IN A LARGE RESERVOIR: RELATIONSHIPS WITH WATER QUALITY PARAMETERS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript entitled “Monitoring algal toxins in a large reservoir: Relationships with inorganic ions” has described the monitoring cyanobacterial toxin concentrations and inorganic ions in monthly water samples from a large reservoir over a 2+ year period, to regulate the existence of any relationships between toxins and common ions. Cyanobacterial toxins have been quantified using ELISA (cylindrospermopsin, saxitoxin) or LCMS/MS (microcystins, anatoxin-A). Additionally, Common anions and cations have been determined by ion chromatography (IC). Anion (Cl-, NO3-, SO4-2) and cation (Na+, Mg+2, NH4+) concentrations varied by location within the reservoir. According to this reviewer, the present work is good and could be beneficial. This work could be accepted in PeerJ after incorporating the following comments/suggestions.
They are:
1.	Please check the manuscript for typographical error.
2.	Some relevant references are missing. For better understanding the following references should be cited and discussed in the main body of the manuscript (ACS Omega, 2018, 3, 6624-6634; Inland waters 2017, 7, 385-400; Toxins (Basel). 2015, 7, 1048-1064; J. Environ. Sci. Health A13 (l): 493–499).
Experimental design: na
Validity of the findings: na
Additional comments: The manuscript entitled “Monitoring algal toxins in a large reservoir: Relationships with inorganic ions” has described the monitoring cyanobacterial toxin concentrations and inorganic ions in monthly water samples from a large reservoir over a 2+ year period, to regulate the existence of any relationships between toxins and common ions. Cyanobacterial toxins have been quantified using ELISA (cylindrospermopsin, saxitoxin) or LCMS/MS (microcystins, anatoxin-A). Additionally, Common anions and cations have been determined by ion chromatography (IC). Anion (Cl-, NO3-, SO4-2) and cation (Na+, Mg+2, NH4+) concentrations varied by location within the reservoir. According to this reviewer, the present work is good and could be beneficial. This work could be accepted in PeerJ after incorporating the following comments/suggestions.
They are:
1.	Please check the manuscript for typographical error.
2.	Some relevant references are missing. For better understanding the following references should be cited and discussed in the main body of the manuscript (ACS Omega, 2018, 3, 6624-6634; Inland waters 2017, 7, 385-400; Toxins (Basel). 2015, 7, 1048-1064; J. Environ. Sci. Health A13 (l): 493–499).


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: HERBIVORE CORRIDORS SUSTAIN GENETIC FOOTPRINT IN PLANT POPULATIONS: A CASE FOR SPANISH DROVE ROADS
Review round: 1
Reviewer: 1

Output:
Basic reporting: I think the start of the introduction, L. 47-59, should be removed. This is really besides the point of your manuscript and is not even tangentially relevant to what your study investigates.

As a general comment to improving the introduction and putting it more in line with what is investigated (importance of drove road vs. landscape characteristics), I may suggest using the framework of plant functional connectivity (in the drove road), as defined by Auffret et al. (2017) in Journal of Ecology, held against the role of structural connectivity (landscape characteristics). This will make the introduction more in touch with relevant theoretical advances in the field and open a good body of literature which will strenghten the introduction. In line with that, why did the authors only consider distance to human settlements as a quantification of landscape factors? There are other landscape characteristics which could be tested such as landscape heterogeneity around each population? On a side note, time since last ploughing is no landscape factor, and since the factor has no relevance, it could be omitted and replaced by factors such as landscape heterogeneity.

The authors should read the collective works of Yessica Rico (beyond the single one cited in the ms) and Michelle DiLeo, including my own work soon to be published: Plue, Aavik and Cousins, Diversity and Distributions (in press, deep link doi.org/10.1111/ddi.12842), for a broader empirical framing of the authors work. Using these papers, it may also be relevant in both the introduction and discussion as to how our collective works may lead to valuable generalizations of plant functional connectivity provided by domestic animal vectors.

In addition, the authors focus consistently on seed flow, but essentially ignore the role of pollen flow in the introduction, as to how that factor is key in outlining spatial population genetic structure, often considered more important than seed-based gene flow. This should be properly incorporated throughout the manuscript. It will help highlight why we should care about looking into seed-based gene-flow as well.
Experimental design: The RQ on genetic differentiation comes out of the blue. Needs a proper introduction beyond the statement on L. 132.

Methods comments

The sampling effort at 13 populations is at the lower end of what could be acceptable for a landscape genetic study, and this is made somewhat worse by the fact that half of the populations are below the 25-30 individuals which is the recommended sampling density for accurately assessing genetic diversity using microsatellites. Also, the authors equally only developed 6 markers, though 10 is commonly strived towards (i.e. the number used by journals to allow publication on the development of SSRs), to ensure a high enough resolution to detect the genetic patterns they are looking for. The authors acknowledge some shortcomings (at least the low number of populations, see L. 368), but I think they should do so more openly on all shortcomings and discussing the various methodological limitations more in-depth.

Why no calculations of raw A or effective allelic richness (Ae) values?

Many data analysis seem to have been executed without a clear rationale in relation to the research questions. Why the bottleneck analysis? Why the IDB analysis? Why the in-depth analysis of population genetic structure via STRUCTURE? The latter makes sense, but it is not clear from the introduction, whereas the former appear executed because they represent standard analysis in population genetic studies, but not because of a clear reason why they are relevant to this study. If they are, elaborate here and elsewhere in the manuscript! If not, omit! If an in-depth analysis of spatial population structure based on Fst is desired, it needs to be properly introduced (so more than L. 132) and related to the paper’s main themes and the analyses itself should be updated, beyond the much-criticized Mantel tests. For suggestions on state-of-the-art approach in doing so, see Plue, Aavik and Cousins in Diversity and Distributions (in press, deep link doi.org/10.1111/ddi.12842).

The statistical analysis needs (much) more detail. Also, one comprehensive GLS-model which incorporates all environmental variables would be more effective and can work on the raw rather than the rarified data by correcting for sample size, e.g., in R-code,

m1 <- gls(Fis ~ (location + distance + ploughing + sample size)^2, correlation = corGaus(form = ~X+Y, nugget = T), method ="ML")

The AMOVA could be replace by a similar more updated technique:

m1 <- gls(fst.dist ~ (location + distance + ploughing + sample size)^2, method = "ML", correlation = corMLPE(value = 0.1, form =…)).

Note that both analyses enable a correction for spatial autocorrelation via the “correlation” term in the model.
Validity of the findings: Results

I would like the authors to start with some summary stats on the genetic population descriptors across loci, populations, etc. To help the reader to get in touch with the genetic data.

Discussion

Obviously, as I am suggesting some improved analysis, this may impact the validity of their current findings. Still, I will make some broad comments on the discussion.

Too lenghty but see my suggestions which will help remove some of your more hypothetical and speculative discussion parts which lack data in support.

L. 382		“significant capacity” I think this may well be a significant overstatement of the current results? All in all, the impact of your drove road is relatively limited to Fis. The position of settlements in the landscape has a larger impact on genetic diversity. I would angle the discussion as such, framing it as in the reworked introduction, balancing functional and structural connectivity.

L. 337-344	This is too speculative. You have no data of your own in this manuscript which could support this. Also, would this high level of pollen flow in the drove, if this is indeed an explanatory mechanism, then not imply clear, higher levels of genetic diversity in the drove? Which was obviously not the case (though Fig. 3 may indeed suggest some non-significant trends in genetic diversity. Bear in mind however that you only have 6 and 7 populations in the drove/landscape, so results should be interpreted with care, and I would not put much faith in non-significant trends).

L. 360-375	As above, I would omit this because of the same argument: I would not put much faith in non-significant trends when only dealing with 13 populations in total. Stick to what you do have.

L. 404-427	There is redundancy in these paragraphs, and they could easily be merged and shortened.
Additional comments: Dear authors,

I have read this manuscript with great interest, as I have submerged myself over the past few years in the importance of domestic cattle as seed dispersal vectors, positively (?) impacting both species and genetic diversity in isolated plant communties. I believe that the paper could make a nice contribution to add more studies underlining the importance of domestic livestock as key providers of functional connectivity in fragmented landscapes. Nevertheless, some work remains to clarify the manuscript further to reach a level acceptable for eventual publication (see my major comments).

Besides my my comments in the remainder of my review, I list a series of minor comments here:

L. 82-3 		“This will … on human well-being”. This sentence skips a few steps as to how biodiversity is relevant to human well-being. Elaborate or omit.
L. 83-86		Omit.
L. 105-107 	“…, hence … Shannon et al. 2009).” Omit.
L. 115 		“fragmentation-derived viability” Rephrase. No clue what the authors mean.
L. 127-132	The system in Germany may not be a pure transhumance system such as the one in the paper, but its sheperding system is still more a transhumance system where animals physically move through the landscapes, compared to true rotational grazing systems in other countries, such as in the Viroin in Belgium (Honnay et al. 2006) or the Stockholm archipelago in Sweden (Auffret et al. 2012, Plue & Cousins 2018), where animals are moved in trucks or boats between their pastures. So, I would not put it as sharply that your transhumance and Rico’s sheperding systems are so different.
L. 133		?? Omit, but keep the part on L. 134, thát is relevant.
L 137		“were strong enough to” Omit.
L. 139		It cannot be that difficult to give those unpublished data, or a summary, to show how many seeds of Plantago are being dispersed. If anything, this may be important to learn how much seeds could be dispersed, putting an important nuance on the strength of the genetic imprint.
L. 147		“genetic differentiation” was not properly introduced, so that this is the first RQ comes as a total surprise.
L. 156		Is Plantago a diploid? Is it gynodioecous like other Plantago species, what would that mean?
L. 158		The species has a soil seed bank. What does that imply for the vegetation genetic patterns? A soil seed bank may slow down genetic changes to the aboveground vegetation (Honnay et al. 2008, Oikos or Plue et al. 2017, Annals of Botany). I think this could be inserted in the discussion, particularly in explaining why you see differences in the Fis but not in genetic diversity?
L. 166		“faster dynamics in annual plants” You mean rapid turn-over in generations?
L. 177		The drove road. A picture would really help, as I have no clue to imagine what such a “road” constitutes. Based on Google, it looks more like a long, quite broad grassland strip crossing the landscape. Most people, have no clue about what your system looks like.
L. 193		Not 20-30, 8-30 to be precise.
L. 199		As the drove road is a road, I wonder how populations where defined? How to limit where to sample?
Table 6, Fig.3 	Can be merged to represent the most key information.
Fig. 1		I would like to see a topographical map underlaying the datapoints. Gives an idea of landscape heterogeneity.

I wish you good luck with the revisions,
dr. Jan Plue


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: HERBIVORE CORRIDORS SUSTAIN GENETIC FOOTPRINT IN PLANT POPULATIONS: A CASE FOR SPANISH DROVE ROADS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Although I am not a native English speaker, I find the manuscript very well-written with a clear and professional English language. The introduction is well structured, although I provided some advice to improve this structure a little bit more. The literature is relevant and updated. Structure conforms to PeerJ standards. Raw data are supplied. Figures require some qualitative improvement.
Experimental design: The sampling design is appropriate with a reasonable number of populations and enough individuals sampled in each population. The main hypothesis is clearly identified in the introduction (Lines 130-132) and the authors did a great job highlighting the knowledge gap that this study fills. I have some concerns with the statistical analyses, particularly with the potential effects that null alleles could have on the estimates of inbreeding and genetic diversity. I also miss a formal analysis relating the genetic differentiation of populations with landscape attributes (presence of drove roads) using landscape genetic tools.
Validity of the findings: Again, I think that new estimates accounting for the potential presence of null alleles in the markers used could provide more reliable genetic estimates. I also think that some speculation could be better phrased to be better identified as speculation.
Additional comments: Garcia-Fernandez and collaborators present an interesting work that investigates an original question. Specifically, they examined whether drove roads are facilitating livestock-mediated seed dispersal using a population genetic approach. The manuscript is well-written, and the results have important implications for ecosystem management. Therefore, I think that this work should be interesting for a broad audience ranging from ecologists to policy-makers. However, I have some concerns with the statistical analyses used that could influence the validity of their results (see METHODS section). I tried to provide some advice in this regard.

Comments for the authors

ABSTRACT
Major comment
Lines 38-43: I found this part of the abstract too speculative. The authors provide information on the genetic diversity and genetic differentiation of populations, but they did not use either indirect or direct methods to investigate gene flow (e.g. paternity or maternity analysis, historic gene dispersal). Of course, gene flow among populations could be a critical factor influencing their patterns of genetic differentiation and genetic diversity, but there are other factors that could be also impacting (e.g. population sizes, historical processes of colonization). I think that it is fine to interpret your results in terms of differences in gene flow, but I don’t think that you can distinguish between pollen-mediated gene flow and seed dispersal as you state in the lines 38-41.

Minor comments
Line 33: I would replace “genetic descriptors” with “genetic diversity and inbreeding coefficients” to be more specific.
Line 43: Given that the main topic is livestock-mediated dispersal and the term “human dispersal” has not been previously defined, it is not straightforward to understand what the authors mean with human dispersal, at least for a reader not specialized on this topic.

INTRODUCTION
The introduction is well-written, developing properly the main topics relevant for the scope of this work. Furthermore, the literature is well referenced, updated, and relevant for this work.

Minor comment
I would suggest improving a little bit the structure reducing the number of paragraphs. Specifically, I think that the first and second paragraphs are very similar and thus, they could be combined into a single one focused on habitat fragmentation as an important threat to genetic biodiversity.
In the same way, I would combine the third and fourth paragraphs into one moving from dispersal as general concept to the more specific mode of dispersal mediated by livestock. Doing this, I think that you quickly introduce the reader on the main topic of the manuscript.

METHODS

Major comment 1
I think that the authors could take advantage of their INEST analysis to obtain more accurate information on genetic diversity and inbreeding. First, some studies have reported better performance of INEST than other software (e.g. Micro-checker; Campagne et al. 2012 in MolEcolRes) estimating null allele frequencies. Second, INEST provides estimates of genetic diversity (He and Ho) and inbreeding coefficients accounting for null allele frequencies in the markers. Third, by comparing a model incorporating and excluding inbreeding as a covariate, you can explicitly test if inbreeding is significant in your populations. I truly think that the manuscript would be beneficiated from this valuable information.

Major comment 2
I have the following concerns with the STRUCTURE analysis:
1. Given the low genetic differentiation among P. lagopus populations, I would suggest including geographic sampling locations as prior population information in our STRUCTURE analysis, as it is recommended in Hubisz et al. 2009.
2. I found quite modest the number of permutations during the burn-in and MCMC (105 and 106). Maybe is a typo and authors meant 10 5 and 10 6; in that case, they should clarify it.
3. Given the low genetic differentiation of the populations, I wonder if the Evanno’s K selection criteria is the most appropriated. As can be observed in the individual bar plots (Fig 2 B and C), admixture is huge. The main disadvantage of Evanno’s method is that you never examine the possibility of K=1 (panmixia). One option could be to examine the mean Ln P(K) and select that K at which the curve reaches the plateau. However, there are other indexes that outperform both delta K or mean Ln P(K) with unevenly sampled collection sites (Puechmaille 2016; Li and Liu 2018 for software implementation of the indexes described in the previous work). For that reason, increasingly more works are encouraging the use of several K selection methods in order to get a more accurate “true” K.

Major comment 3
Given that the authors mentioned the use of a landscape genetics approach (line 145), I miss a formal test examining whether the genetic differentiation among populations is related to the continuous variation across the landscape regarding drove roads. In other words, using a landcover map, you can calculate conductance distances among your populations assuming that drove roads act as corridors facilitating gene flow (i.e., conductance distance). Then you can run an analysis (e.g. Mantel test, MLPE, causal modeling) relating the population pairwise genetic differentiation matrix and the conductance distance matrix. In this way, you can examine straightforwardly your hypothesis of drove roads enhancing gene flow between populations due to livestock-mediated seed dispersal.
Other option, if you prefer to keep a categorical design is to estimate migration rates among your populations using software such as MIGRATE-N. In fact, you could compare migration rates estimated using MIGRATE-N and BAYESASS to compare historical versus contemporary dispersal, if you want to examine whether resident livestock is influencing contemporary genetic differentiation (Lines 186-188).

Minor comments
Line 177: Please, move “hereafter CDR” to line 140 where you define the term for the first time.
Lines 180-181: Does the study species disperse its seeds in June or November? With this information, maybe you could examine asymmetric dispersal in your populations. In other words, if the species disperse its seeds in June, I would expect that southern populations act as source populations and northern ones as sink populations.
Line 195: How many individuals were deposited? “Some individuals” sounds a little bit vague.
Lines 241-244: Why don’t you run separate Mantel test for populations in agriculture matrix and drove roads? Then you could examine if there is isolation by distance in each group of populations and what relationship has steeper slope (i.e., more restricted gene flow). Also, you could examine the four scenarios proposed by Hutchinson and Templeton (1999) regarding the relationship between genetic differentiation and geographic distance.
Line 267: Why don’t you include ploughing history as an explanatory variable in your model?

RESULTS
Minor comments
Line 274: Please, replace “small” with “low”.

DISCUSSION
In general, the discussion is well written, nicely-structured and with a clear take-home messages. In addition, I would like to highlight the good work that the authors have done regarding the implications for the conservation of ecosystem services. I would only suggest considering other factors such as population sizes, colonization history when interpreting their findings (Lines 337-341). Pollinator availability could be an important factor influencing inbreeding coefficients, but also the availability of co-flowering non-relatives (i.e., density of reproductive individuals, asynchrony in flowering phenologies of reproductive individuals).

Minor comments
Line 350-351: this sentence is not clear, please rephrase it.
Lines 369-370: “[…] reduce the occurrence of private alleles”. Considering the modest geographic extent of the study area and the number of markers used (i.e., six), I cannot agree with this statement. There are populations with more than 5 private alleles (LCR01, LMA08 and LMA12).
Lines 429-437: I find this paragraph a little bit out of place here. I would move it to the previous section because it is part of the discussion of your results.

CONCLUSIONS
Conclusions are well-stated and linked to the original research question. However, I think that talking of long-distance plant migration is not limited to the supporting results. Long-distance dispersal could be a mechanism reducing genetic differentiation among your populations, but in my opinion, this hypothesis requires a different analytical approach involving direct estimates of dispersal distances.

FIGURES

Figure 1: I would use a landcover map to explicitly show the location of the drove roads and land use types in the surrounding matrix.

Figure 2: The resolution of this figure should be improved, it is blurred.

Figure 3: It would be nice to increase font size in the axis titles and tick labels. Also, I would replace “I” with “Shannon Index” in the plot “c”.

TABLES
Table 5: Please, include a column stating whether the populations is in a Drove Road or into the agricultural matrix.

Table 6: I think that the authors meant “Genetic descriptors” instead of “Inbreeding coefficient” in the first cell of the table.

REFERENCES
Campagne, P., Smouse, P. E., Varouchas, G., Silvain, J. F., & Leru, B. (2012). Comparing the van Oosterhout and Chybicki‐Burczyk methods of estimating null allele frequencies for inbred populations. Molecular Ecology Resources, 12(6), 975-982.
Hubisz, M. J., Falush, D., Stephens, M., & Pritchard, J. K. (2009). Inferring weak population structure with the assistance of sample group information. Molecular ecology resources, 9(5), 1322-1332.
Hutchison, D. W., & Templeton, A. R. (1999). Correlation of pairwise genetic and geographic distance measures: inferring the relative influences of gene flow and drift on the distribution of genetic variability. Evolution, 53(6), 1898-1914.
Li YL, Liu JX (2018) StructureSelector: A web-based software to select and visualize the optimal number of clusters using multiple methods.Molecular Ecology Resources, 18:176–177.
Puechmaille, S. J. (2016). The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem. Molecular Ecology Resources, 16(3), 608-627.

RECOMMENDED SOFTWARE FOR ESTIMATION OF MIGRATION RATES AMONG POPULATIONS

MIGRATE-N: https://popgen.sc.fsu.edu/Migrate/Migrate-n.html
BAYESASS: http://www.rannala.org/software/


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: HERBIVORE CORRIDORS SUSTAIN GENETIC FOOTPRINT IN PLANT POPULATIONS: A CASE FOR SPANISH DROVE ROADS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The submission is self-contained including all results relevant to the hypothesis that the authors examine. The authors did a great job improving the structure of the introduction and discussion substantially improving the readability of the manuscript. The literature is relevant and updated. The structure conforms to PeerJ standards. Raw data are supplied. Figures still require some qualitative improvement.
Experimental design: As I stated in my previous revision, I think that the sampling is appropriated and the mean hypotheses clearly identified. In the current version of the manuscript, the authors did a good job incorporating new analyses that provide estimates of inbreeding after accounting for null alleles. Although they did not explicitly examine the possibility of isolation by resistance, they did an important effort to include landscape features in their analyses.
Validity of the findings: Although I still think that there is some speculation regarding the effects of drove roads on pollination, the results are strong enough and of interest of a broad audience involving ecologists, policy-makers and managers.
Additional comments: Dear authors,
I really like the outcome of your revision. I think that both introduction and discussion have been substantially improved with a clear structure and a nice flow of ideas. Although I still think that isolation by resistance test would be appropriate, I see the merit of the authors incorporating landscape features in their analyses. Finally, I think that consideration of null allele frequencies in their markers results in more reliable estimates of inbreeding. Therefore, I only have minor comments aimed at providing some feedback to improve the manuscript.

Abstract
L28: What do you mean by “productivity”? Generation of biomass in an ecosystem?
L42: Without any quantitative comparison of pollinator communities between drove roads and agricultural matrix, I still find too speculative this statement.
Introduction
L52 “This genetic impoverishment can limit evolutionary potential.”
L64: What do you mean by “subjected to strong adaptation pressures”?
L68-69: I do not know if I agree with this statement. For example, overpopulation of ungulates in many regions has been reported by numerous studies. I think that this sentence should be rephrased to focus specifically on those groups exhibiting population declines (Large frugivores?)
L76-79: This sentence is quite wordy, try to synthesize it.
L124-134: I think that this paragraph is not necessary. You could include two sentences in the previous paragraph, one indicating the effects of drove roads in pollination and another explaining the effects of persistent seed banks.

Methods
L248: Please, indicate the number of microsatellite markers used in your analyses.
L260: Did you compare the models including and excluding inbreeding? This test is very useful to examine if there is evidence of inbreeding in each of your populations. You should get this information in the output of the analysis.

Results
L373-375: It would be good to provide at least a quantitative estimate such as the coefficient of variation.
A few comments about the results from Bayesass and Migrate:
You should have a migration rare of each population with the remaining populations, but I only see a migration rate for each population. Did you estimate the mean migration rate of each population with the remaining ones? If so, you should indicate it. One option to make more visual the information included in Table 6 could be a network plot. You could be interested in the approach used in Castilla et al. (2016) where migration rates are presented in this way. Sorry for the self-advertisement and of course no need of citing this work!
You must provide the standard errors of your estimates to check if they overlap zero and thus migration is negligible.
It is interesting the difference in the magnitude of historical and recent migration rates. It seems like migration was intenser in the past according to your estimates. I wonder if the decline in the use of drove roads could be linked with this reduction in the recent migration. How do the authors interpret this result?

Discussion
L546-549: Maybe an idea for these future studies could be to estimate mean dispersal distance separately for populations in drove roads and agricultural matrix using the approach implemented in the software SPAGeDi. Probably you will need to increase sampling size (sampling area and number of plants).

L550-552: I do not catch the message in this sentence. Please, rephrase it specifying the ecosystem functions provided by mobile pastoralism and what covers more than a half of the global land.

Figures and Tables
The number of tables is too high. I provide some suggestions in this regard:
1. Move Table 2 to supplementary material.
2. Add geographic coordinates of populations to table 3 and remove table 1. The rest of the information in Table 1 is redundant.
3. Move Table 5 to supplementary material.
4. I think that you could include the information of tables 7, 8 and 9 into a single table. The structure of the models is practically identical. You can maintain the explanatory variables in the first column, then two columns for each response variable including its corresponding coefficient and p-value.

I think that the figures still require some improvement.
Although Figure 1 is illustrative of the landscape and human management in the study area, I don’t think that it is informative. One option could be to move it to supplementary material. Other option could be to combine Figure 1 and 2 into a single figure. I would suggest removing the second panel and maintain the panel with the Iberian Peninsula with the framed area and the landscape map showing the spatial location of populations. Then I would add a third panel with the picture used in Figure 1.
Figure 4: I would suggest removing the grid lines inside the panels and increase font size.

References
Castilla, A. R., Pope, N., Jaffé, R., & Jha, S. (2016). Elevation, not deforestation, promotes genetic differentiation in a pioneer tropical tree. PloS one, 11(6), e0156694.


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: HERBIVORE CORRIDORS SUSTAIN GENETIC FOOTPRINT IN PLANT POPULATIONS: A CASE FOR SPANISH DROVE ROADS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Please check the grammar of some sentences, I found some sentences that miss or have an extra word. Also some sentences lack clarity or I repeated.

Specifically:

Ln55: add: and microevolutionary...
Ln58: add by: is not always possible by just....
Ln60: instead of using often limiting replace by: are needed to sustain
Ln67: remove “measures”
Ln74: I will add to these references, one more recent.
Ln81: add, such as...
Ln86: I am not sure if the word Traditional is the correct here, would it be more: Historic routes
Ln108: rotational
Ln124-127: I don’t understand what meant by “rather than with the use of the landscape that seed dispersal depends on”. Pollinators also will be affected by landscape use, or does the authors meant specifically by the livestock herded associated dispersal?  Please clarify as also I don’t get the idea of the following sentence.
Lines 219 and 276 with 278 and 292 have repeated ideas, foe e.g. calculation of FST with FreeNA and the calculation of Mantel test, please revise and correct.
Experimental design: I have read the revised version of this manuscript and the comments provided by two reviewers. This is the first time I have revised this manuscript and I found that the authors have made a good effort to address each of the comments, the analyses added made the work statistically more sound, so I don´t have further suggestions for analyses.

My only comment on this aspect is regarding the justification of the estimation of contemporary and historical migration rates. After reading the response letter it is clear the purpose and the new information these methods will add to the manuscript, but I don’t think the authors make enough clear within the text, the specific purpose to perform them.

Other comments in methods:
Ln340: Software or R packages to run these analyses?
Ln393: That’s a perfect linear fit! r=1, is that right?
Validity of the findings: Results are sound and the conclusions are well supported based on their own data and available studies.
Additional comments: This is an interesting work adding more evidence on the importance of livestock mediated seed dispersal on gene flow and genetic diversity in agricultural landscapes. As I stated above, after carefully reading the revised version I found the manuscript improved, the methods are sound and the discussion is in line with the provided evidence. I just have few comments that could improve the quality of this work, and the main observation I would make relates to the argument in lines (326-329), where the authors stress that allelic richness is a descriptor that was considered related to seed dispersal in similar studies of Rico et al 2014a, Rico & Wagner 2016, and DiLeo et al 2017.  I don’t think this interpretation is that correct, in such studies allelic richness was used as the best estimate of genetic diversity to evaluate contemporary landscape effects compared to others, such as He., and not necessarily as a proxy linked or related to seed dispersal since also gene flow by pollen or population size are factors involved in genetic diversity estimates such as Ar. For FIS, in case of plants, it does have a pollen flow component which can be due to selfing or biparental inbreeding as specified in Rico et al. 2014. Mol Ecol, and in this work. Thus, I would omit the argumentation of the relation between RiqRare and seed dispersal,which would be incorrect, but certainly its valid to argue the use of this estimate (as did in ln312-314) to (at some level) contrast with previous studies.

Besides this comment I think this work merit publication as it contributes within its field.


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: SCENARIOS OF AVAILABILITY OF WATER DUE TO OVEREXPLOITATION OF THE AQUIFER IN THE BASIN OF LAGUNA DE SANTIAGUILLO, DURANGO, MEXICO
Review round: 1
Reviewer: 1

Output:
Basic reporting: The structure of the manuscript is the classic; there is nothing to say about it.
Experimental design: The method is comprehensible.
Validity of the findings: The article is interesting and could be as a model to transfer to other areas with similar conditions and problems with overexploitation and pollution, the method is comprehensible. This work open new possibilities with the function of the system and the management proposal. It will be interesting that the government consider this work as a part of the management.
Perfect publishable and valid for other researchers.
Additional comments: The aspects that may could be better are the graphics; from my personal point of view are:
The figure 1 must be complete, the orientation and the scale, in the case of the scale if it couldn´t be done there is no problem because in the figure it is marked the surface of the endorheic basin.
The figure 2, in this case the legend is in Spanish and it will be more didactic if the intensity of the color corresponds with the altitude values. In addition, the legend must be organize in equal order, from maximum to minimum altitude.
The limit of the micro-basins must be a line, not a rectangle because it could be associated with a surface.
In the part of “Physical aspects”, I think in the text and not only in the table, it will be fine to specify that the types of clime are the köppen classification.
The hydrography will be more comprehensible and orderly if the figure 6 is added here, and not where is located in the text. This figure has the legend in Spanish and the limits of the basins must be added with a line in the figure. So this will be now figure 3, changing the number of the other figures that follow the text.
The figure 3 is a population pyramid with groups of ages not homogeneous. The legend (man, woman) is in Spanish, but the most important is to add the year. I recommend that the rectangles of the histogram will be designed proportional to the years.
The figure 4 is about uses of land, the legend is in Spanish and to delimit the micro-basins just must appear a line.
The figure 7, the legend is in Spanish and the percentage that it expresses doesn´t specify about what is.
In the article, some phrases are very long; it could be easily to read if there will be short phrases.
In the text, the word sub-basin appear for example in soils, and is the basin.
It is necessary to check all the acronyms, the first time that it appears; it must do it with the complete name of the thing that it represents.