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: ORIGIN IDENTIFICATION OF MIGRATORY PESTS (EUROPEAN STARLING) USING GEOCHEMICAL FINGERPRINTING
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper presents geochemical fingerprinting as a novel approach to assessing the source of problem birds for damage management.  The manuscript is well written.  I have some minor grammatical comments, as well as some comments on the background and literature cited.  One of the reasons the authors list as making starlings a highly successful pest is intraspecific brood parasitism.  The paper cited (Kennedy and Harry 1999), has been incorrectly cited and should be Kennedy and Power 1990.  In reading Kennedy and Power I do not see the support for the statement that the brood parasitism increases success rate and the number of chicks that fledge in starlings.  I would suggest the authors remove this from the manuscript.  The other four reasons for starlings being a “highly successful pest” are more than adequate.  I find the authors reasoning for determining the natal origins of the pest birds to be flawed.  The authors describe deterrent techniques “falconry, noise deterrents, electronic distress calls, bird netting, visual repellents) as eradication techniques.  These techniques should be deployed at the orchards, dairies, and feedlots to prevent damage, not at breeding or origin sites.  Some additional information on the lethal removal and where it is currently occurring that is not helping the damage situation would help strengthen this argument.  A discussion of how deterrent techniques can be ineffective (and many of the techniques listed by the authors are ineffective except netting, which is effective, but can be prohibitively expensive) and that lethal removal, especially of a non-native invasive species can be beneficial would also strengthen the introduction.
Damage at orchards, vineyards, and berry production facilities by starlings has been well documented, and it is generally understood that there is an age difference in starlings that damage these locations.  (Virgo 1971 “Bird damage to sweet cherries in the Niagara Peninsula, Ontario”; Stevens 1985 “Foraging success of adult and juvenile starlings Sturnus vulgaris: a tentative explanation for the preference of juveniles for cherries”; Conover et al. 2007 “Use of decoy traps to protect blueberries from juvenile European starlings”, etc…)  This should maybe be pointed out in the introduction or discussion.
The structure conforms to the PeerJ standards, and the raw data has been supplied.  The description of Figure 3 should include more specifics such as what distance are the authors referring to?  The distance from one end of the cluster to the other, the distance between sites?  Figure 4 I think would be more useful if it only included the adult birds.  With the juveniles included as well the figure is small and hard to decipher.  I find Figures 5 and 6 to be confusing and do not add much to the manuscript.
Experimental design: The research described in this manuscript is original and within the scope of the journal.  The research question has been well defined, with the exceptions noted above.  I think there could be some additional detail described in the methods.  How were the sites for the adult birds chosen, how were the birds confirmed as being adult, especially with the timing of adult problem bird collections (Aug-Dec) and the timing of molt in starlings (Aug-Oct) (Birds of North America Online).  There is literature suggesting that starlings disperse widely from their natal sites (Cabe 1999).  This suggests that the authors methods will only be able to determine the location of juveniles born in the year the geochemical fingerprinting was conducted.  Thus it is not surprising that 58% of the problem birds were immigrants or could not be assigned to a location.
Validity of the findings: No comment
Additional comments: L5: Replace “create” with “cause”
L7: Replace “deterrents” with “devices” or remove “scare”
L7: Remove “only”
L7-9: Do the authors have any literature to back this statement up?  It typically requires more effort to trap birds before they begin to group into large flocks.
L37: “Starling(s) cause significant…”
L38: Although the location of the Okanagan Valley is defined in the abstract, it should also be defined here at first mention in text.
L41: BC is used with no description of what the abbreviation stands for.
L47: Is the damage described in US or Canadidan dollars?
L57: To put the bird removals in perspective it would help to have an estimate of the breeding population of starlings in the Okanagan Valley.
L59: Are the increased starling numbers specifically in the fall?  Is it known how many EUST migrate into the valley in the fall?
L59-60: This logic does not make sense to me.  The techniques described (falconry, noise deterrents, electronic distress calls, bird netting, visual repellents) cannot be applied at breeding locations and be expected to have an effect on damage at orchards and dairies.  If the techniques implied here are lethal this should be specified.
L76: BC should be defined in L41.
L113-115: This statement was already included in the introduction, it should only be in one section and does not need to be repeated.
L266-267:  Is it possible that these 44% are not immigrants?  Starlings are known to disperse widely from their natal origins (see Cabe 1999 “Dispersal and population structure in the European starling”), thus these birds could be breeding in the Okanagan valley, but were born outside of the Okanagan valley.  The method described in this paper would not be able to distinguish these birds from fall migrants.
L130-131: If problem birds were collected between August-December, how were they verified as adult birds?  Juveniles molt in August-October and afterward look very similar to adult birds.  Also, from how many sites and how were these spread around the valley.  What proportion of the number of problem birds in the valley is the 118 bird collection and how representative of the problem bird population are these 118?
L441: Kennedy, E. Dale and Harry W. Power (1990).


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: ORIGIN IDENTIFICATION OF MIGRATORY PESTS (EUROPEAN STARLING) USING GEOCHEMICAL FINGERPRINTING
Review round: 1
Reviewer: 3

Output:
Basic reporting: •	Clear writing, logical flow, easy to read (thank you!)
•	Introduction missing some references and details. See detailed comments and pdf markup.
•	Figures 5 and 6 could be collapsed into one figure with different colour schemes
•	Uncertain if the raw data were supplied
Experimental design: •	Question well defined and fills a relevant knowledge gap
•	Technical approach appropriate. I like how young birds were used to define the elemental origin of older birds!
•	Ethical certificates identified
•	Methods are detailed and reproducible
Validity of the findings: •	Statistics are explained well and are appropriate
•	Findings are discussed in the context of existing research
•	Implications of finding outlined and linked to other research
Additional comments: Thank you for the opportunity to review this manuscript. It was a pleasure to read. My overall comments are minor (see pdf markup and comments below). I trust you can quickly address these to move this manuscript forward in the publication process.

Introduction: Overall very clear. The framing of the problem was well done. One thing that I would like to see added is a short description of the life cycle of Starlings in the area. For example, are the ‘problem’ birds migratory, stop-over, overwintering, ect? You talk about natal origin, which implies these birds are outside the breeding grounds? Or are the birds non-migratory or short-distant migrants? I know the answers to these questions, but a non-avian expert may not. Making this clear at the outset will better frame the problem for the non-expert.  It would also be good to know if the birds show site fidelity to the breeding or wintering areas, or both? From a trace element perspective, I am curious how long do Starlings live? When are the trace element signatures suspected to have been incorporated into the bone tissue of adult birds? Is this a continuous process?

Conclusion: Be clear what the conservation implications are of these finding. For example, how will discerning natal origin help resource managers control problem Starlings? This is stated in the introduction but should be elaborated on here.


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: ORIGIN IDENTIFICATION OF MIGRATORY PESTS (EUROPEAN STARLING) USING GEOCHEMICAL FINGERPRINTING
Review round: 2
Reviewer: 1

Output:
Basic reporting: Revisions make this component much improved. However, the paper needs a thorough read through for numerous grammatical issues.
Experimental design: no comment
Validity of the findings: I wish the paper could have better addressed the issues of uncharacterized sites, but I think they did a reasonable job acknowledging the uncertainty in their interpretations as a result.
Additional comments: I think the authors did a nice job addressing my earlier comments and suggestions. The addition of the table with geological information is quite helpful (bummer that there’s not a nice map of it).  Thanks for including the original data in addition to the z-scored data.  I appreciate the improved citation effort as well. It helps provide context for the material presented here, and maintains a paper-trail for the ideas presented by others. Overall, I think the manuscript clarity if much improved. However, the newly added text needs to be carefully reviewed for numerous writing clarity and grammatical issues. Nice job.

Specific Comments:
L86: Clarify large flocks of starlings

L148-9: I’m not a fan of the inclusion of a strawman hypothesis that we know will be rejected, but maybe that’s personal preference. I would prefer to see a more impactful “alternative” hypothesis, i.e., a statement of what you actually think you will see and why.

L474: Again, clarify starling populations

L556-563: The clarification of likely challenges/alternative explanations here is useful.

L557-558: I found this sentence confusing


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: ORIGIN IDENTIFICATION OF MIGRATORY PESTS (EUROPEAN STARLING) USING GEOCHEMICAL FINGERPRINTING
Review round: 2
Reviewer: 2

Output:
Basic reporting: This paper presents geochemical fingerprinting as a novel approach to assessing the source of problem birds for damage management.  The manuscript is well written with the exception of some minor grammatical considerations (see below).  The figures are relevant and add useful depictions of the results and locations.
Experimental design: The research described in this manuscript is original and within the scope of the journal.  The research question has been well defined.  The methods have been well described and with sufficient detail and information to replicate.
Validity of the findings: The authors conclusions are well stated and are reflected in the data presented.
Additional comments: L7: Replace “divert” with “disperse”; “acclimated” with “habituated”
L31: “…status is considered to be of least concerned…”  Delete “ed” on concerned.  The species classification is “least concern”
L39-40: “Starlings can migrate long distances in a day and can cover a total of up to 1,000-1,500 km over migration periods.” As written this sentence is misleading.  Starlings do not migrate 1,000 km in a single day.
L44: Delete duplicate “around”
L50-51: “Large flocks of starling(s) are known to destroy fruits in vineyards and orchards and depredate cattle feed at dairy farms.”
L59-64: Reconcile these numbers for the readers.  An average of 54,000 birds are removed/year between 2003-2013 yet in 2013 the population in December was 23,592?
L118: Insert “is” after Central Okanagan; insert “of” after up.
L310: spell out kilometer.
L332: delete “and”.
L335: “…that are 100’s of kilometers apart geographically…”
L364-365: “However, some of the problem birds could not be assigned to a source population and were designated as…”  “It might be due to a…”
L369: “Third, it is likely…”
L371: “The use of trace elements in bone tissue in identifying the source population of starling(s)…”


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: ORIGIN IDENTIFICATION OF MIGRATORY PESTS (EUROPEAN STARLING) USING GEOCHEMICAL FINGERPRINTING
Review round: 2
Reviewer: 3

Output:
Basic reporting: Line 84-85: Statement of the null hypothesis. Rather, state the hypothesis.

Figure titles: there are issues with all of them. They need to be stand alone.
For example, if writing 'juveniles' the reader need to know what species. Write 'juvenile starlings'. Same with 'adults'

'locations' = 'locations in the Okanagan Valley, British Columbia'

Do this for all the figure titles.

Figure 3 - '...different the clusters are'. Are what? Are different in relation to each other? the reference samples?

Figure 5 - this is not a heat map.
Experimental design: Yes
Validity of the findings: Yes
Additional comments: Line 63: Bird Studies Canada is now Birds Canada. Also, this reference is not appropriately structured. Did you access this information from the web? It does not appear in the literature cited.

Line 109: do not end a sentence with ect.

Line 395: delete 'like the Okanagan Valley'


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: CRYPTIC DIVERSITY AMONG YAZOO DARTERS (PERCIDAE: ETHEOSTOMA RANEYI) IN DISJUNCT WATERSHEDS OF NORTHERN MISSISSIPPI
Review round: 1
Reviewer: 1

Output:
Basic reporting: The Yazoo Darter, Etheostoma raneyi, has an incredibly small distribution in Mississippi waters. Microendemism is common among darters, and limited distributions are at risk of extirpation due to anthropogenic influences. The topic of the manuscript is relevant to conservation genetics as well as reintroduction or restoration efforts. Previous work on this group included the use of mitochondrial markers (Powers and Warren, 2009) where the authors recovered two clusters of Yazoo Darters and microsatellite data (Sterling 2012) that showed genetically distinct populations in each stream. Based on the limited range of the species, its imperiled status, and evidence of distinct genetic lineages, the authors focus on the Yazoo River system and increase taxon sampling to investigate cryptic diversity in the drainages of the upper Yazoo River.

The methods implemented in this paper are appropriate for assessing the genetic variability within the Yazoo Darter range; however, the presentation and assessment of these methods muddles the question at hand. The introduction states the goal is to understand and elaborate on putative cryptic diversity between the Yocona and the Little Tallahatchie Rivers previously reported by Powers and Warren; however, the discussion focuses on reviewing the diversity within rivers as reported by Sterling 2012. Congruence between the introduction/stated goals and the conclusions drawn from analyses is important for conveying the primary message of this paper. The authors should reflect on the primary goals of the paper and ensure the main message is being appropriately communicated and supported with methods and discussion.

The figures of this paper are not entirely relevant to the content of the article. Figure captions should be expanded to appropriately describe their content.
Figure 1 shows the distribution of Yazoo darters as well as two other Adonia clade species and the “Spring Creek” Darter. After reading the manuscript, I do not understand what this figure contributes towards the paper. There is little to no discussion of E. pyrrhogaster, E. cervus, or “Spring Creek” Daters, and what discussion is present is not relevant to the question of genetic diversity within the Yazoo River. The authors may choose to expand their discussion of these other taxa or remove the first figure from the paper.

Figure 2 should be the primary map for the manuscript. Portions of Figure 1 such as the line of the Upper Gulf Coastal Plain should be included in Figure 2. The caption associated with this figure (and the other figures) needs to be expanded to cover everything presented within it. A good portion of the Materials and Methods (lines 99-106) is dedicated to explaining the sampling area, yet none of the rivers or streams are labeled on the map. In GIS, you can highlight/shade the drainages by HUC (hydrologic unit code). I would recommend coloring/shading the watersheds consistently with the colors presented in Figure 4 and making the numbered boxes and circles white. Alternatively, the authors could color the numbered boxes and circles consistent with Figure 4.

Considering the amount of heterogeneity between the two analyses, the authors should concatenate their cytb and S7 data. I do not like that the S7 tree, which tells a different story than the cytb tree, is delegated to the supplemental material rather than presented and discussed in the main paper.

Figure 4 is fine with the nodes collapsed, given that the authors discuss the lack of internal support for the nodes; however, it may be useful to have the full trees (cytb, s7, and a concatenated tree) included in the supplementary materials

The authors spend some time discussing cryptic diversity and molecular methods used to understand population- and species-level variation. A few recent papers are provided that the authors may find relevant to their discussion:
Geheber 2019: Contemporary and Historical Species Relationships Reveal Assembly Mechanism Intricacies among Co-occurring Darters (Percidae: Etheostomatinae)
Hayes and Piller 2019: Patterns of diversification in a North American endemic fish, the Blackbanded Darter (Perciformes, Percidae)
Near et al., 2016: Systematics and taxonomy of the snubnose darter, Etheostoma simoterum (Cope)
Wagner and Blanton 2017: Do River Drainage Boundaries Coincide with Phylogeographic Breaks in the Redband Darter?

The call for human-assisted gene flow presented in Sterling 2012 is further supported by the genetic analysis presented here. The results of this paper are important for conservation, stream remediation, and population supplementation. With edits to the manuscript listed above, this paper will be a good contribution to the body of knowledge associated with the Yazoo Darter.
Experimental design: The methods implemented in this paper are appropriate for assessing the genetic variability within the Yazoo Darter range; however, the presentation and assessment of these methods muddles the question at hand.

Two portions of the methods require further explanation and elaboration. First, the molecular clock analysis is not sufficiently described (lines 150-152) for reanalysis by future researchers and the results are not presented in the results section. Considering a good portion of the discussion revolves around the timing of glacial cycles and divergence time estimates of the two streams, this needs to be strengthened. The second is the statement in lines 194-195 regarding the use of pairwise genetic sequence divergence. This reason for comparing across all Adonia clade species needs to be needs to be elaborated upon and the statement at line 194 particularly should be justified.
Validity of the findings: The call for human-assisted gene flow presented in Sterling 2012 is further supported by the genetic analysis presented here. The results of this paper are important for conservation, stream remediation, and population supplementation. With edits to the manuscript listed above, this paper will be a good contribution to the body of knowledge associated with the Yazoo Darter.
Additional comments: Other comments are provided in the attached .pdf file.


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: CRYPTIC DIVERSITY AMONG YAZOO DARTERS (PERCIDAE: ETHEOSTOMA RANEYI) IN DISJUNCT WATERSHEDS OF NORTHERN MISSISSIPPI
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1.	Clear and unambiguous English
The writing is overall clear and the English is strong.

2.	Sufficient Literature/Background
Background in the introduction is thorough, targeted to the Yazoo region and the biology of the darter species being examined.

3.	Professional Article Structure
The article contains all the elements of a scientific paper.

4.	Results relevant to hypothesis
While the authors don’t have a discrete hypothesis (they are instead drawing inferences form observed genetic diversity), the results presented are relevant to their research goals.
Experimental design: 1.	Original primary research
The research goal, date collection, methods of analysis, and presentation or results are all consistent with a primary research article.

2.	Well defined research question
The research goal was to investigate cryptic diversity within the Yazoo darter using mitochondrial and nuclear gene sequence data.

3.	Rigorous investigation
This is a very targeted study, with limited scope and conclusions. That being said, while none of the methods or analyses here are cutting edge, they are consistent with current practice in investigations of intraspecific genetic variation in fish species with limited range.

4.	Sufficient methods
The methods utilized are appropriate for the question
Validity of the findings: 1.	Benefit to literature/impact
While it is limited in scope, the paper serves as a valuable baseline analysis of the population genetic structure of this darter.

2.	All underlying data have been provided and are robust
I detected no issues.

3.	Conclusions are clear, relate to hypothesis, and limited to results
Overall yes, but see my comments below.

4.	No unwarranted speculation
There is some speculation in the discussion, but this is clearly presented as a ‘proposition.’
Additional comments: It would be helpful to indicate the watersheds sampled within each drainage on lines 102-106 somewhere on the map on Fig.1, or probably better on Fig. 2.

Line 160, the authors that reciprocal monophyly was ‘moderately’ supported by the Bayesian analysis. In order for support to be ‘strong’, both nodes would need to be supported by 0.95 or higher (a somewhat arbitrary benchmark). However, since one of the has a posterior probability of 0.12 (indicating only 12% of the sample trees recovered that clade), the term ‘moderate’ is a bit misleading. ‘Moderate’ might mean one of the nodes supported by 0.9, for example. These data suggest no or little support for reciprocal monophyly in the Bayesian analysis given that support for both nodes is required.

Lines 161-162. “Phylogenetic trees generated using the S7 gene generally lacked support for samples from the Little Tallahatchie…” It is not clear what object lacked support. The sentence makes is sound as though samples lacked support. A sample can’t really be supported (or not) by the phylogeny. Is the statement meant to imply that the phylogeny based on the S7 data lacked support for a monophyletic clade corresponding with Little Tallahatchie samples?

It is not clear why the trees based on the S7 sequence data were not shown in a figure in the main body of the manuscript. These tree could be included in Figure 3 with the mitochondrial tree (parts A, B, and C for example).

Figure 3 – Are the bubble sizes for LT and YR proportional to the number of individuals sampled or the total number of unique haplotypes?

The authors mention support for the recognition of two species based on the phylogenetic species concept (Lines 181-183), however no specific data are referenced in support of this assertion. Nixon and Wheeler (1990) define a phylogenetic species as "the smallest aggregation of populations (sexual) or lineages (asexual) diagnosable by a unique combination of character states in comparable individuals (semaphoronts).” Are the authors suggesting that diagnosable states are listed in table 2? While these represent discrete characters, the reconstructed phylogenies do not provide strong, consistent support for two distinct clades. Support varies by locus and method of analysis (Bayesian vs. Likelihood). While there is evidence of divergence, raising the potential for two different species is a significant claim and should be clearly supported by evidence. However, very little explanation in this subject is provided in the discussion despite it being a lead point in the section. Given the current understanding of the distinction between species trees and gene trees, the authors might consider modifying the language to suggest the potential for species recognition, barring further analysis of data, both genetic and morphological. If not, there needs to be a much deeper explanation of how the data support the assertion and a nuanced discussion of these data considering known differences between gene tree and species tree inference.

Overall, the authors have drawn some otherwise sound conclusions about the genetic distinctiveness of the populations in these two drainages and made a good case for within drainage translocations. Conclusions regarding species recognition extend a bit beyond the data. Studies such as this focusing on population genetics of vulnerable microendemics are critical to furthering our understanding of how to manage them. This is a strong paper and should be published.


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: CRYPTIC DIVERSITY AMONG YAZOO DARTERS (PERCIDAE: ETHEOSTOMA RANEYI) IN DISJUNCT WATERSHEDS OF NORTHERN MISSISSIPPI
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript meets basic reporting requirements; in several cases statements require clarification and figures require revised labels or heading information, but these have been noted with specific comments in the text.
Experimental design: The manuscript meets the the expectations of experimental design and fits the aims and scope of the journal. In a few cases, additional information is required to clarify minor points regarding methodology and these are noted with specific comments in the text.
Validity of the findings: Findings and conclusions of the manuscript are supported by the data/results presented.
Additional comments: The authors use DNA sequencing of populations of the Yazoo Darter, E. raneyi, to examine phylogeographic relationships and to identify cryptic diversity in this species. The writing of the manuscript is overall clear and effective, the methodology sufficient, and the conclusion are supported by the data presented. They find support for cryptic diversity in that populations from the Yocona River represent a distinct clade and taxon of E. raneyi, which they refer to as the "Yocona Darter". This work makes a good contribution to our understanding of diversity of southeastern US fishes and makes conservation recommendations based on their findings for the focal taxa, which are much needed.

One of the primary concerns that should be addressed by the authors is related to how undescribed species are recognized in the manuscript. Specific comments related to this are provided throughout the text. One, use of names like "Spring Creek" Darter (as in Figure1) is problematic because many readers would have no idea what taxon this refers to; in later tables this is identified as a member of the E. zonistium or Bandfin Darter species group. I recommend labeling as E. cf. zonistium - Spring Cr (or Creek) instead for clarity. I also think using "Yocona Darter" in the text, tables and figures is problematic as this implies an official common name for the taxon which is proposed as a new species, but has not been officially described. This can create taxonomic confusion and could be confusing to the readers that might skim the article, or look at figures to get a quick take-away. I recommend referring to as E. cf. raneyi - Yocona R. (or Yocona River form of E. raneyi). The data clearly support that it is distinct and its not an issue to note and identify that the data support it as a distinct species, however. Also see the use of such annotation for members of the E. bellator and E. brevirostrum species groups, where "common names" are used for undescribed species without . Related to names and population identifiers, there is some inconsistency in use across text, tables and figures that should be addressed as well. I also recommend using E. raneyi rather than "Yazoo Darter" in the text, tables, figures, throughout (or rather than switching back and forth).

I like that the authors use this data to offer more informed conservation actions, however, I think that paragraph could be refined with more specific and clear recommendations based on the totality of all the data that is now available for the Yazoo Darter. Specific comments are in the text.

In general, I think the Figure legends would benefit from a more detailed description of what is shown and consistent labeling of taxa and watershed-drainages or "clades" could be improved and make it easier for the reader to follow the big picture.

There are other minor issues, questions, and points of clarification that should  be reviewed and addressed as noted with comments in the attached pdf.


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

Input:
Title: FAUNA ASSOCIATED WITH SHALLOW-WATER METHANE SEEPS IN THE LAPTEV SEA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Language:
The English requires editing. Aside from general, grammatical errors, one thing the authors should note is that certain terms or words are used in ways that don’t entirely make sense. This might be a translation issue. I have highlighted some of these instances.

Introduction and background:

The authors set the stage well, starting with an introduction to methane cold seeps and continuing with the main thrust of the manuscript: seeps in shallow waters, particularly in the Arctic. Overall, this approach is good and straightaway makes the research questions of the study clear. However, the language needs to be improved overall. I have included suggestions and comments for refining the introduction below, but this is not a comprehensive list, particularly with respect to the grammar.

Lines 36-37: This first sentence is a little clunky- methane gas itself does not provide environments or habitats. And do you mean unique fauna whose nutrition is derived directly or indirectly, largely independent of photosynthetic primary production?

Line 38: distinct response of benthos/benthic community as  expressed as xxx?

Line 41 and 42: you first say Arctic Ocean, and then say HMMV is in the Norwegian Sea. I completely understand the difficulty with the terms, but this terminology is confusing and appears contradictory. Perhaps you can modify it to simply ‘the Arctic’ in line 41, and refer to HMMV being in Nordic waters? Also,  you should probably include references to seep sites in the Barents Sea and the Vestnesa site in lines 42-43 as you mention the most studied Arctic seep sites.

Line 45: the way this sentence is currently structured, it seems like the text in the parentheses refers to the photic zones being at 200 and 1200 m.

Line 48: ‘reaction of macrofauna’ is not appropriate language here. It is not the reactions or the responses of the animals/fauna per se that you are examining. Rather, it is how the benthic community is altered by the presence of methane seepage. Please change this throughout.

Line 50: what depth boundary? Ie, what is the boundary of approx. 200 m a boundary for, with respect to CBEs in shallow vs deep locations?

Line 52-53: modify after bivalves to ‘and overall mainly consists of species not unique to methane seeps.’ It might be helpful to include the aggregating part of the sentence as a separate sentence (e.g., this subset of regular/background Arctic benthic fauna tend to aggregate around sites of methane seepage…)

Lines 58-60: This sentence is supposed to be a general statement about seeps, and not specifically about Arctic seeps. In that case,  seeps tend to have higher biomass but lower diversity compared to the background overall, not higher diversity as stated here. It is true that in the Arctic though, this trend has been questioned (Gebruk et al., 2002, Sen et al., 2018 Biogeosciences) and even shown to not be true (Åström et al., Limnology and Oceanography,  Sen et al., 2019 PeerJ). Please specify and clarify.

Either in in the introduction where gas flares in the Laptev Sea are discussed (briefly), or in the Methods section, some additional detail on the two examined seep sites would be helpful. The figures with the ‘maps’ of the sites and their sampling are white squares and only low resolution bathymetry from Jakobssen et al./IBCAO is used for showing the site locations overall. Some bathymetric maps would be very useful, particularly with locations of flares marked. Is there any information at all on the sources of the methane? In such a shallow setting, this would be useful to know, since gas hydrates are probably unlikely..?

Line 75: change to ‘preliminary descriptions of bottom fauna observed in video are described …..’

Figures:

Figure 1: As stated above, bathymetry maps for the enlarged maps of the three sites would be useful, particularly with gas flares marked on them. This is especially critical since in line 89-90, it says that in 2 years of sampling, station selection was based on where flares were mapped.

Instead of using cruise numbers (AMK 63, 69, etc.), I suggest using years instead.
Instead of a circum-Arctic map at the bottom, it might be more helpful to have a smaller map, showing for example, Russia, or just the Russian/European side of the Arctic. Since it would be possible to show more detail and zoom in more in a map with a smaller extent, the locations of the study sites could then be marked on the map itself, instead of an inset with low resolution bathymetry.

Scales, especially in the enlarged maps would be better being scale bars.

Figure 2: Simple station names would be preferable here (see comments about Table 1).  The labels/legend for the nMDS plot is also very confusing. Please don’t mix colour with symbol: for example, the controls are black, but the legend for site (C15, Oden and Control) is also black, which is confusing. Just one legend would suffice, with each symbol (unique in both color and shape, e.g, purple circle vs red circle) referring to one category. Also, please remove the boxes Primer puts in automatically (such as the SIMPROF box with a  green line, the box in the top left with the basics listed: all these can be mentioned in caption and the text).

Figure 4: Personally, I think that the data in Figure 4 would be better presented as a table.
Experimental design: This is original primary research that falls within the scope of the journal.

Research questions:

The authors do a good job of stating their research questions. Both in the introduction and in the discussion, it is quite clear what the focus of the study is. And it definitely fills an important gap. Arctic seeps in general have not been extensively studied and shallow water Arctic seeps in particular, are conspicuously absent in the literature. The context as well, of comparing shallow water Arctic seeps to the background benthos, and the main results, of finding significant differences in the benthos in response to the presence of seeps is important, making this study a well needed addition to the scientific literature.

Methods:

Overall, the methods are appropriate and adequately described. I have some suggestions though, that are detailed below:

Abstract and first line of Methods: Instead of saying ‘samples were taken……’, state immediately what was done (e.g., grabs and trawls were taken in order to examine macrofauna composition). Similarly, in line 84, please change ‘material was obtained….’ to be more specific.

Lines 85-86 and Table 1: The station names are very confusing. First, background 1-3 is difficult to comprehend, since it is at the C15 seep site and not at a control site. The text here does not mention background sites, it simply says that 12 grabs were done at C15, which appears to include these ‘background’ ones.

Ships and cruises have station names that follow certain nomenclature, but it is not necessary to have those in the manuscript. I suggest simplifying the station names. For example, the site name, with the year, followed by consecutive numbering could be an option (e..g C15_2015-1): At least it is important to use names that immediately make it clear which site is being discussed- it is tough to keep track of the fact that 5947 is C15 but 5953 is Oden.

In the text, it should probably be clearly stated that C15 only was sampled in 2015, and that a different grab was used in this year compared to the other two years of sampling.
Line 101 and 104: please change neutralized formalin to buffered formalin. Please check, but should it be 10% buffered formalin (vs 4% formaldehyde)?

In the Methods overall, regarding the analyses done, the text skips from what was done with grabs and what was done with trawls, which is very difficult to keep up with. I suggest first writing out what was done with grabs and then in a separate paragraph, describing the analyses conducted on trawl samples.

There are some language issues: change ‘weighted’ to ‘weighed’, line 119: density and biomass were scaled up to per square meter, line 118-119: square root transformation does not ‘increase the role of rare taxa’, but it does compress larger values more than smaller values, etc.
Validity of the findings: The statistics and analyses overall are appropriate and I don’t think need to be modified as such. However, I do recommend certain modifications to presentation and discussion of results and analyses.

I don’t understand what C15-seep refers to, since the C15 stations are also seep stations. Understanding this would probably help towards understanding why seep 1 and seep 2 so different from other seep sites, including other C15 seep sites. Is it simply that these two sites form their own cluster?

The authors discuss, in detail, the five clusters that they display in Figure 2. I understand that these clusters showed up at the level of similarity shown. But it would be better to approach the whole clustering aspect with some hypotheses. After all, any number of clusters can be ‘made’ based on the similarity index in question. It is more useful to think first, of possible, or expected clusters and then see if the data follows expected patterns or not. For example, one could expect seep sites, control sites and seep background sites to form distinct and significant clusters. Perhaps one would expect the two seep sites to cluster separately as well. Whatever the case, there should be some justification for the clusters being examined, rather than the fact that they simply showed up. And then one can discuss aspects of those clusters such as dominant species, more or less evenness, etc.

In short, I recommend modifying this aspect of the manuscript to align with specific questions and hypotheses. This is particularly in light of the fact that it appears that the authors do have hypotheses in mind, for example, I think they expected seep sites to be quite different from, and cluster separately, from control sites. So please include this and reshape the discussion and presentation of the cluster analysis and nMDS to reflect this. Please note, this does not mean that you cannot discuss the 5 clusters that are currently discussed: it is absolutely acceptable to discuss expected results and then discuss the obtained results, for example, in this case, you would say that in addition to the expected clusters, an additional cluster was the two C15 sites that did not cluster with other C15 seep sites. Furthermore, discussing the cluster analyses and results within the context of expectations and hypotheses would introduce the idea of seep background sites early on, which is needed. It is not clear whatsoever what seep background refers to (as opposed to control sites) and I assume the authors mean something along the lines of areas peripheral, or on the edges of seep locations. But this needs to be explained early on. Also, it should be noted that the background sites are all from C15, ie, Oden has no background sites.

Table 2 and the Kurskal-Wallis tests for testing differences in abundances of taxa: I am not sure I completely agree with using this. I think it is more important to look at community differences and various aspects of the communities could contribute towards one community being significantly different from another, such as species richness, evenness, abundance of certain taxa, etc. I think this is covered in the cluster analysis and nMDS, and Figure 4 even lists numerous aspects by which the communities differ. So then checking if abundances of certain taxa are significantly different seems redundant and also putting an inordinate amount of emphasis on one aspect that contributes towards community differences.

Please change species number throughout to either species richness or number of species.

The use of ‘non randomly’ is not appropriate and not clear in meaning.

Since trawls were only taken at the seep sites and that too, just one each, instead of concentrating on comparing grab and trawl samples as the main focus of the trawl samples, I suggest using the trawl samples to provide more insight into seep communities.  Some of these discussions can overlap, for example, the fact that dominant species are different based on grab vs trawl samples. But the main value of the trawl samples is not to simply compare with grabs, in fact, that is not even really appropriate given that only 2 trawls were conducted. But rather, the value of the trawls is that they provide another view, for example, they provide data over more continuous area while grabs are more discrete sampling units. Based on the grab data, it was determined that different communities exist, even the two seep sites are significantly different from each other. The trawls can be used to examine inter-seep differences (or similarities) further. Presenting the trawl data only as a comparison to grab data is, I think, not completely appropriate and downplays the value of this data.

Discussion:

Similar to what I have noted for the cluster analysis, the Discussion would benefit from first stating hypotheses or expectations and then discussing the data in light of these hypotheses. Overall, my impression of the Discussion is that good ideas are introduced, but are not developed well and points don’t always flow well from one to another.
The discussion of increased biomass and abundance/density is confusing the way it is split up and in two parts (paragraphs 1 and 3 of the discussion). I understand that in one case, it is overall abundance and biomass and in the second case, you are referring to certain common species. But it is confusing the way it is. Also, the higher than background diversity of Oden warrants a discussion, since seeps and vents usually are seen as having lower than background diversity.

The section ‘taxa responsible for differences’ ends up being more of a discussion about common shelf species being present at the seep site. The heading should probably be modified to reflect this. In fact, this is something that should be developed further, ie, the fact that Arctic seeps host regular benthic species, albeit in higher numbers and even sometimes displaying higher diversity than the surroundings. Your findings therefore correspond with data from other Arctic seeps that indicate that Arctic seeps display a community structure quite different from seeps in lower latitudes and perhaps these ideas could be developed further here. However, later, there is a sentence saying that the seeps are defined by animals that are obligate for reduced conditions (even though only siboglinids are really obligate in that sense, though Decker and Olu have hypothesized that rissoid snails might be seep specific as well).

In the comparison between seeps and control sites, one important result that is not discussed, but really quite key, is that the control sites are more even, while the seep sites tend to be dominated by certain species. While the increase in biomass and abundance and in the case of Oden, even diversity, is important to discuss about the seep sites, the fact that the non seep sites display higher evenness is also a  very important finding that is only mentioned in the results, but not discussed any further.

Note that rissoid snails have been observed also at the Lofoten canyon seep site (Sen et al., 2019 Scientific Reports) and Decker and Olu 2012 (Marine Ecology) have used stable isotopes to determine that rissoid snails at HMMV graze on bacterial mats. Åström et al. are also publishing isotope signatures of Hyalogyrina snails that also seem to be grazers of bacterial mats at Barents Sea seeps (Marine Ecology Progress Series, in press). It would be good to have an image of at least shells of Frigidalvania  found in this study, since it is a new species. The authors mention that it was not seen in video imagery. Could this be due to the size? Rissoid snails at Norwegian Sea seeps are mm sized and are only distinguishable in images if the zoom is turned on.

The trawl data could be used to enhance the discussion on a higher variety of microniches at seeps. For example, since trawls are over larger distances, but grabs were taken near flares, it makes sense that grabs were dominated by Oligobrachia, whereas trawls were dominated by other species. Overall, this discussion needs more input: the provision of more habitat types at seep systems as an explanatory factor for the aggregating effect of seeps, including at high latitude seeps, has been discussed in a number of articles, but they are not referred to here. Neither are some of the niches, such as tubes of siboglinid tubes, bacterial mats and probably most importantly, carbonate rocks formed due to AOM. In fact, carbonates are not mentioned at all. Were they not present at all at the sites?

I like the hypothesis put forward by the authors, about oligotrophic conditions selecting for chemosynthesis based primary production at the shallow depths of the study sites. It is a pity though, that this discussion is so limited and resigned to the very end, almost as an afterthought. Is there any data to support their hypothesis, e.g., sediment organic carbon content at the study sites, seasonal data, etc.?

One point of discussion notably absent is a comparison between the two seep sites. The authors found that though the seep sites clustered together and separately from the control sites, the two seeps themselves formed distinct clusters. And even the trawl data revealed differences in the communities between the two seeps. Is there any environmental data that could contribute towards discussing the differences between the two seeps? Neither porewater chemistry nor sediment pigment data is presented, and bathymetry as well as information on carbonate concretions is also absent. It is hard to believe that no such information at all was collected. Not just for comparisons between the seep sites, but comparing between seep vs control and/or ‘background’ sites should also include information on environmental factors. The manuscript as a whole would greatly benefit from including some environmental information, since seep communities are so strongly determined by local conditions.
Additional comments: Thank you for publishing data on shallow seeps in the Laptev Sea. This will be a good addition to the scientific literature overall, though currently, some changes to the discussion are needed.


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: FAUNA ASSOCIATED WITH SHALLOW-WATER METHANE SEEPS IN THE LAPTEV SEA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a self-contained manuscript, relatively easy to read and understand. It adds to our knowledge of the distribution of species associated with seeps, particularly in shallow waters of the Laptev Sea. References are up-to-date, background and context are appropriate. Figures are relevant but need attention to some details. Raw data (taxa, abundance, biomass) is provided in a Supplementary Document, which this reviewer has not seen. It would be good to confirm that this data is provided for each sample and each trawl.

Figure 1. These maps do not show the location of the methane plumes for each site, nor does it show bathymetric data for context. In addition, it would be good to include scale bars – Lat/Lon is fine, but the length of 1 km, for example, would make it easy for the reader to understand in a glance the distances between sites (and relative to known seep flares).  What does AMK stand for?

Figure 2. Apparent ambiguity: Is A also biomass data square root transformed? Or just B as written.  If just B, what data was used for A? Are bot A and B needed? Or is the info redundant?

Figure 4. Should the order be Control, Seep Background, C15, Oden (seep?), C15Seep?  I.e., place like next to like and provide more descriptive titles? Should Seep Background really be “Control” as well? What about C15? Without some rules for how sites are named, it is hard for a reader to see at a glance what the authors mean to convey.

Lines 142-147: Seems an odd summary, since the focus of the study is on seep vs non-seep fauna. What do the authors expect the reader to take away from this paragraph?  Impossible to contrast seep/non-seep from this.

Line 156: correspondence with presence/absence of seeps – but without showing seep locations on Fig 1, this is impossible for the reader to evaluate.

Line 169: this reder remains confused about whether the C15 station group is seep or background(control).

Line 198: should read “comparison of seep and non-seep station groups”

Line 254: Confusing first paragraph – now the focus is on stations, not station groups.  “All gears” refers to two types of grabs and the trawl?

Line 270: Again, the focus is on stations, not station groups, yet we have learned that there are clusters/groups.  Why are they put back together again here? This does not seem analytically/ecologically sounds\
Experimental design: The experimental design includes 2 trawls across seep environments. Given that seeps are often recognized as vulnerable and colonized by long-lived, endemic taxa, it might be helpful to provide a justification for trawling. This reviewer recognizes that this could be a sensitive point, but felt it must be made; in this reviewer’s opinion, trawling as part of an experimental design for seep studies should be discouraged, unless an environmental impact statement makes it clear that there will likely be no serious harm. A survey with remote-sensing instruments (i.e., cameras) would have been ideal as a means to assess megafaunal diversity and distribution, rather than destructive trawling.  I think for this work, it is important to include the trawl data, but perhaps the authors could craft a way to indicate this is a less than ideal approach for assessing sensitive deep-sea habitats (with a brief explanation), with a note that in this case, it was expedient given tools available and that elsewhere seeps at such shallow depths do not support endemic taxa? The point I hope would be conveyed is that trawling is not what the deep-sea scientific community (or at least, many members of it) considers to be best scientific practice.

There is a bit of circular logic, defining seep sites by location and then defining seep sites by the faunal assemblage. The reviewer understands what was done, but perhaps the authors should be explicit in the methods about how they will define a seep based on the fauna?

Even anecdotal evidence of differences or similarities of seabed substrata among sites would be useful.  Were there authigenic carbonates at the seep sites? Any differences in sediment quality?

There seem to be some imprecision and over-statement.  Two examples from the abstract:
“The aim of this work was to understand the effect of seeping methane on benthic macrofauna at depths 60-70 m.”
The work does not look at the effect of seeping methane on benthic macrofauna. It does provide descriptive measures of faunal assemblages, some of which are located in close proximity to methane flares, from which association with methane seeps is inferred, but no measure of methane is provided, no direct association between macrofauna and methane concentration is reported.  And it may be that sulfide, which is typically co-produced with methane may have as much or more of an ‘effect’ in structuring benthic communities.  It is impossible to say from this data, though one may speculate.

“The development of specific methane seep communities at such a shallow depth apparently is related to pronounced oligotrophic environment on the northern Siberian shelf.”
Again, there is no experimental evidence of this; the authors do write “apparently”, but perhaps could be more explicit by expressing this as an hypothesis.

This reviewer has not scoured the ms looking for other ‘over-statements’.  These are not unusual to discover in initial submissions, but the authors would do well to look for these and turn any remaining unjustified statements into hypotheses and discussion of alternatives.

A key concern, as mentioned above, is how stations and station groups are analyzed either as sites or groups and then interpreted. There is a confounding of habitat types when the analysis is by site, as the authors show very well.
Validity of the findings: Given the finding of groups, the validity of site analyses is in question.

And as also noted above, some hypotheses are presented as fact, which is not valid.
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: FAUNA ASSOCIATED WITH SHALLOW-WATER METHANE SEEPS IN THE LAPTEV SEA
Review round: 1
Reviewer: 3

Output:
Basic reporting: see below
Experimental design: see below
Validity of the findings: see below
Additional comments: General: This is an interesting study that expands our knowledge of methane seeps to the shallow waters of the Siberian Arctic. The data are appropriately analyzed and conservatively interpreted. I have a number of relatively minor concerns that I itemize below. I believe, however, that the manuscript could be more clearly presented and have a greater impact than in its current draft. The manuscript needs to be edited by an English speaker to improve the grammar, syntax, and word choice. There are numerous grammatical errors and awkward sentences. I also found it very hard to follow because it was not always clear what was a seep community and what was reference. It is important to identify sites by station number so they can be cross referenced with other studies, but for a reader unfamiliar with the stations, cruises, etc. it makes it very difficult to follow and interpret the results. As I point out below, it is also important to show the spatial relationship between the samples and the flares.
Introduction
There needs to be more background on seeps in general. The introduction assumes the reader is well acquainted with seeps in the Arctic and at lower latitudes. One or two paragraphs should be sufficient. And there needs to be more review of the input of phytoplankton vs. methane derived carbon to seeps and the relationship to depth as that relates to the conclusions (expand line 49).
There also need to be more details on the Laptev Sea seeps. What are the characteristic features of the seep field (l 64-65)?
More details are need on the earlier cruises (l 69-72) or omit this section.
Methods
You indicate that seeps were identified by acoustic methane flares. It would be very helpful to indicate the relationship between the samples and the flares. You report that several grabs were off the mark as determined by their contents (which is circular reasoning). A map of grabs relative to the flares is needed.
What is the relationship between the trawls and seep sites. The maps need to clearly identify these relationships. I don’t think the trawl data contribute that much to the story, but frankly it is hard to tell because I don’t see their spatial relationship to the seeps.
L 85. This is where the description of the sample sites needs more clarification. Identifying sites as C15 and Oden are fine, but each sample needs to be identified as seep or non-seep.
L 47 Some of the sites from Åström et al., 2016 are less than 90 m.
L 100 ‘most’ grabs. Not all?
L 111 More detail on these indices. What H’- log10 or log2 or ln?
Results
L 156 More detail is needed here to help the reader see the patterns you are talking about.
Figure 1 As noted, the description of stations and their relationship to the seeps is very hard to follow. Clearly identify what is seep and what is background/reference. C15 has both.  Which is station 5625 for example? A reader needs to be able to get all they need from a figure and legend without refereeing to the text or table.
Figure 6 is not useful.
Table 2. The means of each of the stations need to be reported and then the statistical results of the KW tests can be reported in one column. The current format makes it very hard to see the results and impossible to see the magnitude of the differences.
Discussion
In general, there needs to be more discussion of the results in the context of other methane seep studies, Arctic and non-Arctic. The discussion is very narrowly focused and does not relate the patterns in the Laptev to other seep areas.
L 345 But Åström et al., 2018 used a 0.5 mm mesh. Some speculation on why none of the Arctic seeps have large bivalves would be welcome.
L 364 More discussion is needed on the importance of habitat. Carbonate precipitates as a result of anerobic methane oxidation and this enhances hard substrate and habitat complexity.  Work in the Arctic and elsewhere has addressed this.  The relationship between the n-MDS results and the microhabitats needs more support. You refer to ROV work in the area. What do images reveal about the habitat?
L 373 This is the only paragraph that really tries to interpret the results in a larger context. How do the primary productivity values compare to other Arctic seep areas? Is there a continuum? Are you suggesting you only get a methane response in shallow water in oligotrophic areas? What if there is strong pelagic-benthic coupling in deeper areas, would you not expect a response? That is an interesting hypothesis that needs to be developed more fully even if you can’t completely address it with your results.  Maybe a table comparing seeps, depths, water column productivity, etc. would be instructive. I can even see a conceptual model; some similar ones exist for vents.
You also need to discuss the differences within a site but between station types (Figure 2). There are seep effects and there are other spatial patterns, you neglect the latter.


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: FAUNA ASSOCIATED WITH SHALLOW-WATER METHANE SEEPS IN THE LAPTEV SEA
Review round: 3
Reviewer: 1

Output:
Basic reporting: see below
Experimental design: see below
Validity of the findings: see below
Additional comments: The authors have done a good job revising the manuscript and responding to the reviewers’ comments. I still have a few issues with the manuscript, which I outline below. These are relatively minor and though I feel they should be addressed should not prevent the manuscript from being accepted.
1.	The language is much improved, but is still in need of an English speaker editor. The following are some of the lines where the syntax, grammar, word choice, or preposition is wrong: 15 (awkward phrasing), 28 (among not between),34 (awkward), 37 (wording), 42 (same as line 15), 44 (certain increase??), 69 (for is wrong preposition), 74 (awkward), 86 (conduct not conduit), 90 (awkward), 107 (gear not gears, or better yet methods), 179 (wide range is awkward), 243 (densities), 259 (elsewhere not randomly???), 339 (not statically reliable? Not significant?), 498 (short arctic months is awkward).
2.	Line 157. Dunn’s test usually follows a Kruskal-Wallis why Tukey? Corrected for what?
3.	Line 247 Some place the total abundance needs to be reported and included in statistical tests/\
4.	L 472 Need to cite: Åström, K.K.L., Carroll, M.L., Sen, A., Niemann, H., Ambrose, W.G. Jr., Lehmann, M.F., Carroll, J. Chemosynthesis influences food web and community structure in high-Arctic benthos. Marine Ecology Progress Series 629:19-42. doi.org/10.3354/meps13101
5.	L 491 see papers by Åström. This is the key issue with the paper. You cannot separate the impact of the carbon source and habitat heterogeneity. Few can in this system. But, you need to be more explicit about the confounding issue.
6.	Your main point is lost. You need to draw a stronger comparison between oligotrophic and more productive areas. At least make it a separate concluding paragraph. There has been work done in a few other shallow water areas (Argentina for example; M.E. Bravo; mebravo@iado-conicet.gob.ar), that should be cited or referred to.
7.	I do not see the point of Figure 6. You cover the material in the text. A table with the percentages of the top 10 species would be more informative than the figure, which has very limited value. Can you make some predictions about other shallow areas?


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: FAUNA ASSOCIATED WITH SHALLOW-WATER METHANE SEEPS IN THE LAPTEV SEA
Review round: 3
Reviewer: 2

Output:
Basic reporting: Update and check suggested references and add references to support your statements in the article.
I recommend and overall check of the English language. Some parts of the text is confusing (eventually because of insufficient English?) and needs clarification.
Experimental design: No major comments.
See details for the attached document.
Validity of the findings: Authors provide support for their concluding findings. Community descriptions of fauna associated with shallow seeps in the Laptev Sea. Seeps are different from non-seeps and they highlight the distinct species Oligobrachia sp.
Additional comments: This is an interesting study because of its location (Arctic Siberian shelf) of these special type of habitats (cold seeps) and the depth of the study site. The study adds in new information of benthic communities at Arctic methane seeps. It is a strength that both seep and non-seep areas are assessed. I find the manuscript in need of both some general improvements and edits (grammar and minor figure edits). I believe, however, that the manuscript would improve by adding a short section or comment on pelagic-benthic coupling or productivity to match the discussion and links to the shallow seep-water systems and especially to the comments/statement in the last section of the discussion.


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: PUBLIC PRIORITIES ON LOCALLY-DRIVEN SEA LEVEL RISE PLANNING ON THE EAST COAST OF THE UNITED STATES
Review round: 1
Reviewer: 1

Output:
Basic reporting: Attached
Experimental design: Attached
Validity of the findings: Attached
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: PUBLIC PRIORITIES ON LOCALLY-DRIVEN SEA LEVEL RISE PLANNING ON THE EAST COAST OF THE UNITED STATES
Review round: 1
Reviewer: 2

Output:
Basic reporting: I have now reviewed the manuscript authored by Dr. Carpenter titled: “Public priorities on locally driven sea level rise planning on the East Coast of the United States”. In this manuscript Dr. Carpenter present and analyses survey data obtained from 503 people affiliated with coastal communities on the east coast of the US. The goal of the survey was to assess the values of the public and stakeholders on sea level rise planning. I believe that the information collected and synthesized by Dr. Carpenter could be helpful for management and planning efforts. The English was clear and unambiguous. References appeared suitable, although: you may want to briefly (1-2 sentences) describe likert-type scales and provide citation.

I believe that the author should consider improving the presentation of his information. I would encourage synthesizing the information in figures, which may be a better way to communicate (e.g., findings about vulnerability to hurricanes for residents vs non residents could be plotted in a bar chart to contrast the differences, the table could still be included), pie charts (or other figure types may also help). Providing high quality and informative figures may make the article more appealing to readers. I would suggest that the author refer to tables, figures (or provide effect sizes) when making a statement, such as on lines 268-270 or to justify each finding. I found the discussion and conclusion very atypical, and I would suggest improving these sections. I would also justify each findings by referring to figures, tables and statistics.
Experimental design: This was a basic survey and randomization was not considered for this study
The statistical analyses were also fairly basic (e.g., a more thorough analysis would have possibly involved the use of hierarchical models) but given the descriptive nature of this manuscript, these advanced analyses may not be necessary.
Validity of the findings: With respect to the choices of tests, I would suggest picking one test or the other (parametric or non-parametric but I wonder why include both). I would also provide the appropriate tests for the t-test (homogeneity of variance [the author mentioned Levene’s test but it is not included in the results], and normality test, the two group means and standard deviations. By the way, these tests do not provide information about the magnitude of the effect, so it may be useful to compute the effect size (e.g., arithmetic difference and associated uncertainty, e.g., 95%CI around the estimate of effect size).
Additional comments: Minor Comment:

l. 31 you may want to add measure of uncertainty.
I would suggest improving the format of the figure, in my opinion it does not meet publication standards.
You may want to briefly (1-2 sentences) describe likert-type scales and provide citation.
l-155 to 157, I would think that this information could be moved to the methods section (instead of the results).


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

Input:
Title: PUBLIC PRIORITIES ON LOCALLY-DRIVEN SEA LEVEL RISE PLANNING ON THE EAST COAST OF THE UNITED STATES
Review round: 2
Reviewer: 1

Output:
Basic reporting: Although, the authors addressed the comments point by point, I feel like some of the added text was unclear and not well written (see two examples below).
"Likert-type responses are a method to measure, among others, things that are perceptions that cannot be directly measured (Boone, 2012; Carifio, 2008). "

"Given the large sample size and clearly marked scale, or these controversies, the analysis of this data takes a hybrid approach by providing descriptive statistics including means, but the means are primarily used to describe the frequencies of responses."

I strongly encourage the author to work on improving the writing of the added text throughout the paper.

Also please clarify the following:
For example, in a real options approach, adaptation measures that can be exercised in the future as scenarios unfold can be developed while acknowledging the uncertainty associated with them (Dobes, 2018; Linquiti and Vonortas, 2012).
>Definition of "real option approach" is unclear.

In my opinion the format of the figure should be improved. I would suggest adding legends to the vertical axes on the figures (Figs. 3 and 4)
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: ON THE IMPORTANCE OF SPATIAL SCALES ON BETA DIVERSITY OF CORAL ASSEMBLAGES: A STUDY FROM VENEZUELAN CORAL REEFS
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. English used throughout the manuscript is clear and unambiguous.

2. Literature references are complete. They are sufficient and adequate to the topic presented and discussion of results.

3. Professional article structure, figures, tables. Raw data shared.

The authors comply with the structure that is required for this type of article, where they include relevant and complementary images to the manuscript, as well as raw data shared in a CSV text file.
However, the authors should consider next comments for some figure captions for clarified the information presented.
Figure 1: Mention which sites correspond to each region.
Figure 2. Mention that in all PCO ordinations, the variation of coral assemblages is shown at the site level nested into locations.
As a suggestion, I have seen in the whole manuscript, which is used "coral community" and "coral assemblage" in a similar way. I believe the most appropriate is to use "coral assemblage" instead of “coral community” for avoiding confusion.

4. Self-contained with relevant results to hypotheses.
The hypothesis of the article is presented in the lines 95-97. However, I consider this hypothesis very simple and does not provide enough details of coral beta diversity variation concerning the presence of different environment setting described along the Venezuelan coast. The hypothesis should be more explicit, where the particular hypotheses of each spatial scale considered in the experimental design are described.
Experimental design: This work conforms to the aims and scope of the Peer J journal.

This work provides relevant information to know the variation of the composition and coverage of coral species in the western Caribbean. However, their approach and experimental design are not adequate to answer the questions asked in this work.
I consider that this study has a rigorous investigation performed to a high technical and ethical standard, based on non-extractive benthic surveys following the guidelines by the Global Coral Reef Monitoring Network-Caribbean (GCRMN), and using the photoQuad software to identify coral species and their coverage.

Methods and data analysis were described without enough details, and it is not totally possible to replicate them.

Lines 117-123. The proposed experimental corresponds to a fully-nested and unbalanced multifactorial model, where the factors were: i) Region with three levels (West, Center, East); ii) Location with seven levels (2 to 3 localities per region); iii) Reef sites, 4 to 7 per locality; iv) Four transects per reef site. Sampling effort was obtained with 60 photos per site (15 per transect).
It is necessary to mention there are localities with coastal and oceanic influence, and some of them are continental or insular. The oceanic locality has different oceanographic conditions than coastal localities, as mentioned in the discussion section. Likewise, there is a difference in the environmental conditions between continental or insular localities. On the other hand, is the human impact different across all localities and reef sites? It is known that anthropogenic impact can affect the variation of coral assemblages. Therefore, it is necessary to explain, if the analysis of the fully-nested model of the spatial variation (i.e., longitude and latitude) of the coral assemblage, includes the natural variation of the sites when considering their coastal/oceanic, continental/insular influence, as well as the effect of human disturbance.

Inline 136, it is mentioned that two types of matrices were obtained using photo-quadrats, one with the relative abundance of coral species, and the other with data on the coral species presence/absence. For this, I reviewed the raw database that the authors included along with this article; thus, I have several comments:

i) Why were relative abundances of the species used and not the absolute abundance that represents the current live cover of the coral species? I believe that the absolute cover represents the current conditions of coral assemblage, as well as the change of its beta diversity across different spatial scales.
ii) When reviewing the raw database, I found that the lowest values per species are 20% relative abundance. I consider that this value is high for those species of low abundance and restricted distribution, which can be considered as rare. The latter species are those that most contribute significantly to beta diversity.
iii) The taxonomic resolution of the identification of any species is fundamental for the analyzes that evaluate the variation of its beta diversity. In the raw database there are the following categories: Other (Scleractinian encrusting), Other (Scleractinian foliose), Other (Scleractinian massive), Other (Scleractinian plate), and Other (Scleractinian solitary / other); as well as several genera of coral with undetermined species, which can be considered as coral taxa. In the case of the "Other" categories, each category is considered as a particular taxon in the analyzes; however, it is not known how many taxa exist within these categories. Although in these categories, the relative abundances are low, and the frequency is few, numerically they are relevant when analyzing beta diversity because this potentially increases the species turnover. In this work, how is it justified to use the database with these categories, and how can this affect the estimation of the variation of the coral species beta diversity?
iv) Photo-quadrats were used as true replicas nested within the transects. However, about 50% of 2,134 photo-quadrats have zero relative abundances, since I consider that no species or taxa of corals were recorded. I believe that this is a serious problem since there are a large number of zeros in the replicas with which the average dissimilarities of the species in the multi-scale nested design are estimated, which should affect the estimation of beta diversity. One option to reduce this bias is to use these photo-quadrats as Pseudo-replicas nested within the transects. Thus, the transects could be used as true replicas with the composition and average absolute coverage values of coral species. If this option is considered, a spatial scale would have to be eliminated in the experimental design. Thus, it would only be:
Y = Region + Localities(Region) + Sites(Localities (Region)) + error
If the authors consider not to follow this suggestion, then they should justify how this large number of zeros in the samples (photo-quadrats) does not numerically affect the estimation of the dissimilarities of the species across the different spatial scales analyzed.

Lines 139-145. It is necessary to describe the pre-treatment of data to be able to build the similarity matrices of Bray-Curtis to develop the PERMANOVA model and PCO ordination.
I want to comment that in order to carry out the analysis of the beta diversity assessment, it is essential to know which species favor the species turnover rate, or well, the species dissimilarities within each spatial scale studied. In this study, PCO ordinations were only used to visualize the change in species similarity at the reef site level, where Pearson correlations> 0.7 were used to identify which coral species contribute most to the structure of coral assemblage. I consider that to complement this analysis (PCO), it is necessary to perform a similarity percentage analysis (SIMPER) based on the same experimental design (fully-nested model), pre-treatment and similarity matrix used in the PERMANOVAs. This SIMPER is to identify and estimate the species that contribute most to the beta diversity (average dissimilarities) change at each spatial scale with significant differences (see PERMANOVA Table).

Lines 146-147. The information described on how the canonical analysis of principal coordinates (CAP) was done only mentions that it was done with the coverages of scleractinian corals and their latitudinal and longitudinal position. This information is not enough to understand how the CAP design was carried out since it is not known if the CAP was performed at the level of photo-quadrats, transects, reef sites, or locations. What kind of species similarity was used to perform the CAP?
I believe that the results of the PERMANOVA model should be used to make this analysis (CAP) and use the spatial scale that most contributed to the explanation of the variation in the change in the dissimilarity of coral species. In this case, the spatial scale of the reef sites can be used.
On the other hand, why were latitude and longitude only used as explanatory variables in the CAP? There are many variables associated with them, such as the upwellings along with the change in longitude, and the oceanographic variables associated with the latitude. Is it possible to obtain information on these variables (upwellings and oceanographic variables), perhaps with values on an ordinal scale, to make a more robust analysis? It would be interesting to know if the authors could have other environmental variables at the reef site scale, in order to improve data analysis, such as rugosity (topographic complexity), depth, other structural elements of the habitat (eg, live coral cover, macroalgae cover , sponges, turf and other types of substrates), and human impact variables. These kinds of variables can be used as predictive variables to explain the variation of the beta diversity of coral assemblage? With this information, it is possible to perform analyzes such as a canonical redundancy analysis (RDA) or a canonical correspondence analysis (CCA).

Lines 149-150. The differences in beta diversity were tested across different spatial scales using a test of homogeneity of dispersions (PermDisp) based only on presence/absence Jaccard similarity, based on the criteria of Anderson et al. (2006). But to complement the results of PERMANOVA, why was the Bray-Curtis similarity not used to carry out the PermDisp? In order to be able to infer whether the variation of the change in the assembly of coral species is given by location effects, dispersion effect or both.
On the other hand, when reviewing Table 2, the results of each PermDisp by spatial scale correspond to a one-way analysis. How can its use be justified, since the fully-nested design cannot be incorporated in the way the analysis was done? For example, I mean that by observing the significant variation of the smaller scales, and when analyzing the result obtained at the level of transects, PermDisp analyzed and tested the homogeneity of the dispersions of all transects but without considering the structure of the nesting: Transects(Sites (Localities (Regions))).
In the case of the analysis of beta diversity partition based on the strategy of Baselga and Orme (2012), it was performed in the same way as PermDisp, because the change in beta diversity, and their respective components, were only tested by spatial scale regardless of the nesting design. It would be interesting to know how the contributions of the species turnover and nestedness change within each region.
Finally, it is necessary to mention which were the samples used to develop the PermDisp and the partition of beta diversity by spatial scale. For example, were transects used to analyze the spatial scale of reef sites? Were the sites used to analyze the locality spatial scale? If so, the nested design was used in some way.
Validity of the findings: The results are well written and match what was found in the data analysis. However, if the authors decide to make some of the suggested changes in the used methods, some of the results of the different numerical analyzes may change.

Lines 178-189. The results of the PermDisp and beta diversity partition show that small and local scales are the most important to explain the variation of beta diversity, which suggests that environmental and spatial heterogeneity at this scale are essential to explain the coral species turnover. In that sense, it is important to consider other data analyses that assess the relationship of the change in the composition and cover of coral species with environmental variables (habitat structure, human or other) on a local scale (e.g., reef sites). Likewise, it is relevant to know which species favor dissimilarities (or beta diversity) and with which environmental variables they are related.
The discussion section is well written, and a good relationship of the results is made with published literature. However, this section may change if the reviewers consider making some changes to the methods used.

Line 206-209. What are the other spatial scales associated with residuals?

Lines 284-285. There is no analysis in this work to be able to accept the statement that upwelling alone is not sufficient to explain the extremely variable nature of the coral assemblage.

Lines 292-295. I suggest giving greater emphasis to the importance that coral assemblages have greater beta diversity on local scales. This suggests that there may be significant environmental heterogeneity within reef habitats, which could mean that coral assemblages still have adequate conditions on the coasts of Venezuela in comparison with other Caribbean areas.

Line 300. Delete the parenthesis in the year of the appointment (Zvuloni et al. 2010).

Line 320-322. It is mentioned that "upwelling-related processes could be targeted as potential candidates to explain longitudinal variation of coral communities, whereas oceanographic/coastal processes could explain latitudinal variability". While on lines 284-285, the opposite is mentioned: "upwelling alone is not sufficient to explain the extremely variable nature of coral community". What is the correct position of the authors concerning the relationship of the upwelling effect on the coral beta diversity?  I recommend exploring whether it is possible to evaluate the effect of these variables (upwelling effect and oceanographic/coastal processes) on the variation of coral assemblage.
Additional comments: The work performed by Miyazawa et al., entitled “On the importance of spatial scales on beta diversity of coral communities: a case study from Venezuelan coral reefs”, makes a multiscale analysis to identify the greatest variability of the coral assemblage beta diversity on the coast of Venezuela. For this, the authors carried out fieldwork where they obtained a considerably extensive sampling effort in different regions, locations, and sampling sites.

Their results are interesting and make a relevant contribution to scientific knowledge and the understanding of the processes of the variation of species turnover in coral ecosystems. However, I found some troubles in the section of materials and methods. I consider that this article should clarify some details of the data analysis and the results, as well as other details that should be addressed by the authors. Therefore, I consider that this article cannot be published in the form as it currently is. Authors could consider doing several corrections I have suggested.


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: ON THE IMPORTANCE OF SPATIAL SCALES ON BETA DIVERSITY OF CORAL ASSEMBLAGES: A STUDY FROM VENEZUELAN CORAL REEFS
Review round: 1
Reviewer: 2

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


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

Input:
Title: ON THE IMPORTANCE OF SPATIAL SCALES ON BETA DIVERSITY OF CORAL ASSEMBLAGES: A STUDY FROM VENEZUELAN CORAL REEFS
Review round: 1
Reviewer: 3

Output:
Basic reporting: several issues, see below
Experimental design: several issues, see below
Validity of the findings: several issues, see below
Additional comments: The subject of the ms is important for many aspects related to biodiversity, however this ms has some apparently serious issues that should be resolved

Estimating β-diversity requires an adequate estimation of the α-diversity of coral assemblages to be compared. However, at local scales α-diversity (transect? site? in this study) may differ due to location, reef, reef zone, zone patchiness, community history, environmental setting, biological interactions and catastrophic events; as elsewhere in the reef ecosystem.

Since adequate estimates of species diversity are directly related to sampling effort, the sampling design should take into account the potential sources of variability at the different sampling sites, and its effect on sufficient sample size. One way to do this is to find a sample size that will be sufficient in all instances, thus allowing for direct sample comparison.

However, this study is based on a standard sampling protocol and the reader wonder if the sampling was adequate to properly address the questions posed. I believe that addressing in detail the following points would give credibility to the study:
1.	How similar were the seven study sites in terms of reef zonation, exposure and general setting?.
2.	Why CHI site is not considered as part of the East region?
3.	Demonstrate that transect length was adequate for each surveyed site and that four transects is a sufficient number of such transects per site
4.	Please explain the spatial layout of the transects on each site and how such layout was decided
5.	Please explain the pros and cons of a systematic transect sampling, instead of a random one to assess diversity.
6.	Please explain why 15 photos were taken per transect instead of the 30+ that could be obtained (NOTE: regarding the assertion on line 128 that transect photos of the same transect are replicates: As images are taken along a limited space along the transect, instead of randomly on the study site, they are pseudo-replicates; true replicates would implicate a random layout).

An issue of great concern is related to the above in conjunction with a unit sample size image of 80 by 90 cm, image that is further subsampled by 25 random points. Perhaps if communities were composed by rather small size colonies such approach would be OK, but not so if coral assemblages are dominated by relatively large colonies because these will occupy large image sections or whole images and this will further reduce sample size for diversity estimation. This may be the case in this study as the ms indicates that Orbicellas, Pseudodiplorias and Colpophyllias dominate (line 302-303, Fig 2).

As this is a rather important concern I tried to resolve this doubt by means of the supplemental raw-data sheet provided, however the *.csv file has a sort of continuous line format useless to discriminate species/sample info (so, it is not truly supplementary materiel). Nevertheless, is possible to observe a large quantity of zeros in every line, presumably corresponding to different species values, further increasing the above concern. On the same tenet relative homogneization at the regional levels could also be a result of sufficient sample size. All these require a detailed clarification by authors.

Given the above, I consider that the above questions have to be properly addressed to consider  publishing this study

However, a few more comments to the authors:
•	An issue of over dispersion may severely affect the permanova analysis, so it is necessary to validate such analysis.
•	it may be that the transect factor level is difficult to justify. If so, I suggest to reanalyze with site as the lower level
•	Latitudinal relevance could be related to island vs continental, perhaps a post hoc site comparison could help in clarifying this
•	Justify the inclusion of correlation vectors on the PCO plots and its interpretation in that particular type of diagram
•	Explain the values in the axes of the PCO diagrams and what each plot means
•	It will be adequate to explain how a dispersion analysis could be applied to absence/presence data

While the ms is well written much of it has been said before. In the introduction by Beselga and several other authors; in coral community and β-diversity patterns sections by many other authors as well. I will suggest, once the methodological issues are resolved to concentrate in the homogenization of diversity problem and in this case to what extent estimates of nestedness and turnover could be a sampling artifact over valid estimates.


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: ON THE IMPORTANCE OF SPATIAL SCALES ON BETA DIVERSITY OF CORAL ASSEMBLAGES: A STUDY FROM VENEZUELAN CORAL REEFS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The English used in this second version is from my point of view is clear and unambiguous.
This manuscript presents an adequate introduction that introduces to the main problem addressed by this work. All literature cited is necessary, and it was correctly cited.
The structure of the article (manuscript, figures, tables, raw data, and supplementary material) complies with what is requested in the instructions for the authors.
This work presents relevant results related to the hypothesis presented.
Experimental design: This second version used an experimental design that tests the proposed hypothesis and achieves the objectives of the work. This new experimental design is more explicitly understood why it is important to analyze the spatial variation of coral assemblage among different scales.
Statistical analysis models agree to this experimental design. The numerical methods used are correct to analyze the spatial variation of the coral assembly at multiple spatial scales.
The assessment strategy of coral beta diversity was also adequate to get important results on how species turnover and nestedness vary at different spatial scales.
This new version provides more detailed and clear information on the methods and analyses used, which allows us to replicate them.
Validity of the findings: The results of this work show that coral assemblages in Venezuela have an important spatial variation. Thus, their species composition and coverage were mainly explained by local and intermediate scales due to greater spatial heterogeneity. This result supports an important contribution of coral species turnover at these spatial scales. All the presented results are supported by several statistical analysis.
The conclusions are appropriately stated and based on the results and the stated hypothesis.
I found only a few minor details:
Line 82. Change the lowercase letter g of the word Gonzalez to a capital G.
Line 200. Remove the first parenthesis in ((Figure 3).
In Figure 3 use italic letters for scientific names of coral species.
Additional comments: First of all, I congratulate the authors of this article as they improved it considerably because they followed most of the suggestions made in the first version.
I consider that this version of the manuscript has the necessary quality to be accepted and published in Peer J, once minor corrections are corrected.


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

Input:
Title: ON THE IMPORTANCE OF SPATIAL SCALES ON BETA DIVERSITY OF CORAL ASSEMBLAGES: A STUDY FROM VENEZUELAN CORAL REEFS
Review round: 2
Reviewer: 2

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