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: GLYCOSYLCERAMIDE MODIFIES THE FLAVOR AND METABOLIC CHARACTERISTICS OF SAKE YEAST
Review round: 2
Reviewer: 1

Output:
Basic reporting: See the confidential note to the editor
Experimental design: See the confidential note to the editor
Validity of the findings: See the confidential note to the editor
Additional comments: OK Accepted


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: GLYCOSYLCERAMIDE MODIFIES THE FLAVOR AND METABOLIC CHARACTERISTICS OF SAKE YEAST
Review round: 2
Reviewer: 2

Output:
Basic reporting: The heatmaps (Fig 1 and Fig 2) are uninformative and unprofessional, mostly because the values are not properly normalized to facilitate visualizations of patterns and differences in the compound concentration. Why don't use MetaboAnalyst to generate the heatmaps?
Experimental design: The experimental design chart should be more professionally done and as Fig 1 to help understand the manuscript
Validity of the findings: No comments
Additional comments: Since the current Figures are not informative and there are not so many metabolites, it is more appropriate to have a table listing the concentrations (and p values) of significant metabolites as done in many metabolomics publications (not as supp. material)


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

Input:
Title: EXOTIC LAGOMORPH MAY INFLUENCE EAGLE ABUNDANCES AND BREEDING SPATIAL AGGREGATIONS: A FIELD STUDY AND META-ANALYSIS ON THE NEAREST NEIGHBOR DISTANCE
Review round: 1
Reviewer: 1

Output:
Basic reporting: Dear Authors,
I have had the privilege of reviewing your manuscript sent to PeerJ for eventual publication. After reading the manuscript with great interest, I can say that it contains valuable information that helps us to understand much more the ecological relationships between top predators and their trophic resources. You make a very complete introduction, a comprehensive literature review, and provides an excellent background to demonstrate how your work fits into the broader field of knowledge. Figures are clear and explanatory enough. Supplementary material substantially helped to me to better understand your analyses. The Hypothesis and predictions are clearly exposed. Statistical procedures are adequate, and easily understandable. However, I have detected a number of shortcomings diminishing the general robustness and the communicational effectiveness of the manuscript. Below, I indicate the main shortcomings you should address.

Title
I think that title is little precise. Perhaps a more appropriate title is: It is abundance and breeding spatial aggregation of eagles driven by an exotic lagomorph in Patagonia? A meta-analysis on the nearest nest distance offers some evidence. I suggest this because your analysis has certain limitations that prevent categorically assure that abundance of eagles is directly influenced by the abundance of hares. (see Experimental Design section).

Abstract
The abstract should directly to reflect the contents of the manuscript in a precise, concise and informative manner so that it can stand alone. Your abstract does not meet these requirements. I suggest you re-elaborates the abstract by doing the following:
(i) Synthetize the two first sentences in only a short, informative, and significant affirmation, or simply delete them;
(ii) Remove the first affirmation. It does not contribute anything;
(iii) State your aim or hypothesis. For example: We examine the potential relationship between abundance and breeding spacing of the Black-chested Eagle (Geranoaetus melanoleucus) and abundance of the European hare, its main prey, in the Argentine Patagonia;
(iv) Orderly and concisely describe your study design (e.g., study area, date), field procedures, and analysis. For example: We did this through three steps. First, by using a correspondence analysis, we analyzed the field abundance of six species of raptors, including the BBE, in relation to the hare abundance. Second, we estimated the breeding spacing of the BBE in two selected site with high abundance of hares by using the nearest neighbor distance (NND) metric. Finally, we evaluated if NND in BEE deviates from the expected distance according its body weight by performing a meta-regression including others raptor species with similar ecological requirement,
(v) Provide your results following the same order of the above-mentioned procedures. Here you should indicate the values of the NND in the two selected sites with high hare abundance, and that such values deviated from expected; and
(vi) Replace the last affirmation by a comment or conclusion more directly related to your results or hypothesis testing.

Introduction
Perhaps this section could be shortened. In paragraph 5 (lines 84-98) you provide information that is not relevant to the paragraph’s central idea (lines 91-98). I suggest removing it because the same information is given in Methods section. In the last paragraph (lines 100-112), you should note that the idea in the first sentence is similar to hypothesis statement. Please, try to be more precise and effective in writing this paragraph. For example, you should to say: Here we hypothesized that abundance and breeding spacing of the BCB eagles in Patagonia will be strongly influenced by the abundance of its principal prey, the exotic European hare. Then, include your predictions. Finally, you should offer some comment on the significance of your study. All comments related to methods should be removed as this is explained later.

Methods
In the Species Study subsection, line 129, the reference Ferguson-Lee & Christie 2001 is not a primary reference, and it is not necessary here.

In the Raptors and Hare Densities subsection you should indicate what and how many sites were included in your analysis for establishing the relationships between abundances of the raptors and the abundances of hares. This information is not provided here nor Fig. 1. Note that this an important information for better understand your design.

In the subtitle “Nearest neighbor” you should add “nest” at the end.

In the Bibliographic Search and Meta-analysis subsection, lines 181-182, you affirm that “To compare our results with other similar species we conducted a bibliographic search of studies disclosing NND of other raptors worldwide”. I think that you do not do this to compare precisely your results with other studies, but you do this to detect if the nearest nest distance of the bee deviates from expected in relation to body weight. Please, review. In the second paragraph of this subsection, line 201, you should briefly justify why you use a random-effect model, and some additional dots of information. For example: What were the random variables? What was the statistical power?

Results
In the last paragraph of this section, you do not say what you should really say: The average NND was lower than expected in relation to body size, indicating that eagles tended to reduce their reproductive spacing.

The subtitle “Relationship between body size and NND in raptors” should be rephrased as “…raptor body weight and NND.

Discussion
In line 277, Form is From?. In the first sentence in the paragraph 4, lines 289-290, you repeats a same idea than in the above paragraph. I suggest delete it.

Conclusion
You should rather mention something about how did your analysis answer your questions. Also you should recognize limitations of your study, and how they could be overcome in future research.

References
Here, you should be careful with style of journal. I have detected that literature is not appropriately referenced.
1.- Delete all point after the initial letters of author name, excepting the last author.
2.- Give the complete name of journals (lines 326-327 and 439-440).
3.- Write the paper title with capital initial letter only when you initiate the sentence. Of course, proper names should be given in capital initial letter too (lines 335-336, 367-368).
4.- Provide the volume of journal in line 385, 402, and 456.
5.- All journal titles should be given with capital initial letter (line 387, 394, 442, 465, and 488). 6.- The reference of Martin and others 1996, and Vitousek 1990 are incorrectly referenced. The correct citation of Martin and others is Martin 1996. In the case of Vitousek 1990, the original paper was published in Oikos 57: 7-13.
7.- In line 478, Buteo polyosoma should be written in cursive.
8.- Conventionally, The Auk, The Wilson Bulletin, The American Naturalist, El Hornero, etc, are  referenced without “The” or “EL”.

Figures
Figure 1 is little informative. On the map you should indicate the following: (i) roads or highways where you made the census, and (ii) location of site where you evaluated raptors and hare abundances. In figure 2, what axis correspond to hare abundances and what to the raptors abundance?

Language
In general, English is good, but requires revision by a native English-speaking researcher. The main aspect that should be reviewed is morphosyntax.

Coherence
I feel that when explaining your analysis procedures there is a certain lack of integration of the pieces of analysis that try to test your hypothesis. For example, the explanation about of use of meta-regression to find expected and observed body weight is not well assembled to previous NND analysis.
Experimental design: Your research question is clearly defined, relevant, meaningful, and is try to fill a knowledge gap about how abundance of an exotic prey can drive the breeding spacing of top predator. In general, the field work appear be rigorous and exhaustive. Statistical procedures and analysis tools are all adequate. Method are described with sufficient information to be reproducible. However, you need provide much more details about your research and analysis protocols.

1.- As above mentioned, you should explicitly indicate what and how many sites were included in your analysis for establishing the general relationships between abundance of raptors vs abundance of hares. Although you provides these information as raw information, readers need rapidly know the number of sampling units sustaining your analysis. In addition, for immediate transparency, you should provide a table with number of each species in each sampling site, without the need to review supplementary material.

2.- As also above mentioned, it is important you justify why you use a random-effect and mixed-effect models, providing additional dots of information. For example: What were the random variables? What was the statistical power? What was the effect size?. Perhaps, you also could shortly mention advantage and limitation of using meta-analysis. In many cases statistically significant findings would not reflects a true biological effect.
Validity of the findings: Although all analyses are correct, there is an important variable that was not included here, the spatial availability of nests. The absence of this variable in the study makes results partially inconclusive. For example, distribution and abundance of raptors, excepting the eagles, could be also influenced by availability of nest substrates. The greater closeness of Falco sparverius with eagles in the correspondence analysis may also be due to the fact that the first, which does not consume hares, can nest in rocky cavities. On the other hand, Buteo polyosoma shows a tendency to nest in trees (What was the availability of trees in the studied sites?). Undoubtedly, as you well claim, territoriality may be strongly influencing the presence of B. polyosoma in sites with eagles. However, if we do not know the availability of nesting substrates, we cannot know how this variable is influencing the assemblage structure of Patagonian raptors. On the other hand, although the local high abundance of hares could cause an eagle aggregation, if there are not an aggregate availability of nesting substrates, then couldn't really have a reduction in breeding spacing. Please, explain and discuss much more why such variable was not taken in account in your analysis. Was availability of nesting substrates "evenly" distributed throughout the study region?

Finally, as above mentioned, you should better connect your results to the original research question. It is very important here that you recognize the limitations of your study, and how they could be overcome in future research. Limitation recognizing does not really invalid your findings, only make your research more transparent and honest.
Additional comments: Ideally, to test your hypothesis with strength, you should have compared the abundance and breeding spacing of eagles before and after the introduction of the European hare. Of course, this is impossible due to the lack of historical information about it. To cope with this, the ideal is to have compared the abundance and breeding spacing of eagles in areas with high and low abundance of hares. The measurements should have been made simultaneously (to control the effect of time), and on sites with similar availability of nesting substrates. If such conditions could not be met for logistical reasons, human costs, or natural conditions (e.g., similarly high abundance of hare in the entire study region, distribution of markedly aggregated nesting substrates), then it is clearly understandable why you do not answer your question in that way. I assume that for this reason you explore a more indirect way of testing your hypothesis: the "distance to the nearest neighbor nest" metric. This is a very creative and intelligent way to find answers to your research questions. However, as I mentioned earlier, there are several information gaps that need to be filled. Please explain and better justify your research design considering the comments given 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: EXOTIC LAGOMORPH MAY INFLUENCE EAGLE ABUNDANCES AND BREEDING SPATIAL AGGREGATIONS: A FIELD STUDY AND META-ANALYSIS ON THE NEAREST NEIGHBOR DISTANCE
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this paper, the authors examine raptor abundances and breeding densities of the Black-chested Buzzard-eagle (BCBE) in northern Argentinean Patagonia in relationship with abundances of an introduced lagomorph, the European hare. Authors also conducted a review and meta-analysis on the relationship between Nearest Nest (or Neighbor) Distances and body size for other eagles and related raptor species.
The article is well written. However, there are multiple issues that should be attended before this manuscript is ready for publication. References on the relationships between body mass and spatial distribution included in the manuscript should be revised since they are mostly for mammal species (Damuth 1981). Also the factor to correct body weight in the meta-analysis (exp -0.75) is the proposed by Damuth (1981) for mammalian herbivores. In fact, White et al (2007) found a weak relationship between density and body mass for birds with significantly lower exponent of -0.22.
Experimental design: Following are some concerns with regards of data analysis and experimental design.
First, component analysis is a graphic method employed to examine relationships between categorical variables. In their analysis, however, authors want to examine the relationships between continuous variables (species densities, individuals per square kilometers). Others parametric or non-parametric method providing values of the statistical significance of the relationships you are examining would be hence more suitable for your data set.
Second, authors analyze BCBE nest densities and NND statistics considering solely the abundance of one of its main prey as the driver of nests spatial arrangement. Such analysis was performed with data gathered in two areas with similar prey abundance and nest densities. While prey abundance can be an important factor determining nesting success and productivity of any bird species, spatial arrangement of breeding territories may be limited by other determinant landscape components, such as for example the availability of suitable nesting sites. This is especially true for a species requiring specific substrates for nesting as is the case of BCBEs (i.e. cliff-nesting). In this line, the two areas examined in this study were selected taking into account the availability of cliffs (Line 170) and a pre-existing high abundance of eagles nests. Hence, it is possible that the observed spatial arrangement and density of eagle’s nest may be the result of other habitat features (e.g. topography) rather than prey abundance. The fact that eagle’s densities in these two areas remain as high as those observed 20 years ago (although with a slight decline similar to that observed in hare populations according to the authors, Lines 293-296) also suppose a more stable and persistent component of the environment, such as nesting sites availability, rather than a temporal feature (prey abundances or availability) as the driver of eagles breeding densities. Otherwise, and aiming to test your hypothesis that hare density is determining eagles nest densities, you should provide information on NND for the target species across different scenarios of hare abundances (such as, for example, the remaining areas in your study site where hare surveys were conducted) but controlling by habitat characteristics (i.e. same or similar availability of potential nesting sites). Is important to note that selection (or exclusion) of species to be considered in the meta-analysis may also be affected by habitat spatial heterogeneity and clustered distribution of potential nesting or foraging sites as you agree in the case of fish-eating species that relies on spatially discrete water body sources (Line 188). Authors may also acknowledge that the case they are analyzing here for BCBE could be similarly affected by process and patterns that determined the exclusion of species from the analysis because such a clustered spatial characteristics (e.g. colonial breeding or other social traits). Thus, other specie-specific sources of variability on NND statistics should be considered.
Finally, I miss more detailed information about your sampling design and data analysis procedures. For example: How many transects were surveyed? (I found that information on the supplementary raw data sheet but this information is not in the text). As the study period extended during several years (2012-2014), where these transects repeated across the same season or where surveryed through different seasons? In that case, how did you deal with repeated measures or year effects? The manuscript will be improved by clarifying if the monitoring effort was equally distributed between years and surveyed areas by, perhaps including a table as supplementary material. Statistical procedures and the election of mixed or random-effect models in the meta-analysis are not explained in detail. For mixed effect models you should indicate moderator variables employed.
Validity of the findings: The experimental design and the statistical procedures employed need to be revised since weak in part authors findings and conclusions. Bustamante et al. (1997), which seems to be one of the first studies of the species in your study area, found that nest sites of BCB eagles where no located in areas with the higher European hare abundances. Furthermore, Bustamante et al (1997) report on differential foraging habitat-selection of adult eagles in comparison with immature individuals also supports a landscape component in the distribution of eagles rather than only prey abundance. These results contrast with the interpretation of your own results but they are no discussed in your manuscript.
Additional comments: General comments
L 104. NND acronyms is used ambiguously either for Nearest Neighbor or Nearest Nest Distance. Please, be consistent with its usage.

L 151. Change to read “During the austral summers 2012-2014…”. Also the 4000 km of roads surveyed during the study are referenced to the figure 1 but no roads are indicated in such map.

L 161-164. Correspondence analysis is a graphical method applied to examine relationships between categorical rather than continuous variables. See my previous comments with regard of the selection of statistical methods.

L205-209. Which was the moderator effect in these mixed-effects model?

L135-136. This sentence is supported by two references but a similar statement on the proportion of hares in eagles’ diet in lines 94-96 is supported by other two different references. Please, clarify. In addition, the lowest value reported for European hare frequency in eagle’s diet in a particular sampling site is 15% (Trejo et al. 2006). You should consider this value through the manuscript when refereeing to the proportions in which hares are represented in eagle’s diet.


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: EXOTIC LAGOMORPH MAY INFLUENCE EAGLE ABUNDANCES AND BREEDING SPATIAL AGGREGATIONS: A FIELD STUDY AND META-ANALYSIS ON THE NEAREST NEIGHBOR DISTANCE
Review round: 2
Reviewer: 1

Output:
Basic reporting: Basic reporting
Dear Authors (Barbar et al.)
I have again had the privilege of reviewing your manuscript #23439 resubmitted to PeerJ for eventual publication. In my opinion you did an excellent job in attending my comments and critics. I am fully satisfied with your responses to my queries and suggestions, and I can say that the information contained in the manuscript is now much clearer and more robust. Sincerely, I have very few new comments to add about this second version of the manuscript.

Title.
Ok.

Abstract
Ok. However, I suggest some few changes.
Line 17. Replace “Patagonia, Argentina” with “Argentine Patagonia”
Line 18. Replace “used resource” with “prey consumed”. The first term is too ambiguous and broad.
Line 27. Replace “…any other raptor in the Patagonian guild” with “…any other raptor species in the study area”
Line 29-31. For now, this conclusion is somewhat pretentious since your study have certain limitations and we do not really know what happens at the community level. Since your study is hypothesis-based, perhaps a better affirmation would be: "Our results support the hypothesis that high local abundance of prey leads to a reduction of the breeding spacing of its main predators, possibly due to that high prey concentrations breaks reproductive territoriality ...", [or alike].

Introduction
My only criticism here is that this section still seems quite extensive. If possible, synthesize a little more.

Methods

Study area.- Line 116, Replace “…in this area” with “on the entire study area”.
Study Species.- Lines 134-136. Perhaps would be informative if you provide some approximate estimation about nesting frequency in these substrate types.

Raptors and hare densities.- Lines 151-152. Please, indicate why you did survey raptors on this hourly range. Are all raptor species more active during the morning? or, Was the field work subject to logistic restrictions obligating to realize surveys only during first half of the day?

Results
Line 235. Here you affirm that the only significant variable affecting eagles abundances was the abundance of hares based on a p-value = 0.047. However, nowhere in the manuscript you indicate the threshold p-value on which you based to determine the level of significance. Please, indicate this in the Methods section.
Line 240-242. Here you should also comment somewhat on inertia percentage, apart you mention in the Fig. 1.
Line 266. Replace “field area” with “study area”.

Discussion
Line 278. In my opinion, the term “enhance” is very broad. I suggest replace with “change” or “modify”.
Line 1. 291-293. This idea is not well understood. Rewrite.
Line 324-326. I think this last statement has some value, but you must make it clear this is rather a speculation.

Coherence
From my point of view, objectives, hypotheses and methods are now much more integrated which has improved the overall coherence of the manuscript.
Experimental design: Experimental design
With new data analyzes and much more detailed explanations, the experimental design and statistical procedures are now much more comprehensible and coherent. Although you indirectly demonstrate a relationship between reproductive spacing and abundance of hares, I think that your experimental design allows to gather information that supports your hypothesis. In addition, your experimental design is reproducible.
Validity of the findings: No comments
Additional comments: Comments for the author
I am very pleased for your huge effort to improve the presentation of your manuscript. I thank you for having responded to all my interventions. I must say that many of the suggestions were made not to satisfy my own doubts or ignorance, but to benefit the understanding of the readers, many of whom (particularly students) may not be familiar with the methods used. On the other hand, as you already know, science is not a matter of "absolute" if not to gather evidence that supports a specific hypothesis. In this case, you gather enough information that supports your research hypothesis. Of course, future studies may corroborate or refute your hypothesis.


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

Input:
Title: A NEW LARGE-BODIED THALATTOSUCHIAN CROCODYLIFORM FROM THE LOWER JURASSIC (TOARCIAN) OF HUNGARY, WITH FURTHER EVIDENCE OF THE MOSAIC ACQUISITION OF MARINE ADAPTATIONS IN METRIORHYNCHOIDEA
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Ösi et al describe a new species of metriorhynchoid thalattosuchian from the Lower Jurassic of Hungary. While highly fragmentary, the new specimen contains enough information to be diagnosable, fills in some much-needed information on postcrania of non-metriorhynchid metriorhynchoids, and represents the earliest evidence of thalattosuchians in the pelagic realm. I think this is a generally well written and executed manuscript. I have a number of minor issues and formatting suggestions, but nothing that should unduly delay its publication.

Comments:
Pelagosaurus typus - the authors typically write out the full genus and species name when discussing this species. However, in some places it is abbreviated as Pe. typus, and in others as P. typus (e.g. towards the end of the phylogenetic results section). I'm assuming the use of "Pe. typus" was meant to clarify as Platysuchus is also discussed extensively (and Peipehsuchus occasionally). The authors should be consistent.

Lines 73-79: This entire paragraph seems more like discussion to me rather than introduction. It presents and interprets results of analyses the paper hasn't yet described. This paragraph actually sounds more like a "conclusions" paragraph than anything. I recommend this be removed from the introduction. This will probably require writing a new final paragraph for the introduction. Otherwise it will end very abruptly.

Lines 134-135: "A very rough sketch…" - I'm not sure why this sentence was included as it seems irrelevant.

Line 138: "preserved in laminated limestone" - These specimens are preserved in shale, rather than limestone assuming the authors mean the incredibly numerous specimens from the Holzmaden region of Germany (Posidonia Shale).

Lines 224-225: "distinct anterior acetabular flange…" - It would be nice to see side by side comparisons of this feature of the ilium of Magyarosuchus and Pelagosaurus. Also for the surangulodentary and angulodentary grooves. Perhaps a figure showing these could be added (in the supplement would be fine if there isn't room in the manuscript for more figures).

Line 241: "anteroposteriorly extending grooves…" you name these grooves in the diagnosis (surangulodentary and angulodentary) - they should be named here as well.

Line 254: "… form the shallow lateral side of the coronoid process" - ? The dentary doesn't typically contribute to the lateral side of the coronoid process in other thalattosuchians.

Lines 260-261: "shelf is present that has a slightly elevating medial side" - could this shelf be an articulation surface for the surangular?

Lines 262-271: In the figure for this specimen, the authors have labeled the external mandibular fenestra (or where it would be if the specimen weren't crushed), however they make no mention of that in the text here. This should be discussed as this is a feature lost in metriorhynchids. They should also discuss the deformation that has closed the EMF to explain why it is not visible in the figure.

Lines 272-273: I agree it is too fragmentary to describe in detail. However, is there any surface ornamentation visible? It looks like there might be from the figure, but it's hard to tell. If there is ornamentation, this should be mentioned as you discuss the ornamentation of the other mandibular pieces.

Lines 291-292: "are devoid of pneumatic foramina" - While true, I don't think this bears mentioning - I don't know of any crocs with pneumatized vertebrae.

Line 292: "neural arches are fully fused to the centra…" - this is typically used as a measure of ontogenetic stage (e.g. Brochu 1996; Irmis 2007). The authors may wish to note that the closure of these sutures support that this was a very mature individual (in agreement with the large size).

Line 300: "lumbar" is typically a vertebral classification for mammals (and their relatives). I would use "dorsal" here.

Lines 309-310: "… neural arches seem to be fused, the neural spines are separated" - I'm not sure what the authors mean here. Are they saying that the centra are unfused, the neural spines are separate, but the zygopophyseal articulations are fused? More clarity would be helpful here.

Lines 336-337: description of sacral ribs - The authors may want to mention here how the sacral ribs of this specimen differ from the elongate, slender sacral ribs of metriorhynchids (but are similar to those of Pelagosaurus).

Line 339: "probably represents the first sacral rib" - does its articulation surface match that of S1?

Line 363: Is this "triangular boss" the same thing as the postacetabular process (as labeled in Fig. 6)?

Line 366: "bard-shaped" - I don't know what this means.

Line 377: "a widened distal end" - Perhaps emphasize that the distal end is much wider than the proximal expansion. Also, is the ventral part of the distal expansion broken off? Is the expansion asymmetrical (i.e. is the dorsal portion more expanded than the ventral?)?

Line 435: "is the two-third of the second or third metatarsals" - I'm not sure what this is trying to say. Is this specimen the distal two thirds of one of these metatarsals? The sentence might just be missing a couple of words.

Line 448: Fig. 6C - Do the authors mean 7C? Figure 6C is a sacral rib.

Lines 460-461: "anterior margin of the osteoderms… overlap the posterior surface of the anteriorly following osteoderm" - This sounds backwards to me (though the wording is a bit confusing). The posterior margin of each osteoderm should overlap the anterior margin (and anterolateral process) of the following osteoderm.

Lines 472-473: "ornamented by the proportionally largest pits among thalattosuchians" - did the authors quantify this? It doesn't look noticeably different from some other specimens I've seen (e.g. some S. bollensis, Teleosaurus, or Pelagosaurus osteoderms). Maybe a figure of side by side comparisons would help?

Lines 475-481: The authors don't make any mention of the ventral osteoderms being sutured to one another, though this is indicated in the figure.

Line 489: "are also in an 'in review' manuscript" - As these datasets have already been published in Ristevski et al., I'm not sure there's any need to reference an 'in review' manuscript.

Lines 572-573: "Postosuchus kirkpatricki lies outside the clade…" - I don't think this statement is necessary. The authors rooted their tree on Postosuchus, so this relationship is forced by your input parameters. The same goes for the other two analyses rooted on Gracilisuchus. Gracilisuchus lying outside of Crocodylomorpha was forced a priori by designating it as the outgroup.

Lines 625-626: "internal relationships are becoming less sensitive to where in Crocodylomorpha Thalattosuchia is recovered" - The issue of thalattosuchian relationships changing based on location within the larger crocodylomorph tree were discussed previously by Jouve (2009 - the Teleosaurus description) and Wilberg (2015 - the outgroup paper).

Lines 634-635: Magyarosuchus is referred to twice here as "Magyarosaurus". The authors should check the rest of the manuscript to ensure that there are no other references to "Magyarosaurus".

Lines 672-673: "some features still unknown in these…" - These features aren't really "unknown" in S. bollensis or Pelagosaurus as complete caudal series are known for both. I think the authors mean that this Magyarosuchus caudal vertebra possesses a morphology different from that of teleosaurs and Pelagosaurus.

Line 727: "P. typus, which is typically 2-3m in length" - unimportant side note:  there is a very large Pelagosaurus skull at the Stuttgart museum. The specimen number is kind of hard to read in my photographs, but I think it is "SMNS 91.102" - it is labeled as "unusually large skull". Just eyeballing it from my pictures, the total body length should be around 4m based on the cranial/body length regressions in Young 2016, which is still smaller than your estimates for Magyarosuchus.

I didn't look over the References section in any detail, but there appear to be at least a few minor issues (e.g. the Hua and Buffrénil 1996 citation is partially in bold, and "vertebrate" is misspelled). Some references include both the journal issue and volume, while others only include the issue. The authors should check over their references for consistency.

Minor grammatical issues:

Lines 90-91: Urweltmuseum Hauff is in a different font than the rest of the manuscript.

Line 94: the word "the" should precede "specimen" in this sentence.

Line 147: the word "A" should precede "vibro-tool".

Lines 181-194: some, but not all, specimen numbers end in a period. Is this intentional?

Line 199: "for thanking his donation" - this doesn't seem like the right wording. Maybe "in thanks for his donation"?

Line 223: I think the word "rami" is unnecessary here.

Line 280: the word "the" should precede "crown surface"

Line 304: I would use the word "presumably" rather than "supposedly" in this context.

Line 372: "is only the distal half preserved" - should be "only the distal half is preserved"

Line 442: "precize" should be "precise"

Line 479: "avoid" should be "devoid"

Line 483: "Analysis" should be "Analyses"

Line 640: There is an unnecessary line break in the middle of this line.

Line 739: "questions" should be "equations"

Line 762: "usually" should be "unusually"

Comments on figures:
Figure 3 caption - "dentale" should be "dentary" throughout
	-	"… compressed to each other preventing to outline" - this is odd wording. Maybe change to "the specimen is dorsoventrally compressed, artificially closing the external mandibular fenestra", or something like that.

Figure 3 - the grooves visible in A are given specific names in the diagnosis (surangulodentary and angulodentary) but are just called "grooves" on this figure. I think they should be labeled more specifically on the figure (or at least. In the figure caption). The authors could leave the "gr" label on the figure and just change the figure caption to indicate that "gr" = surangulodentary and angulodentary grooves.
	-	I think it would help in interpreting these dentary fragments if the alveoli were outlined (maybe with a translucent gray oval). Some of their locations are labeled, but I think they would be clearer with some sort of emphasis. I also think some lines indicating sutures or contacts between bones would be helpful. The angular and surangular are labeled on G, but their contacts aren't that clear.
	-	There are some lines pointing to something on H and I without a label.

Figure 4 caption - Are there specimen numbers for the teeth shown in A, B, and G? The tooth in C has its own number.
	-	Which teeth are shown in H-I? Are these just magnified views of the tooth in G or two different teeth?

Figure 4 - in part I, the carina is somewhat out of focus near the top of the image. Would it be possible to retake this photo with a greater depth of field? Also, there is a scale bar in this image, but it is not indicated here or in the figure caption what the scale represents (mm?).

Figure 5 - It is somewhat difficult to determine which images are of the same vertebra(e) in different views (e.g., on first impression, I would assume H is ventral view of the vertebra shown in I and J). Maybe it would be helpful to box them off (i.e. box around A-C, D-C, F-H, I-J, and K-P). A similar argument could be made for figures 6-9, but these are generally more obvious.

Figure 10 - The caption refers to the trees as A and B, but they are labeled "Hastings & Young matrix" and "modified Andrade matrix". Also, the trees are mislabeled. The one labeled Hastings and Young is the Andrade tree, and vice versa.
	-	On both of these trees "GONIOPHOLIDAE" should be "GONIOPHOLIDIDAE"
	-	There is something off with the font in these figures (and in Fig. 11). It looks like some of the text has been compressed (top to bottom), and some has been stretched when the authors were resizing the trees.
	-	Minor points: I'm not sure I like the gray ovals behind the trees. The darker one behind the lower tree especially reduces the contrast between the black text and the background making the words more difficult to read. If the authors wish to retain the ovals as a way to obviously separate the trees, perhaps they could lighten up the gray color. It doesn't have to be very dark to set it apart from the white of the page.

Figure 12 caption - Magyarosaurus should be Magyarosuchus.

Table 1 - "dentale" should be "dentary" throughout. "coracoideum" should be "coracoid"

Comments on supplementary files:
Data file S1 - There are still some track changes comments in here.
	- Some formatting issues in tables (particularly S5.2). Also, the character # column is too narrow starting with 425 of H+Y matrix
	- Parts S4 and S6 appear to be identical (the Wilberg matrix stuff)
	- Citation for von Meyer 1831 has a weird giant "2" next to it (Wilberg, 2015a has a giant "4")

Data file S2 seems to be an Excel format version of the Wilberg matrix, which is also provided as a nexus file in data file S6. Probably only the nexus file is necessary.

Data file S3 is also the Wilberg matrix info already included in S1.

I had an issue opening data file S4 (I assume the H+Y matrix?) - Mesquite gave the error message "There was a problem reading the character matrix Character Matrix.  It appears that the file is corrupt ( taxon 140, character 17 (section of matrix as stored: "osaur ????"))."
	- Thus, I was unable to double check the results of this analysis (though I don't expect there to be any issues). The authors should check this 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: A NEW LARGE-BODIED THALATTOSUCHIAN CROCODYLIFORM FROM THE LOWER JURASSIC (TOARCIAN) OF HUNGARY, WITH FURTHER EVIDENCE OF THE MOSAIC ACQUISITION OF MARINE ADAPTATIONS IN METRIORHYNCHOIDEA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript “A new large-bodied thalattosuchian crocodyliform from the Lower Jurassic (Toarcian) of Hungary, with further evidence of the mosaic acquisition of marine adaptations in Metriorhynchoidea” will be an interesting contribution to the knowledge of basal thalattosuchians. The manuscript is well organized and writing is clear. The figures of the specimen are clear. Nevertheless, some modifications are needed in order to be accepted for publication.
Some comments are highlighted in the pdf.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Diagnosis:
I not convinced about the use of the body length as a diagnostic feature. May be the authors can start the sentence as follow: Large size metriorhynchoid thalattosuchian with the following unique combination ….. and delete the sentence “large body size (estimated body length: in the range of 4.67–4.83 m)” from the diagnosis.

Institutional abbreviations:
Lack the name of the institutions that correspond to the acronyms BSPG and MNHN.

Description and Comparisons:
Comparisons of postcranial elements need to be improved. It would be nice to see more comparisons with other teleosaurids species. This is done in a few places, but not consistently throughout the manuscript. Also, some elements (dorsal vertebrae, ribs, ventral armor) have not any comparison with other taxa.

Discussion:
The assumption of a ventral deflection of the distal tail on M. fitosi is only based on one incomplete and isolated caudal vertebra. I not convinced that there is enough evidence to support this hypothesis. In my opinion, the authors need to make a more persuasive case about that.


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

Input:
Title: THE PERFORMANCE OF CLEANER WRASSE, LABROIDES DIMIDIATUS, IN A REVERSAL LEARNING TASK VARIES ACROSS EXPERIMENTAL PARADIGMS
Review round: 1
Reviewer: 1

Output:
Basic reporting: I have carefully read the MS entitled “The performance of cleaner wrasse, Labroides dimidiatus, in a
reversal learning task varies across experimental paradigms” by Marcadier and colleagues. The authors trained cleaner wrasses in a left-right choice followed by a reversal learning. The clear were subdivided in 4 experimental groups which differed according to details of the procedure and the apparatus. Results of the experiment showed quite clearly that reversal learning performance varies according to the experimental group.

I find the study very interesting. The effect of methodologies on cognitive abilities tests for non-human animals is possibly very important in comparative research, yet very few studies deal with the problem. Objectively, the study provides few critical data on this problem, as it is not clear what exactly caused the observed effect; however, it might be an important contribute to the journal because it will help catching the attention of other researchers on the problem.

I did not find any major issue on the experimental design, experiment execution, analysis and interpretation of the results, with one exception. It is not clear whether the authors prevented the fish to find the food reward based on odour cues. Once controlled this detail, I would be happy to see this MS published.

Writing overall is clear. I think however that the manuscript might be improved in some parts. Below, the authors will find a list of suggested improvements. Further, I think the authors ‘forget’ to cite two very important papers that investigated the very same issue on fish. I am a bit unpleased to recommend these papers as I am one of the authors. However, these suggested papers are so similar to the study here reported that I think the authors cannot avoid to report and discuss them. Details about these two papers and other suggested citations are given below.
Experimental design: Please see comments on possible odour cues.
Validity of the findings: no comments
Additional comments: L26 I am not an expert on spatial abilities but I think the terminology used by the authors might be unappropriated. The use of the term ‘spatial discrimination’ assumes that fish used a spatial strategy to solve the task, such as they learned to discriminate two positions in the tank and they learned that the reward was in a specific position; however the fish could have used non-spatial cues to solve the task; for instance, the fish could have learn to choose the stimulus at their right or left, a strategy which is based on egocentric rather than spatial cues. A correct term here might be ‘spatial task’, which assumes that the specific task is spatial, but not that the fish solved it with a spatial discrimination. I have been corrected about similar terms by researchers more expert on the topic. Thus, I think the authors should carefully check their wordings and eventually correct here and elsewhere.

L64 I think the reader would expect to see some references here.

L70-97 In this long paragraph the authors give many details about studies on primates. I see that they probably do so to make the reader understanding the importance of their works. I think they can reduce this long paragraph in few lines, and/or remove one of the examples (e.g. the one on inequity).

L99 Is there one addictional empty space between “compared” and “the”?

L98-113 Inside or after this paragraph it is the right place to discuss the previous studies on fish that manipulated small details of the procedure/apparatus and found different cognitive performance.
In the study “Gatto, E., Lucon-Xiccato, T., Savaşçı, B. B., Dadda, M., & Bisazza, A. (2017). Experimental setting affects the performance of guppies in a numerical discrimination task. Animal cognition, 20, 187-198”, my colleagues and I trained guppies in a discrimination task identical to the one of a previous study (Bisazza, A., Agrillo, C., & Lucon-Xiccato, T. (2014). Extensive training extends numerical abilities of guppies. Animal cognition, 17, 1413-1419); however, we independently changed details of the apparatus and procedure compared to the previous study. We found that most of these changes produced a reduced discrimination performance of guppies.
In the study “Lucon-Xiccato, T., Dadda, M., Gatto, E., & Bisazza, A. (2017). Development and testing of a rapid method for measuring shoal size discrimination. Animal cognition, 20, 149-157”, we modified one of the most used paradigm based on spontaneous behaviour to study discrimination in fish, the shoal choice. We found that three very small modifications in the experimental apparatus substantially improved guppies discrimination abilities. I believe that these two studies together are one of the most clear evidence that fish cognitive performance measure is affected by methodology.

L178 How can the authors be sure that none of the fish learned to find the reward following odour cues? This must be proved or the entire study might not be valid.

L190-192 I would like to see a statistical test showing that there was not effect of the initial reward side. This has been previously proved to be affect fish learning in similar spatial tasks (see this study from my lab: Miletto Petrazzini, M. E., Bisazza, A., Agrillo, C., & Lucon-Xiccato, T. (2017). Sex differences in discrimination reversal learning in the guppy. Animal Cognition).

L201 With 8 individuals per treatment, the authors might have failed to control with another issue of comparative psychology: the use of small sample size and the presence of individual differences in learning abilities (see these two papers: Thornton, A., & Lukas, D. (2012). Individual variation in cognitive performance: developmental and evolutionary perspectives. Philosophical Transactions of the Royal Society of London B: Biological Sciences, 367, 2773-2783; Lucon-Xiccato, T., & Bisazza, A. (2017). Individual differences in cognition among teleost fishes. Behavioural Processes. ).

L214 Odd parenthesis at the end of the sentence.

L237 Have the authors try to use a chi-square test to see whether there is a significant difference between the number of fish learning the task in the different conditions? This would be a stronger evidence of the effect

L248 I would add a covariance test between the score of the initial learning and the one of the reversal learning of the subjects. Maybe an ANCOVA fitted also with treatment as factor.

L275 In one of the paper that I have previously suggested (Gatto et al.), there is a result interesting for this paragraph. Fish trained with a transparent panel in front of the stimuli that forced the fish to wait in front of the stimuli before making the choice did not improve discrimination learning performance.

L304 Did you record the trials? This would allow to test the idea of fish trying to pass from one stimulus to the other despite the transparency.

L317 Spatial discrimination is not relevant for cleaners or simply less important for their ecology? Maybe the authors can use a conditional phrase.

L331 I am not sure whether “colour” properly describe the variation of the apparatus. Maybe the opacity?

Fig 1. What about drawing the transparent part of the apparatus as a empty clearer bar? This would help the reader to identify the part in the figure...


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

Input:
Title: THE PERFORMANCE OF CLEANER WRASSE, LABROIDES DIMIDIATUS, IN A REVERSAL LEARNING TASK VARIES ACROSS EXPERIMENTAL PARADIGMS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Although this paper is well-written, I do not think the introduction and discussion show sufficient background on this topic. The effects of the details of a task on performance are not only well-studied, but could be said to be characteristic of large swathes of comparative cognition. This is not a new insight, and I am uncomfortable with the authors presenting it as such. This isn't a matter of whether the ideas and experiment in this manuscript are sufficiently "novel" (although they are presented that way by the authors), but more that it gives a false impression about the state of the field of animal cognition.

I have a couple of examples from the introduction where the authors are present commonplace ideas in comparative psychology as either unexplored or very recent (all of which can also apply to the discussion and conclusion):

64-69: The idea that species might differ in attention/motivation and this might affect performance in tests of cognition is not new, and did not originate with Lotem & Halpern (2012). Bitterman's tests of cognition across species in the 1960's were specifically controlling for this, and Alan Kamil wrote extensively about this as a possible barrier to progress to comparative studies of cognition in the 1980s (I strongly recommend his "synthetic approach to animal intelligence" from 1987, for example). This also applied to 327-330, which reads as though this insight has come about in the last couple of years.

70-73: An enormous amount of research in comparative cognition is about how slight modifications of paradigms influence performance. This is particularly true for studies of spatial memory. See for example the comparison between pigeons tested in a regular radial maze (Bond, Cook & Lamb, 1981) and in an open field maze (Spetch & Edwards 1986). Or Michael Brown's work in the early 1990's on the effect of radial maze arm length on performance in rats. These are just some early examples, there are many more from recent years. Lots of journals publish these studies frequently (e.g. The Journal of Comparative Psychology, Comparative Cognition and Behaviour Reviews, Learning & Behaviour, the Journal of the Experimental Analysis of Behavior, Journal of Experimental Psychology: Animal Learning & Cognition). These studies are interested in what these changes tell us about the mechanisms at work, so the aims might be a little different from the comparative study of cognition which you are trying to push forwards, but they are fundamentally the same.

74-97: In this vein, I think the examples used are a little odd. Not only is there a large literature dedicated to examining the effect of these kinds of manipulations, but the examples you give are also from social cognition. I understand the point you are making with this example, but I feel an example from spatial learning would be more apt.

98: The role that ecology plays (or might play) in learning is also well studied. I can see you want to refer to work on cleaner wrasse, but Kamil & Krebs and others covered similar ground in the 80s with their studies of food-storing birds (and Kamil's later work on transitive inference). Even in hardcore associative learning, it have long been known that some things can be associated together much easier than others, in ways that make ecological sense (smell+sickness or light+shock). Again, I am not objecting to this experiment, but I would like the authors to acknowledge what has come before, to prevent it feeling like they are trying to reinvent the wheel.

330-331: It might not be the authors intention, but this sounds as though good experimetnal design is a novel concept! We have known that experimental design matters in comparative cognition for the last 100 years! This shouldn't be news to anyone in animal cognition. I also think this sentence is rather unfair to your study: you can change parts of a task and still have a good experimental design. The idea that a perfectly designed experiment will unambigously get at "cognition" is just not true. Cognition is a collection of mechanisms taking in and processing multiple types of information and then guiding a wide range of behaviours. Variation in sensory systems, species typical motivations or behaviours, as well as capacity to act in terms of morphology (hard to teach a fish to point, for example), mean that no test will ever be perfect. But how animals change their performance when you change the test can tell you something about how they solved it, the mechanisms they used, and the information they learned. By pulling that apart (using experiments like this one), we can get at the mechanisms involved and then maybe explore how the properties of these mechanisms vary across species (food storing birds is a great example here). It won't be achieved by just one test (or even a battery) though.

In addition:

I do not like the term "cognitive performance". You are not directly measuring cognition, you are measuring behaviour which could be impacted by all kinds of factors (motivation, perception, morphology) of which "cognition" is only one. Just say "performance", or preferably "performance in this task".

Change "cognition test" to "spatial discrimination test", this was not a general test of cognition, but rather a specific one.

I am not sure that you can say that spatial learning is not ecologically relevant to these fish. Space is one of the few areas which is almost always ecologically relevant to (mobile) animals. Do these fish not have any locations they return to, or avoid?
Experimental design: I thought the experimental design was fine.
Validity of the findings: You seem to have found that your fish appear to learn some spatial information faster under certain conditions than under others. Rather than attributing this to differences in "cognitive performance", which suggests that cognition is homogenous and continuous, might I suggest thinking about how the fish might be solving the task and how this might be affected by the modifications you introduced (both in terms on mechanisms/processes such as discrimination or attention or associative learning, as well as the information they learn).

Space is not a single cue, and spatial tasks can be solved in a number of ways. Did the fish learn the location? Or did they learn a direction to swim? Or even the "geometry" of the arena? Do any of these impact how the fish respond to the changes? Does the poor performance in the reversal mean that they are preferentially using spatial information to solve the task (and so struggle when the spatial location of food changes)?

I think it would be helpful to look at some of the psychological work on this (as referred to in the section above) and see why, for example, people think that arm length affects radial maze performance. These studies would appear to be very relevant to the experiment you designed, and understanding more about why these differences might occur would be genuinely beneficial for moving the field forward. I seriously doubt there is such a thing as an "ideal" test of animal cognition which can be applied to any species and the results easily compared. If we are to make useful comparisons, it won't be based on performance in a test, we will need to understand the mechanisms and how they differ, and studies like this one are important for that. I just don't want to see it overlook all the progress others have already made on these topics in the last 50 years.
Additional comments: I do not think this study is flawed, but the introduction, discussion, and conclusion all ignores large areas of research on animal cognition. As a result, this manuscript  describes this experiment as more novel than it actually is, and presents ideas about the influence of the task and ecology on performance, which have been discussed and widely accepted in the more psychological end of the field for decades, as fresh and new. This is unfair to the psychologists who have spent the last 50 years working hard on the kinds of experiments the authors are saying haven't really been done. It also presents an inaccurate account of the state of animal cognition in 2017, which matters as younger researchers reading this manuscript or researchers in animal behaviour unfamiliar with animal cognition will take it as fact.

I think the introduction would need to be rewritten, to take account of what has been done before, and provide an accurate overview of the field of animal cognition. As would the conclusion and parts of the discussion.

I also think reading up on what has been done before would benefit the interpretation of these results. There is a lot of work tweaking spatial tasks such as radial mazes, water-mazes, open-field mazes, as well as the details of procedures including reward sizes, reward timing, inter-trial intervals, fixed ratio versus fixed interval reinforcement, and  much more. I know the authors are interested in comparing "cognition" across species, but I think looking less at performance itself and more about what performance might tell us about the mechanisms/information learned would be a good start. And also provide some much needed cross-over between experimental psychology and behavioural ecology!

P.S. Sorry to be so pedantic and editorialising a bit, but I really like animal cognition, and it pains me when people overlook all of the remarkable work done on this topic in model psychological systems like rats and pigeons over the past 50 years. This work is highly relevant for the evolutionary and ecological approach both I and the authors would like to see, but doesn't get as much attention as it should by those trying to take such an approach. Ignoring animal psychology work means that biologists interested in cognition risk slowly reinventing the wheel, and I for one would rather that didn't happen.


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

Input:
Title: THE PERFORMANCE OF CLEANER WRASSE, LABROIDES DIMIDIATUS, IN A REVERSAL LEARNING TASK VARIES ACROSS EXPERIMENTAL PARADIGMS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Comment 1: Clear, unambiguous, professional English is used throughout.

Comment 2: Line 28 and throughout: I have seen "two-alternative forced choice tests" written as "two-alternative forced-choice tests." May want to consider editing to stay consistent with what is in the literature.

Comment 3: Line 74-97: Although very clear and demonstrative of the authors point, I found this example to be somewhat lengthy and tangential. Additionally, both examples (Lines 74-97 and 98-113) to be somewhat primate-centric. I would recommend the authors include other examples from the literature that are shorter and more relevant. For example, see Cheney et. al. (2013) and Pintor et. al. (2014)

Comment 4: Line 99: Extra space between "compared the"

Comment 5: I would avoid the overuse of transitional phrases ("for instance" on lines 73, 93, 99).

Comment 6: Lines 123-126: I think it would be helpful to explain the specifics of the foraging tasks that can be solved, so that the reader understands how the plates are used.

Comment 7: Lines 134-135: Have these extrinsic factors been shown (empirically) to influence the outcome of tests? If so please provide citations. Also, please explain how distance swam before a decision must be made is expected to influence choice.

Comment 8: Lines 142-145: Similar to Comment 7, I think that the authors should spend more time explaining their hypotheses and predictions, so that the reader is better prepared to understand the author's interpretation of results in the discussion. In other words, please explain how "accentuating the separation between the two discreet choices and/or giving the fish a longer time" is expected to influence performance.

Comment 9: Structure, raw data, etc. seem to meet journal standards. Figure 1 is clear and well-designed.

Comment 10: Figure 2: I would consider using an asterisk to indicate statistical significance. Also, I would capitalize titles of experimental treatment remain consistent with captions, Figure 1, text, etc.

References:
Karen L. Cheney, Cait Newport, Eva C. McClure, N. Justin Marshall. (2013) "Colour vision and response bias in a coral reef fish," Journal of Experimental Biology 216: 2967-2973; doi: 10.1242/jeb.087932

Pintor, L.M., McGhee, K.E., Roche, D.P. et al. Behav Ecol Sociobiol (2014) 68: 1711. https://doi.org/10.1007/s00265-014-1779-7
Experimental design: Comment 11: This manuscript appears to be original and falls within the Aims and Scope of the journal.

Comment 12: The research question and purpose in filling a gap in knowledge is clear.

Comment 13: Investigation appears to meet high technical & ethical standards.

Comment 14: Methods are described in detail, but I would recommend providing an image or video of the plates used with the reward/bait on them (either in the MS or in supplemental information).

Comment 15: Lines 155-157: Editing required - there may be an extra “(“ ?

Comment 16: Line 155: could the authors explain what

Comment 17: Lines 155-156: Were the biological market experiments performed with actual clients or plates similar to the ones in the present experiment? Could this have influence performance at all? More of an explanation here would he helpful.

Comment 18: Line 160: Were the fish habituated to the clear partition? It seems that the clear partition could have influenced performance (e.g., lines 282-284)

Comment 19: Lines 205-206: Are the authors confident that the fish were watching/paying attention to the plate that was removed? I can imagine a sceniero where the subject made a correct choice and begin eating immediately with its attention directed away from the other plate while it was being removed. Perhaps this is not the case, but without a video or images it is unclear.
Validity of the findings: Comment 20: Results are beneficial to the literature

Comment 21: The statistical analyses used seem appropriate, however I do not have experience using these specific tests and would therefore defer to the expertise of the editor and other reviewer(s).

Comment 22: Conclusions are well stated, but I think could be better linked to the original questions/predictions (by providing more information in the introduction, see comment 7).

Comment 23: Line 282: The subjects would only form an association if they observed the other plate being removed (see comment 19).

Comment 24: Lines 267-269: This may be speculation, but I am wondering if an alternative explanation could be that the subjects could see which plate contained the reward from a further distance (i.e. when it could see both plates from further away and see which was baited)?

Comment 25: Line 287-289: Do the authors have any inclination as to whether this happened in their experiment? Did they observe subjects frequently running into the transparent partition?

Comment 26: Line 287-294: This description is slightly unclear: In Figure 1. it appears that the fish always approach the choice from the front. Do the fish instead deviate to one side of the aquarium and follow the wall, ending up in a choice because of their initial inclination to follow a wall?
Additional comments: I found this paper to be an enjoyable read and think it is a welcome contribution to the literature. I think it could be a bit stronger by including a few relevant references, images/videos, and a more detailed explanation of your predictions in the introduction (i.e., how and why would changing each of these specific parts of the experimental procedure result in differences in the performance of subjects in your task).


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

Input:
Title: THE PERFORMANCE OF CLEANER WRASSE, LABROIDES DIMIDIATUS, IN A REVERSAL LEARNING TASK VARIES ACROSS EXPERIMENTAL PARADIGMS
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comments
Experimental design: No comments
Validity of the findings: No comments
Additional comments: The authors modified the manuscript following my suggestions or they clearly explained their experimental choices.

I think the manuscript is focussed on the interesting point. I do not have other methodological concerns and the language is clear and easy to follow.

I think this interesting study can now be considered for pubblication.


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

Input:
Title: THE PERFORMANCE OF CLEANER WRASSE, LABROIDES DIMIDIATUS, IN A REVERSAL LEARNING TASK VARIES ACROSS EXPERIMENTAL PARADIGMS
Review round: 2
Reviewer: 2

Output:
Basic reporting: - I believe that the authors have addressed my previous concerns and have improved the introduction (background/context, hypotheses, etc). I noticed just a few minor things upon review:

- Line 63: I think that the sentence "For instance, numerical abilities in fishes are often tested through shoal size discrimination as in many species, a solitary fish will naturally join the largest of two groups of conspecifics (e.g. Hager & Helfman, 1991)" may need revision.
"As in many species" stands out as odd. Perhaps add "and" before "as in many species" ? Or move "As in many species" toward front of sentence?

- Line 71: Do the authors mean "improved performance"?
"Increased performance" strikes me as meaning increased participation vs. improvement in testing/success.

Lines 129-132: I think it is good that the authors have discussed the distance needed to swim to the plates in the introduction. However, this statement still does not explain what the prediction is: I would suggest the authors consider replacing "impact" with "increase" or "improve" or "positively affect" if this is indeed their prediction (ie "This increase in distance, and hence the time required before making a choice, also has the potential to increase the accuracy of decisions...").

- I do not see the letter codes (to indicate significance) in Figure 2. Apologies if I am missing something, but I have reviewed this figure several times and I do not see the "different letters at the top" as stated in the caption...
Experimental design: No further comments on the experimental design.
Validity of the findings: No further comments on the validity of the findings.
Additional comments: I think the authors have done a nice job of addressing my comments and discussing points presented by all reviewers.


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

Input:
Title: PELAGIC LARVAL DURATION, GROWTH RATE, AND POPULATION GENETIC STRUCTURE OF THE TIDEPOOL SNAKE MORAY UROPTERYGIUS MICROPTERUS AROUND THE SOUTHERN RYUKYU ISLANDS, TAIWAN, AND THE CENTRAL PHILIPPINES
Review round: 1
Reviewer: 1

Output:
Basic reporting: needs a rewriting by a fluent English speaker.. many phrases are imprecise and vague and not standard usage and, as well, there are glaring errors with dropping of plurals- like "various PLD(s) and growth rate(s) of" & dropping of indefinite and definite articles and prepositions, like "(The) population structure of fishes", "(a) handful (of) congrids" & "breed at (a) (single?) specific spawning area".
Many references, esp. for larvae are old and/or referring to gobies- completely different fish models.
discuss Leis et al 2013 review (Does fish larval dispersal differ between high and low latitudes?)
Experimental design: the data are fine, it is the presentation and discussion that are below standard
Validity of the findings: discussion is inadequate.. some statements are unsupported, some citations do not match the phrase they are being referenced to.. the authors need to carefully go over the wording of the discussion to limit it to what exactly they know based on what from the literature.
Additional comments: specific comments by line
> 38 several means less than many.. and there are many factors!
> 42 PLD is not used to predict population structure... use site-attached instead of benthic, which means sitting on the bottom.
> 44 PLD often "correlates", just not very well.. how about "PLD has been found to strongly influence population structure only in..."
> 51 "distinct early life history traits, leading to specific PLDs" I have no idea what this means, vague terms, everything on earth has "distinct traits".
> 53 "remain unclear and barely evaluated".. some people's entire careers evaluate this! so not barely!
> 57 the unusual leptocephalus is not important at all.. it is the pelagic larval stage that is meaningful.. the actual length of the PLD.. for example, many labrids have the same PLDs and the same lack of genetic structure- the actual shape of the larva is irrelevant.
> 60 & 62.. English grammar, need to use "have been" instead of "were" for things that happen continuously in the recent past...
> 63 varying PLDs
> 68 "genetic structure among populations, geographic areas or environmental systems" is vague.. populations are in different areas, and "environmental systems" is a meaningless word.
> 69 use "explored thoroughly".. "discussed" implies it was studied well but not discussed well.
> 71 Anguilliformes
> 86 fish have sperm, not semen
297: with a long PLD and lepto stage, being spawned in the intertidal would not be expected at all to cause retention.. maybe for fish that brood large eggs in the intertidal, maybe, but never eels.
299- no despite necessary- they are long PLD larvae.. "distinct" PLD is meaningless.
303- there must be some dispersers.. these statements are baseless..
307- sentence is incomprehensible- ecological explanations irrelevant to long distance transport- dispersal occurs with the infrequent offshore dispersal, not any retained larvae.. genetic homogeneity can be maintained by a single disperser every 100 years..
312: "Self-recruitment(s) of leptocephali are also observed more often than dispersal in".. they cannot have shown that- it would be impossible to study how many dispersed..
317- "longer PLD implies that some larvae might recruit from remote populations".. but cooler water means slower growth and/or longer PLD, so can never separate those two causes.


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: PELAGIC LARVAL DURATION, GROWTH RATE, AND POPULATION GENETIC STRUCTURE OF THE TIDEPOOL SNAKE MORAY UROPTERYGIUS MICROPTERUS AROUND THE SOUTHERN RYUKYU ISLANDS, TAIWAN, AND THE CENTRAL PHILIPPINES
Review round: 1
Reviewer: 2

Output:
Basic reporting: Clear, unambiguous. Literature references are sufficient. Structure of article is sound, data are presented relative to specific questions/hypotheses.
Experimental design: Question is well-defined and relevant. Investigation performed with high technical savvy and method provide sufficient detail to replicate.
Validity of the findings: Sound, well executed. Interpretation of data is meaningful and clear.
Additional comments: This is a study that includes 195 specimens analyzed for 1,336 nucleotides of concatenated cyt b and coi sequences from one species of moray eel surveyed in SE Asia. Their goal was to assess PLD and genetic structure. They find that eels with longer PLD and lower otolith growth rate were at higher latitudes with colder water; i.e. faster growth and shorter pelagic periods in warmer temperatures. They find low genetic structure at this scale, which is not surprising given previous phylogeographic studies of morays. Generally, I find the study to be interesting and very well executed. With some minor mistakes, the manuscript is well written, the figures are clear and interpretable, the data is presented fairly plainly, and the analyses and interpretations seem very sound. I have no problem seeing this published as it stands or with very minor revision.

The only criticism I can provide is just a suggestion that the premise or setup could use some finessing. There is a known, but shaky, relationship between PLD and genetic structure. PLD is known to be high in morays and genetic structure is known to be low or nonexistent. The authors find that PLD is indeed high and genetic structure is very low. The paper is better presented as a descriptive piece. It's a straw man to present the finding of low genetic structure as anything but expected. The interesting stuff here is yet another moray with empirical estimates of PLD, the finding of differential PLD across latitudes even in this fairly modest spatial scale, and the repeated finding of low genetic structure in another moray. The introduction sets this up a bit as if it is a question whether or not PLD will be long and genetic structure low - whereas that finding is all but expected.

Minor edits:
"	Results: no missing data? Please clarify extent of any missing markers from concatenated dataset
"	292: title, larval not "lraval"
"	294: change "the gene flows" to "gene flow"


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: PELAGIC LARVAL DURATION, GROWTH RATE, AND POPULATION GENETIC STRUCTURE OF THE TIDEPOOL SNAKE MORAY UROPTERYGIUS MICROPTERUS AROUND THE SOUTHERN RYUKYU ISLANDS, TAIWAN, AND THE CENTRAL PHILIPPINES
Review round: 1
Reviewer: 3

Output:
Basic reporting: This study is an assessment of links between population-level differences in pelagic larval duration (PLD) and population genetic structure. This is an innovative idea that has not been tested previously to my knowledge.

There were a number of minor typographical errors (see below) but these are readily corrected in a few minutes. Overall the English was very good, and the result is an efficient, highly-readable report. Introduction is informative and succinct, literature is well covered, overall structure is appropriate. With one or two exceptions, see below, figures are clear and justified.
Experimental design: The research is within the scope of PeerJ and the study is well-designed. Statistical analyses are robust, using the very conservative Bonferroni correction. The only criticism that could be leveled about study design is that the tidepool snake moray occurs from Africa to Micronesia, so that the geographic scale of sampling could be expanded profitably. However, the authors know this, and I won’t criticize them for lacking unlimited funding and resources.
Validity of the findings: The results include significant differences in PLD along a latitude (or temperature) gradient. Authors conclude that differences in PLD between sample sites are not due to population genetic isolation, but due to differences in environment. This conclusion seems robust.

The only significant phi-st between sites was with Liuqiu versus Checheng, closely situated sites in southern Taiwan. Liuqiu also had the longest and most variable PLD. Authors address this in Discussion, invoking possible long distance recruitment within the South China Sea. Perhaps add a sentence at the beginning of this discussion that Liuqiu is significantly different from almost every location with phi-st prior to Bonferroni correction (which is highly conservative).
Additional comments: 138 Call-outs for Figures 5 & 6 are out of order. Maybe eliminate the call-outs as they aren’t needed here.

228-229 and elsewhere: P values should have same number of significant figures.

Table 1 should have a horizontal line between Japan and Taiwan.
Table 3 could go in supplemental information, a bunch of nonsignificant phi-st values.
Figure 7 could also go in supplemental information, as it is peripheral to main theme.

Rewording Suggestions
32 ‘Gene flow’ should be singular
33 Perhaps replace ‘poor’ with ‘weak’.
51 Replace ‘undergo’ with ‘experience’.
56 Delete ‘handful’.
62 “There are only a few studies…’.
65 ‘Areas’ should be plural.
95 ‘Zones’ should be plural.
100, 171 Numerous
126 Replace ‘have been indicated’ with ‘are typically’.
133 replace the first ‘in’ with ‘the’.
163 ‘pairwise’ should be lower case.
204 Sampling
211 ‘Structure’ should be singular.
245 I think this should be ‘metamorphosis’.
249 This should read ‘four other eel species…’
256 This should read ‘…to this check should contain most of the leptocphalus stage…’
287 This should read ‘…other transient oceanographic events…’
302 ‘gene flow’ should be singular.
304 this should read ‘…effectively a handful of migrants…’
306 ‘…timescales of tens…’
309 ‘…maybe a possible…’

Overall, an innovative study design that should be emulated in other fishes, to test the generality of findings. This was an informative, enjoyable read that should appeal to the broad readership of PeerJ. Congratulations to authors.

Possibly Useful Reference:
Selkoe KA, Gaggiotti OE, ToBo Lab, Bowen BW, Toonen RJ. 2014 Emergent patterns of population genetic structure for a coral reef community. Mol. Ecol. 23, 3064–3079. (doi:10.1111/mec.12804)


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: PRIMARY PRODUCERS MAY AMELIORATE IMPACTS OF DAYTIME CO2 ADDITION IN A COASTAL MARINE ECOSYSTEM
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a clearly-written and scholarly submission, which sets up the study well in the context of what is known about biological feedbacks to ocean water chemistry from both field and laboratory experiments, as well as natural variability of carbonate chemistry along coastlines. The figures are germane to the story and are internally well-described to a reader.
Issue 1: The only issue that I found with respect to how the manuscript was written applies to the construction of statements regarding relationships among variables, and inference of cause and effect. In my experience, linear regression is applied to a variable (y) that responds to another variable (x), the latter being measured with less error, experimentally manipulated along a gradient, or expected to be a causal factor in the relationship. When one reports the results of a linear regression, characteristically y is related to x. So I found the construction in the manuscript confusing in a couple of places:
Abstract: “Net community production was strongly related to pH, pCO2, net ecosystem calcification, and changes in O2 concentrations.” Accordingly, I would expect to find NCP on the y-axis, and the four other variables each to contribute to variation in NCP. However, I don’t think that this cause-effect relationship (that water chemistry affects NCP) is what the authors intend. An additional point about the construction of this sentence: it is written as if the change over 6 hours is only relevant to a single variable (O2), but results in Fig. 3 emphasize the change in pH and pCO2 as well. It might work, for instance, to write that “under ambient conditions, tide pools with higher NCP also showed larger daytime increases in pH and oxygen, larger declines in pCO2, and higher rates of NEC.”
Methods line 229: The same issue arises here, where four variables are listed (as above, but without O2) but without any indication of which is the response and which the predictor in linear regression analyses, therefore the expectation of cause and effect. So these methods could usefully be rewritten to be clear about which are predictor and which are response variables, as well as to add O2 (as a response variable in relation to NCP, I think – although reduced major axis regression that makes no assumptions about more variation in the y- than x-direction might also work).
Line 260: Same issue – reverse so that the response variables are related to the predictor variable of NCP
Line 285: Same issue – could be rewritten to emphasize not just “relationships among”, but the logical linkage from NCP to improved pH to better conditions for calcification. And on line 288: currently written as “the relationship between x and y”, but typical construction is “the relationship between y and x” (although, again, here as these are two variables expected to be indices of photosynthesis, then their correlation, rather than linear regression results, may be a better approach)
Experimental design: The methods, calculations, and statistical analyses all contribute to a strong test of how biological communities differ in their daytime capacity to draw down carbon (thereby changing pH and pCO2) under the almost-closed field conditions of tide pools at low tide. I was particularly impressed with the attention to best practices in the reporting of carbonate chemistry variables.
Issue 1: Figure 3C, line 229, and line 262: Also worth testing whether NEC is related to the abundance of calcifying organisms. I get that the positive relationship between NEC and NCP is compelling, but a priori I would expect that more calcification occurs when more biomass is present to calcify. Maybe this is tricky because calcification by mussels, Tegula, and coralline algae are not necessarily occurring similarly (but one might also say that about the photosynthesis of the different encrusting and upright fleshy algae…). But I think it would be a relatively quick check, and allow a reader to know that there was not some confounded variable (more primary producers and shelled organisms in some pools than others) driving the relationship in Fig. 3C. In essence, such a test allows a conclusion about whether daytime calcification is driven by per capita rates responding to ambient water chemistry, or to abundance of calcifiers.
Issue 2: There is one last issue in regards to methods, which I will bring up although I don’t think it can really be fixed at this point: how great it would have been to include a tidepool-sized tub of seawater with no benthic organisms present, as a better way of defining the intercept in Fig. 2 (which assumes a linear relationship) AND an excellent proof that the yeast digesters actually added CO2 to the tide pools. That is, since one of the major conclusions of the paper is in regards to variable capacity to ameliorate CO2 addition, depending on NCP, it would be helpful to have samples with very low NCP, as this would confirm the treatment of CO2 addition and help inform that macrophytes are the key players. I personally am satisfied with the conclusions drawn from the existing range of NCP available in the 10 tide pools, but the authors might be a little more circumspect about the certainty of intercept, given the extrapolation beyond data (as in abstract line 31).
Smaller issues:
Line 183: I think that these calculations (NCP, NEC) apply only to tide pools under control treatments. If so, please specify. If not, then I am confused about how it would be possible to infer NCP and NEC from the change in DIC, given that there is an external source when the yeast incubators are bubbling into the tide pools.
Line 188: is a single value used for the density of seawater? I notice that in Silbiger and Sorte 2018, a single value is used, but here the density may change if there is evaporation and salinity changes over 6 hours.  I doubt it matters much one way or the other for the calculation, but as written, it is ambiguous.
Validity of the findings: The authors have generally done an excellent job of drawing conclusions from their data. I have already brought up issues of language and experimental design above, which may need small attention in the discussion.
Issue 1: Lines 306 ff are the most speculative, in which daytime drawdown of carbon is stated to improve water chemistry in ways that would more than offset high CO2 and low oxygen from nighttime respiration. I actually think that the authors have missed the most compelling piece of information in this regard, which comes from Silbiger and Sorte 2018 - they show, for some of the same tidepools, that regardless of the fraction of primary producers in the tide pool, nevertheless water chemistry at night converges to a similar low pH. This means that high daytime NCP may not necessarily result in any higher respiration at night, therefore the minimum pH conditions may be rather insensitive to community composition.
Additional comments: The manuscript was a pleasure to read and has definitely stimulated new thinking on my part about the short-term drawdown of carbon by seaweeds.


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: PRIMARY PRODUCERS MAY AMELIORATE IMPACTS OF DAYTIME CO2 ADDITION IN A COASTAL MARINE ECOSYSTEM
Review round: 1
Reviewer: 2

Output:
Basic reporting: Please see general comments.
Experimental design: Please see general comments.
Validity of the findings: Please see general comments.
Additional comments: This well written paper describes the effects of macrophytes in mitigating the effects of CO2 addition in Californian tide pools. Although the data are quite limited in their scope, having been collected over a period of 6 hours on two consecutive days, I find the results to be interesting and well-supported. The authors do include some caveats about the limited sampling (only during the day), but I think they should both expand those caveats (only during the spring, only at low tide) and bring them to the front of the paper rather than leaving them to the end. I would also emphasize the caveats around using tidepools, which are really a best-case scenario for identifying these effects, as a proxy for coastal environments writ large.

My other comment is statistical. This dataset strikes me as a good opportunity to use an ANCOVA, multiple regression techniques, or something similar to simultaneously evaluate the effects of CO2 addition and macrophyte abundance. Given the hypotheses presented and the conclusions drawn, one would expect there to be an interaction between CO2 addition and macrophyte abundance such that adding carbon dioxide would have a stronger effect on pH and pCO2 when macrophytes were rare and a weaker effect when they were present. The additional advantage of this approach is that one could partition the variance among these variables. Yes, the authors currently conclude that ignoring the macrophytes causes one to misunderstand how the system is functioning, but it remains unclear to me exactly how important variation in macrophyte abundance really is. Sure, the p-values are significant, but is this a major force in these pools or is it something that only explains a bit more of the variance than one would have explained otherwise? If the authors decide to retain their current statistical approach, I would like to see a justification for not using alternatives such as multiple regressions or ANCOVAs.

Minor comments by line number

51-59: Much of the variability in pH along the coast, in both space and time, is driven by patterns of upwelling. I would be willing to bet a modest sum of money that upwelling dynamics are a more important spatio-temporal forcing variable in the California Current system than local photosynthesis, at least at scales beyond tidepools, semi-contained bays, and other bodies of water with high residence time relative to their volumes. Upwelling deserves at least a mention here as a source of pH variation along the coast. There are several papers by Feely and others to support this.

103-105: In the context of this study, the range of pool volumes and surface areas are at least as interesting as the means, and should also be reported.

122: Please provide the exact dates.

131-133: That seems like a reasonable assumption to me. But how similar were the two days in terms of the weather? Brighter sun on one of the two days could influence photosynthesis, and a stiff breeze could result in increased mixing within the pools and perhaps increased loss of CO2 to the atmosphere.

144: Was there any spatial heterogeneity in carbonate chemistry within the pools? I don’t have a good sense for how quickly CO2 would diffuse or mix out into the entire pool, and if there would be a gradient of CO2 concentration moving away from the air stone.

155: mV is a unit, not a variable. You can say that you measured pH by recording the voltage in mV.

184-190: Although tide pools are closed systems in terms of water at low tide, they are not closed to the atmosphere. Were the pools gaining or losing CO2 across the water-air interface over the course of 6 hours? If so, pool surface area : volume would matter. Is it worth including this as a term in your statistical model, or at least ruling out differences in SA:V between treatments? Or can you justify this effect being so small as to be negligible? Ah, I see you do consider this (line 199 and onward), but it isn’t clear how this was done. You would still need to know the surface area of the pool (not the surface area of the bottom) relative to the volume, and I don’t see that listed a measured variable.

216-217: How was invertebrate biomass calculated? Count data multiplied by some standard for each invertebrate species? Or something else?

234, 273: My natural inclination is to compare Figure 1 to Figure 4 to understand this point. However, Figure 1 is a rate (change per hour), and Figure 4 is an absolute change. I don’t think you need to change the figures, but it would be worth pointing this out so that readers don’t mistakenly assign meaning to the differences in y-axis scaling.

280: Confusing: isn’t the rate of pH change positive for all pools? I assume you mean that the addition of CO2 increased the positive rate of pH change.

281-282: If macrophytes buffer the system by drawing down CO2, how would adding CO2 enhance their ability to draw down CO2? It would be worth trying to provide a potential mechanism for that surprising result.

308: Perhaps daytime benefits to calcification outweigh (unmeasured) night-time costs, although I think you need to state that the effects of macrophytes have not been quantified at night to determine their actual importance. However, reduced calcification is not the only effect of ocean acidification. Couldn’t macrophytes indirectly harm other species at night through physiological effects of elevated CO2?

340: The word “essential” seems overly strong here.

Figure 1: The y-axis is a bit of a mind bend. I would add a second set of y-axis labels to the right hand side of the plots (the frame around the graph already provides a second y-axis on the right), and label the area above zero as “pH increases more rapidly with CO2 addition” and the area below zero as “pH increases less rapidly with CO2 addition”. At least, I think that is what the graph is telling me. A similar statement can be included on panel B for effects on pCO2.

Figure 2: Put a box around your legend so that the reader doesn’t mistake your symbol legends as data points. Or you could move the legend outside of the frame.

Figure 4 legend: The 2 in pCO2 is not subscripted in one instance.


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: PRIMARY PRODUCERS MAY AMELIORATE IMPACTS OF DAYTIME CO2 ADDITION IN A COASTAL MARINE ECOSYSTEM
Review round: 1
Reviewer: 3

Output:
Basic reporting: The authors examine the biological and chemical interactions in seawater, using tidepools to look at these interactions in situ. They link tidepool composition to changes in seawater carbonate chemistry within tidepools. The study uses a paired experiment in 10 tidepools where CO2 is added with yeast (n=5), then switching the treatments to examine the effects.  The effect of the CO2 appeared more related to the composition of the tidepool (particularly photosynthesizers) than to the treatment per se. The methods, results and figures are generally clear.
Experimental design: The study uses a paired experiment in 10 tidepools where CO2 is added with yeast (n=5), then switching the treatments to examine the effects. While the scatterplots presented seem a little sparse, the message still seems robust and convincing.
Validity of the findings: The study demonstrates the local effects that biological processes of photosynthesis and respiration have on coastal seawater chemistry and is thus worth publishing. Again, the sample size is not great, but the patterns are clear.  I have several comments for the authors, but all are relatively minor and can be addressed with the data on hand.

On L176 – Be clear about what was measured versus what was estimated with ‘seacarb’. TA was measured, I gather. However, it was never reported (that I could see), but only used for estimating calcification. The authors should be cautious about using the change in TA to infer calcification because there is evidence that the primary producers change alkalinity through the process of fixing carbon. See e.g. Brewer and Goldman 1976 L&O, Stepien et al 2016 PlosOne. These studies suggest that TA changes are occurring independent of calcification rates and the authors should consider this possibility in their NEC estimate. It is likely the case that their NEC estimates may be confounded with other processes.
Additional comments: Abstract – Sentence “Effects of CO2 additon on pH and pCO2 were not apparent unless we accounted for seaweed surfgrass abundances” is a bit vague.

L 145: the statement ‘due to nonlinearity in the carbonate parameters across time …” seems important. Does this nonlinearity reveal anything about the proposed ‘buffering’?

Fig 4 caption – the phrase “when community composition was not taken into account” is vague. It is simply the result. And in some ways, it seems that this should come first – then the exploration of plant biomass, etc. The SE bars are large and also motivate investigating the composition.

There were several instances where I thought that the authors could have used a more foundational or exact citation:
L 49: Wootton et al. 2008 PNAS, Thomsen et al 2010 Biogeosciences
L 67: The Nielsen et al citation is a non-peer reviewed report and contains no data showing any ’buffering’ and is thus not an accurate citation for the statement. Additionally, the Silbiger and Sorte citation has some of the same data reported here – correct? So I suggest that the authors examine other studies. One suggestion is Semesi et al. 2009 MEPS would be better. Or Delille et al 2000 Polar Biology

In general, the authors should be more rigorous about their citations of macrophyte effects. My take is that there are several papers that show variable carbonate parameters inside of any area with dense macrophytes (Frieder, Koweek), but these do not necessarily show ‘buffering’ and are not always compared with areas without macrophytes, limiting our inference. Just a cautionary statement for all.