Datasets:

CleverShovel

/

paper_reviews

like 1

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.

Title: HOW HAS OUR KNOWLEDGE OF DINOSAUR DIVERSITY THROUGH GEOLOGIC TIME CHANGED THROUGH RESEARCH HISTORY? Review round: 3 Reviewer: 1

Basic reporting: In general, I followed the course of the paper. The structure and referencing are sound, the text mostly unambiguous, and the relevant raw data available. I did, however, note a few typos, omissions and ambiguities. These are addressed, by order of their appearance in the text, below: Line 64-65: “(e.g. (Sepkoski et al. 1981); Sepkoski Jr (1993); Alroy (2000b))” – the bracketing around the first reference here is inconsistent with the second two. Line 69-70: “At the present, the first argument appears to be the best supported by analytical evidence” – I feel that this needs its own references explicitly tied to it, as it is something of a bold statement. Line 131: “(November 2017; note a new download was performed subsequent to peer review)” – When was the new download performed? Or was that the download performed following peer review? If the former is the case, were all the analyses repeated on the new download? If so, why report the previous one? Line 169: “We stopped at 1991” – Is there any particular reason for this cutoff? Was it due to computational constraints, deemed a sufficient sample, or is something about the post-1991 record considered fundamentally different to the dinosaur record from before then? I think all of these positions are defensible, but would like to know the author’s thought process on the matter. Line 413: Typo: should read "steadily increasing" or "steady increases in". Line 414: Typo: should read Jurassic here instead of Cretaceous (I think?). Line 435: “meaning that we cannot interpret anything from these results with any high level of confidence” [emphasis added] – Really, this means that we cannot interpret anything with any level of confidence – it is 95% or nothing, after all. Line 489: It should probably be noted in the discussion of it here that the Smith & McGowan (2007) method has seen substantial criticism (e.g. Sakamoto et al., 2016) - it would help inform the next few lines discussing about how this influence has apparently been mitigated since. Line 554: There is a break between two sets of references here – I think that it is just a single series of citations that has been broken, but it may be that a sentence has been deleted. Please check. Line 627: “This find is somewhat contrary to that of Sakamoto et al. (2016)” – Do you have any idea as to where this discrepancy may come from? I suppose it may be a result of the temporally biased nature of sauropod phylogenies – relatively few titanosaur taxa were included in phylogenies as of 2016, and so may result in underestimated speciation/cladogenesis rates. It may be relevant to consider imperfect phylogenetic coverage as a point in support of count-based diversity metrics, even when they require correction for sampling. Alternatively, it may represent a taxonomic decoupling between genera and per-species dynamics. I appreciate this is all currently speculative, I was just curious. Figures The time (x) axis in Figures 4-12 is quite cluttered. Maybe it would be clearer if they were modified to feature a standard, coloured, geological timescale as the x-axis? Experimental design: The research question that the analyses were conducted to address is well-identified. The methodology is generally transparent, save for one ambiguity I would like to clear up. Lines 149-150: “These databases are based on a comprehensive data compilation effort from multiple workers and represent updated information on dinosaur taxonomy and palaeontology at this time.” – Just to be clear, how do your (e.g.) cumulative frequency plots of named genera (Figure 2) deal with taxa currently considered invalid? Are only taxa currently considered valid included at all; does the curve simply reflect the total number of named genera regardless of current validity; or are all taxa named within each time bin included, but with those later deemed invalid subtracted from the appropriate time bins? Taxonomic revision represents an (arguably) equally important contributor to our developing understanding of diversity patterns as does discovery, so this is highly significant and so must be stated as clearly as possible. Currently, my understanding is that for the occurrence-based analyses you are using the taxonomy as of 2015 in all of the two-year bins? This would be appropriate as it eliminates another potential variable to focus on sampling, but this needs to be explicitly stated in the main text to ensure that the reader does not confuse it with a comparison of the ‘state of knowledge’ of dinosaur diversity through publication history. An additional cumulative plot of genera considered valid in each bin may add some nuance to Figure 2, though. My more substantial concern with the experimental procedure conducted herein is that bootstrapping of results, in order to calculate confidence intervals, was apparently not performed. This is expanded upon in section 3 below. Validity of the findings: I am satisfied that the results presented herein are broadly valid and agree that they are worthy of publication. I applaud the authors for publishing negative results, something universally acknowledged as important but relatively rarely actually performed. I also think that this study will be useful as a starting board from which further analysis can look into other potential biases, as discussed in the text. Most importantly, I think that the chief conclusion – that ‘global’ signals are highly uncertain due to their nature as a gestalt of heterogeneously-sampled and unstable regional data – is both valid and significant to a field in which ‘global’ curves remain commonplace. However, I am concerned in that only mean subsampled diversity values are reported and compared, with 95% confidence intervals apparently not calculated. This is highly problematic when the results are then used to lend support to purported evolutionary events across the Jurassic-Cretaceous boundary (e.g. 519-521): even error bars on the ‘global’ results would help to allow this claim to be appropriately evaluated. I appreciate that it is already obvious that there will be low statistical power in many time bins in particular regions, and that estimating error is less likely to have an impact on interpreting the main results comparing subsampled diversity between 1991 and 2015, given that results are generally similar aside from very different individual points. Wide error bars are already pre-empted by the chief conclusion that ‘global’ patterns are highly uncertain due to instability in individual regions but including them would help quantify this. In addition, given that an implicit practical aim of this study is (presumably) to indicate where in the sampling curve is “good enough” to estimate diversity in an exemplar case, would that not most appropriately be handled by inspecting when the 95% confidence intervals first show substantial/total overlap with those calculated for data from 2015? Additional comments: In summary, although I do see virtue in the approach and interest in the results that would merit publication, I do still have some concerns that I, ideally, would like incorporated into the analyses, and at the very least acknowledged in the discussion. My primary concern is the lack of consideration of confidence intervals in the interpretation of a genuine biological signal across the Jurassic-Cretaceous boundary: I also would appreciate clarification on how changes in taxonomy were handled. Still, I do think that the results herein are worthy of publication. Although there is partial overlap with some previous studies, collaboration of previous works and dissemination of negative results are both uncommon yet important in science. In particular, the main conclusion from this study (that “global” diversity patterns in the fossil record are highly problematic) is one that really cannot be stated enough. I hence feel that I can recommend it for publication in PeerJ, provided that the above comments are satisfactorily addressed. Still, as these revisions will require re-analysis in order to generate confidence intervals, I would appreciate the opportunity to see it again.

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.

Title: COMPARATIVE GENOMIC ANALYSIS OF A NEW TELLURITE-RESISTANT PSYCHROBACTER STRAIN ISOLATED FROM THE ANTARCTIC PENINSULA Review round: 1 Reviewer: 1

Basic reporting: no comments Experimental design: no comments - The experimental design is valid. Research question is well defined and meaning. Methods are described with sufficient detail and information to replicate. Validity of the findings: no comments - The results and findings are also valid. The manuscript highlights the diverse nature of the Psychrobacter genus, provide insights into potential mechanisms of metal resistance. The data is robust and conclusions are well stated. Additional comments: The manuscript 21147 “Comparative genomic analysis of a new tellurite-resistant Psychrobacter strain isolated from the Antarctic Peninsula” the draft genome of a strain of Psychrobacter and comparative analysis with other diverse Psychrobacter strains. This high tellurite-resistant strains was identified as Psychrobacter glacincola and ~100 metal resistance genes were identified. Comparative analysis showed strain BNF20 was evolutionarily divergent from other Antarctic Psychrobacter isolates. In general, I think this manuscript merit to be published in PeerJ. 1. This manuscript has more than 30 pages, in my opinion, it should be abbreviated. 2. line 110-line 112, are there any references or data to support this phenomenon? 3. line 126, “Bacteria were isolated at 25 ℃”, I wonder why the authors isolate bacteria at 25 ℃ and not at lower temperatures (5 or 10 ℃), for it well-known that Antarctic is the coldest on Earth. 4. Results 3.1, in my opinion, it is not sufficient to identify the strain as Psychrobacter glacincola merely based on 16S rRNA gene sequence and fatty acid composition. 5. line 255-256, “(King George Island,-266 62.183183, -58.933355)” should be deleted. 6. line 295-296, please make it clear that rRNA genes are organized as cluster or operon. 7. line 363-366, “sp.” should not be italic. 8. line 420-421, do Bacillus and Burkholderia belong to the same genus?

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.

Title: COMPARATIVE GENOMIC ANALYSIS OF A NEW TELLURITE-RESISTANT PSYCHROBACTER STRAIN ISOLATED FROM THE ANTARCTIC PENINSULA Review round: 1 Reviewer: 2

Basic reporting: The authors reported the genome sequence of a new Antarctic bacterial species and provides a bunch of bioinformatics and experimental analysis that genetically and phenotypically typify/characterize such new species. #General language issues# The paper is well written although some points may deserve an additional editing, for example: • Line 49 and 50: missing subject ‘Finally, investigating the presence and taxonomic distribution of ter genes in the NCBI´s 49 RefSeq bacterial database (5,398 genomes, as January 2017), revealed that 2,623 (48.59%) showed at least one ter gene.’ 2,623 what? Authors should add ‘genome’ or ‘organism’ or ‘bacteria’ or similar. Same in the following line: “At the family level, most (68.7%) harbored one ter gene and 15.6% exhibited five (including P. glacincola BNF20).” Most …? The subject is missing. • Line 52: “Overall, our results highlight the diverse nature of the Psychrobacter genus” What do authors exactly mean with ‘diverse’? Here a rephrasing may help clarifying the general scope. • Line 268-269: “Previously, it was identified as P. inmobilis by partial 16S rRNA gene sequence analysis” I would rather suggest: “Initially, it was erroneously identified/labeled as P. inmobilis based on partial 16S rRNA gene sequence analysis” • Line 311-312: “No genome exhibiting >96.5% ANI and 60% alignment fraction was found, suggestive of genomes belonging to the same species” Here text is highly misleading. #Tables and figures# Caption in Table 2 is incomplete, it should be edited to include also reference to the third column. “Table 2. Minimal inhibitory concentrations (mM) of different metal(loid)s for P. glacincola BNF20” Authors could possibly add ‘compared to MIC for E. coli BW25113’ (or similar). Experimental design: no comment Validity of the findings: The author state that about 100 genes possibly conferring resistance have been found in the genome, however these results are not supported by experimental tests (except few cases). Could you please give some details? How do you explain the discordance? Additional comments: I would suggest to clearly state that only 16S RNA is available for the strains used in the phylogenetic tree. Readers may in fact argue that those strains should be also used in ANI test. This would also enforce the statement in the abstract ‘… the bacterium was identified as Psychrobacter glacincola BNF20, making it the first genome sequence reported for this species.’ which is not reported elsewhere.

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.

Title: COMPARATIVE GENOMIC ANALYSIS OF A NEW TELLURITE-RESISTANT PSYCHROBACTER STRAIN ISOLATED FROM THE ANTARCTIC PENINSULA Review round: 3 Reviewer: 1

Basic reporting: no comments Experimental design: no comments Validity of the findings: no comments Additional comments: The revised MS peerJ-21147 has been revised according to the reviewer's comments, and the major comments have been answered clearly in " peerj-21147-Letter_to_the_Editor_05JAN2018.doc".

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.

Title: COMPARATIVE GENOMIC ANALYSIS OF A NEW TELLURITE-RESISTANT PSYCHROBACTER STRAIN ISOLATED FROM THE ANTARCTIC PENINSULA Review round: 3 Reviewer: 2

Basic reporting: no comment Experimental design: no comment Validity of the findings: no comment Additional comments: The authors have addressed all the weakness present in the previous version of the manuscript

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.

Title: ANTS CONTRIBUTE TO POLLINATION BUT NOT TO REPRODUCTION IN A RARE CALCAREOUS GRASSLAND FORB Review round: 1 Reviewer: 1

Basic reporting: . Experimental design: . Validity of the findings: . Additional comments: 12 December 2017: Referee's report for PeerJ on Michael Rostás, Felix Bollmann, David Saville, Michael Riedel "Ants contribute to pollination but not to reproduction in a rare calcareous grassland forb " This an interesting and well-conducted study following a clear logic. It confirms in the example of an Euphorbia species that ants are no effective pollinators of plants having no special adaptations to ant pollination. This message is not new but still valuable. However, and this is one of the merits of the paper, the authors also observed seed germination and showed that ants have a clearly deleterious effect on that forb species. The authors also made credible that the high micro-site fidelity of Formica cunicularia should lead to geitonogamy which adds to the well-known deleterious effect of pollen sterility caused by metapleural gland secretions. Demonstration of pronounced micro-site fidelity of Formica cunicularia was surprising for a myrmecologist. These ants, as many other species of the subgenus Serviformica, do not establish territories, are subordinate to most other, even smaller, ants when encountering them at a food source and were believed to explore their home range in search for food opportunistically and at random. At least the assignation "random" is has to be deleted now – the activity of individual foragers is apparently directed to rather narrow sectors just as in the foragers of the dominant Formica rufa group species (subgenus Formica s.str.) which exploit and defend rich and very long-lasting food sources. I recommend acceptance of the paper with minor changes or additions. I suggest the following (a) The authors have stated " We conclude...that ants, although the most frequent visitors, play a negligible role in the reproduction of E. seguieriana." Integrating all facts we know, the authors should better say that ants definitely play a deleterious role in reproduction of Euphorbia segueriana the more as one other point was not addressed by the authors: If one considers that Serviformica ants occupy the flowers for a considerable time and that they are predatory on diverse insects, they will reduce the visiting frequency of the flowers by the true (flying) pollinators – even if it is probably a rare exception that the F. cunicularia can successfully catch such a pollinator on the very top of the plant. The pollinators are chased off at least (see also discussion of this issue in Claessens & Seifert 2017). (b) There is a rather weak literature survey for sources referring to the area of observation: the Holarctic and Central Europe in particular. The only plants in Central Europe that are specially adapted to ant pollination are the two orchid species Coeloglossum viride and Chamorchis alpina (Baumann & Baumann 2010, Claessens & Kleynen 2011, 2016; Schiestl & Glaser 2012, Claessens & Seifert 2017). As this strongly contrasts the situation described here, the issue should be commented by more than a single sentence. (c) The message of Fig. 5 is poor. Delete? Keeping the anonymity of the referee is not necessary. With best wishes Bernhard Seifert Suggested literature: Baumann, B. & Baumann, H. (2010): Pollination of Chamorchis alpina (L.) Rich. in the Alps by worker ants of Formica lemani Bondroit: first record of ant pollination in Europe. – J. Eur. Orch. 42 (1): 3-20. Claessens, J. & Kleynen, J. (2011): The flower of the European orchid - Form and function. – : Jean Claessens & Jacques Kleynen, Geulle: 440 pp. Claessens, J. & Kleynen, J. (2016): Orchidées d'Europe, fleur et pollinisation [Orchids of Europe, flower and polination]. – Biotope Éditions, Mèze: 448 pp. Claessens J, Seifert B 2017: Significant ant pollination in two orchid species in the Alps as adaptation to the climate of the alpine zone? – Tuexenia 37: 363–374. Schiestl, F.P. & Glaser, F. (2012): Specific ant-pollination in an alpine orchid and the role of floral scent in attracting pollinating ants. – Alpine botany 122 (1): 1-9.

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.

Title: ANTS CONTRIBUTE TO POLLINATION BUT NOT TO REPRODUCTION IN A RARE CALCAREOUS GRASSLAND FORB Review round: 1 Reviewer: 2

Basic reporting: excellent Experimental design: creative Validity of the findings: very convincing Additional comments: This study examines a rare Euphorbiaceae plant species with flowers that are most frequently visited by ants. The investigators conduct some creative experiments, marking individual ants with different colors on the plants on which they were observed, and saw on subsequent days that the ants never seemed to visit other plants, indicating that all their movements were likely within individual plants (and presumably back to their nests). From this they reasonably conclude that the ants may transfer pollen but only for geitonogamous pollination. Exclusion experiments were employed to demonstrate that plants need visitors to their flowers for fruit set, but that flying insects provide most of the effective pollination (not significantly different from open controls), whereas plants with only ants visiting their flowers set less than one-third of the fruit of other plants. Furthermore, the seeds from those ant-only plants did not germinate well, suggesting there is some inbreeding depression operating. There were two ants species observed visiting flowers, and one carried much more pollen than did the other. However, a larger proportion of the pollen grains taken from the bodies of the first species were inviable. The scientists implied that the pollen grains were inviable due to the antibiotic secretions of the metapleural glands of the ants, but I wonder: How long is pollen viable when not in contact with ants? And what proportion of fresh pollen is viable? Maybe they know, and did not include this info in the paper. If not, I suggest that it may also be a function of the amount of time spent on the body of the individual ant, for in many plants pollen is viable only for one or two days, and it is possible that pollen stays on an ant so long it may simply be old. This elegant study was quite comprehensive, but only the pollen viability question was left it my mind. Perhaps the authors can comment on that possibility or provide some more evidence that it was the ant secretions that rendered the pollen inviable. Actually I see from the data table on pollen viability, they evidently present data on the natural proportions of viable pollen from flowers – is that correct? And so just a little more comparison and explanation would be helpful. In Fig. 1 caption - I think the term ‘cyathium’ should be used as it is one only that has the ant on it. It may be reasonable to eliminate Figure 5. Fig. 8 caption – if * means that, what do *** mean? Maybe better to put different letters above the bars.

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.

Title: CHIMPANZEES (PAN TROGLODYTES) DISPLAY LIMITED BEHAVIOURAL FLEXIBILITY WHEN FACED WITH A CHANGING FORAGING TASK REQUIRING TOOL USE Review round: 1 Reviewer: 1

Basic reporting: No comment. Experimental design: I have one major concern (pertaining to the authors’ objectives and hypothesis-testing framework… or lack thereof) that needs to be addressed before I can recommend this manuscript for publication. A couple of minor specific comments should also be addressed. Validity of the findings: No comment. Additional comments: This study aimed to investigate the capability of chimpanzees to alter their behaviour in response to an artificial foraging task (i.e., liquid-retrieval task) in which viable solutions became gradually restricted in captive chimpanzees originating from two separate subgroups with different experiential histories, and after providing them with limited exposure to scaffolding towards a novel tool technique. Overall, this is a well-written manuscript on an interesting topic with key implications for our understanding of the evolution of cumulative culture in our hominid ancestors. The Methods, Results, and Discussion sections are strong and well laid out. However, I have one major concern (pertaining to the authors’ objectives and hypothesis-testing framework… or lack thereof) that needs to be addressed before I can recommend this manuscript for publication. A couple of minor specific comments should also be addressed. MAJOR CONCERN: I think the “study aims” section (Line 120-134) should take a more robust hypothesis-testing approach. In the present version of the manuscript, this section is much too general, descriptive and vague (“This may be anticipated to impact their problem-solving abilities”; “this study also considers the impact of subgroup membership upon task performance”; “we examined whether chimpanzees could acquire novel tool behaviour through exposure to favourable affordances”). After providing a very interesting background review of the literature on behavioral flexibility and conservatism in tool-use and tool-making tasks, I am wondering why the authors did not use some of the theoretical aspects they introduced (e.g., the “copy-if-dissatisfied” social learning strategy) and the potential asset of their study conditions (i.e., a group of subjects originating from two different subgroups with different experiential histories) to generate at least two competing/alternative hypotheses (e.g., behavioral flexibility versus behavioral conservatism… or functional fixedness), each of them being associated with a series of testable and mutually exclusive predictions. Without this framework, I started reading the Methods, Results, and Discussion sections with no specific expectations in mind, which, I believe, may seriously weaken the impact of the study. MINOR CONCERNS: To what extent the authors’ results could be interpreted in terms of “functional fixedness”, which is not mentioned in the paper? As a reminder, functional fixedness is the disinclination to use familiar objects (including tools) in novel ways, and as such, is a likely inhibitory factor in tool innovation? (cf. Brosnan and Hopper, 2014). Line 381: “although we are not aware of any direct experimental evidence for such hypothesised effects.” – Please read the fascinating observational and experimental studies of the developmental processes and indirect social influences (via behavioral artefacts) underlying the acquisition tool use and tool-making techniques (Pandanus tools) in wild New Caledonian crows, and showing that juvenile birds learn these complex behaviors by manipulating parents’ (and others’) discarded tools and using counterpart artefacts (i.e., negative template of the tool after removal from the thick and enduring Pandanus leaf) as easier starting points for tool-making (e.g., work by Jennifer Holzhaider, Gavin Hunt and Russell Gray).

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.

Title: CHIMPANZEES (PAN TROGLODYTES) DISPLAY LIMITED BEHAVIOURAL FLEXIBILITY WHEN FACED WITH A CHANGING FORAGING TASK REQUIRING TOOL USE Review round: 1 Reviewer: 2

Basic reporting: Dear authors, This is an interesting study on the ability of individual chimpanzees to change their behavior when a task changes. Experimental design: There are two main points I’d like more information on throughout: 1) Examine within-subject changes in behavior of effective vs not effective solutions depending on which phase the response was recorded in (see more details below). 2) Say something about why you tested them socially in the introduction and how you predict this to influence your measurement of flexibility and innovation. Validity of the findings: My more detailed comments follow below. Additional comments: L33: define “conservatism” or just say what it is rather than using jargon L39: explain a bit how flexibility supports problem solving L41: define “culture” and “cumulative culture” L42: say something about the tension in cumulative culture between modification of the trait through flexibility and needing to have high copying fidelity. The latter is often thought to be the main facilitator of cumulative culture (e.g., Hunt & Gray 2003). L46: how do you predict these traits (flexibility, innovation, social learning) limit cumulative culture in chimpanzees? L52: Logan 2015 and Logan 2016 are the same paper. The 2015 version is the preprint at bioRxiv and the 2016 version is the peer reviewed published version. You can delete the Logan 2015 citation. L59: did the differences in flexibility support or refute predictions? L60: why are “individual differences” important to cumulative culture and flexibility? A bit more explanation will help place these results in context so the reader can follow your argument. L64: were individual differences not found in corvids and great apes because they weren’t investigated? Why the switch to interspecific for these taxa and what does this level of explanation contribute to furthering your argument about flexibility and cumulative culture? L71: define conservatism L73: point out that it might reflect the flexibility of the innovating individual(s) (but not those that subsequently used the innovators’ technique/material choice). L82: I’m not sure how you consider innovation distinct from flexibility. It would be good to define innovation in the first paragraph of the introduction. L101: indicate whether the great apes were successful on the multi-access box task. L102: explain how the juice retrieval task works. L113 and 117: in the discussion, you don’t mention what your results indicate with regard to whether chimps copy if dissatisfied or explore if dissatisfied. If you didn’t intend to test these predictions, I would exclude the discussion of them from the introduction. L120: given your study aim, what were your predictions? L129: explain how the different life histories might impact their problem solving abilities. L133: explain what the favorable affordances were and how they differed from scaffolding. L137: of the 18 individuals, how many were from which subgroup? L148: were chimps tested individually? It looks like it was a mixture of individually and with others present. If others were present when an individual was being tested, did you account for their opportunity to learn about the task socially? L159: transparent or opaque tubes? L161 and 162: inner or outer diameter? L172: how much previous experience did the chimps have with the different tool options? If some tools were novel, did you check to see if they were afraid of them? It sounds like some individuals had been previously rewarded for using sticks. It would be good to mention their reinforcement history with each material and discuss how this might influence their tool preferences in the tasks. L175: was the juice reachable using their hands/lips/tongue at a depth of 7cm? Which of the tools provided were functional in stage 1? L176: was the “bait” the juice? How many attempts could occur during each session or did the session end after the juice was reached the first time? Were the number of different tool choices/attempts per session accounted for in analyses? L177: how did you determine the end of a session? Why is it important that the tube was emptied of liquid at the end of each session? Did the chimp observe the emptying? L180: depth 7cm again? L185: explain which tools were functional and which were not. L189: I’m not sure how the number four was arrived at for the inserted stick sessions. L195: why were chimps allowed access to the empty tube and tools between sessions? Did you record whether they attempted to use any of the tools on the tube between sessions? If they did, in the absence of a reward, they may have learned not to prefer certain tools. L209: kudos for citing R packages! L214: could the technique also be “not effective”? L227: did all 18 individuals observe another interacting with the task? L237: novel to them in terms of this was the first time they had used the technique, but not novel to them because they had seen another use this technique? It is important to separate when individuals acquire information versus when they use information if you are testing something about innovation. I would think innovation is when an individual invents a new solution to a problem without having seen others perform that solution. L243: what does “potential across phases” mean? L244: since the functional techniques differed according to phase, effectiveness should be classified only with regard to the phase that the response variable was recorded in. So a hand response in Phase 2 would be Not Effective, whereas it would be classified as Effective in Phase 1. This will be really important for determining whether individuals changed their behavior according to the phase. If this wasn’t already accounted for in the model (it looks like it wasn’t), I would recode the response variable for effectiveness (yes/no) by phase and tool type and rerun the analyses. In the case of the stick, you could break them down into two categories: long (functional only in phase 1) and short (functional in both phases?). Categorizing the response variable in this way will allow you to determine whether individuals changed their behavior according to the phase. The within-individual behavior change will be the key to determining whether individuals exhibit flexibility. L268: because of what I brought up in the previous comment, it’s not clear whether individuals are rarely choosing Always Effective tools in phase 1 because they are effectively getting the juice using the Partially Effective tools, which is why they then increase their use of Always Effective tools in phase 2. I think categorizing tools as either effective or not according to which phase they are in will be key for understanding the results. L284: why were only 4 individuals in this phase? How were these individuals chosen? L286: if Frek and Kindia didn’t retrieve the reward even though it just needed to be licked off of the leaves they pulled out of the tube, were they motivated to participate in the task? It appears that there was no food deprivation prior to testing to increase their motivation in the tasks. How do you know that juice is a high enough reward to motivate them to try hard in tests? L287: which individuals are “the four individuals who encountered the leafy stick solution first-hand”? It’s not clear whether these are Kindia, Edith, Frek and Pearl or not. L308: what reward was Manrique et al (2013) using in their tests and was there food deprivation prior to testing? Could this help explain the differing chimp results on a problem solving task? Or perhaps the multi-access box is easier to solve than the test you gave? L327: in at least a few individuals? At the species level? Specify at what level you think flexibility is occurring. L331: which study lacked social information, the Davis et al study? L332: if I understand phases 1 and 2 correctly, they had the opportunity to socially learn about the functionality of the tools by watching conspecifics. These individuals would serve as “demonstrators”. I’m having trouble following “Had the chimpanzees in this study failed to discover ‘Always effective’ techniques, this lack of social information would be a plausible explanation for the relatively diminished behavioural flexibility observed”. Your chimps did have access to social information about effective techniques and they discovered many effective techniques. L393: explain a bit more about “cultural biases” - the preexisting behaviors in the group, which vary among groups, will be the ones more often used? L399: explain what “favourable affordances” are. L483: what factors would you recommend exploring? Table 1 caption: mention that all individuals observed others attempting/solving the test using a variety of techniques (if this is true). Table 2: break “Effective in all phases” into 2 columns, one for each phase so readers can see which techniques were effective or not in each phase. Table 2 caption: note at what hour phase 2 started. Table 4: excellent that you provided the full model results! Could you note which effects were fixed and which were random? If random effects aren’t included in the table, please add them. Edinburgh_Dipping_data.xlsx: rows 330, 602, 806, 910, 911, 972, 1106, 1225, 1271, 1496, 1497, 1552, 1553, 1671, 1672, 1804, 1805, 1836, 1837, 2058, 2059, 2123, 2239, 2491, 2769, 2770, 2799, 2819, 2892, 2922, 2936, 2962, 2976, etc are empty. Were they excluded from the analyses? If they were, they should be deleted from the data sheet to avoid confusion. Were the Unknowns excluded from the analyses? Supplemental Article S1: - Fig S1: y-axis should say “Always effective” I think. - Table S1: add random effects to the table. Indicate in the table that Phase refers to Narrow condition and that the intercept includes the Wide condition. I hope these comments have been useful! All my best, Corina Logan University of Cambridge References Hunt, G. R., & Gray, R. D. (2003). Diversification and cumulative evolution in New Caledonian crow tool manufacture. Proceedings of the Royal Society of London B: Biological Sciences, 270(1517), 867-874.

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.

Title: CHIMPANZEES (PAN TROGLODYTES) DISPLAY LIMITED BEHAVIOURAL FLEXIBILITY WHEN FACED WITH A CHANGING FORAGING TASK REQUIRING TOOL USE Review round: 1 Reviewer: 3

Basic reporting: This study by Harrison and Whiten investigates behavioural flexibility in chimpanzees by providing them with different apparatuses that afford different solutions. In the first experimental phase (“Wide Tube”) the juice contained in an apparatus tube could be accessed by using either both bare hands alone or else by recourse to a wide assortment of materials available beside the apparatus. In a second phase (“Narrow Tube”) the opening of the tube was made narrow, thereby rendering inefficient some of the tools and impeding previous solutions. In a third phase, an attempt was made to investigate the structure of their behaviour by observing whether the four chimpanzees might recognize the appropriateness, for accessing the juice, of a suitable tool placed inside the tube, thereby affording a clue that could guide their choice in future. The results showed a moderate amount of behavioural flexibility because even when chimpanzees’ use of an invariably effective technique increased by 50-fold in the ‘Narrow Tube’ phase, as compared to the previous “Wide Tube” one, the apes were reluctant to relinquish previously-employed albeit now inefficient strategies. Nevertheless, in the “Wide Tube” phase those strategies still comprised 50% of all individuals’ attempts and “no individual that made more than one attempt used “Always effective” techniques for a majority of their attempts”. The “scaffolding” provided by the experimental design did not seem to exert any significant change on behaviour. The high percentage of “Partially effective” attempts in the new “Wide Tube” phase owes to the prepotence that those behaviours rewarded hitherto had acquired in the first “Narrow Tube” phase. Both the Introduction and Discussion need refinement and clarification. The authors talk of cumulative culture, behavioural flexibility, individual innovativeness, copying of behaviours by conspecifics, etc. It is understood that cumulative culture can emerge only when some individuals are able to innovate solutions that spread horizontally and are passed from one generation to the next. All the topics included in the Introduction and Discussion are appropriate and relevant, yet in the interest of clarity it would be helpful to organize the information in separate sections or paragraphs: for instance, clustering studies that investigate individual innovativeness in order to differentiate them from those that address social learning of newly-acquired behaviours. Also, it would be convenient to separate clearly those studies in which the changes of the apparatus task wholly prevented subjects from using responses rewarded previously, from those which did not prevent them from using old albeit less efficient techniques. In contrast to previous reports, the flexibility observed here could be simply because the old strategies had become so inefficient as to provide no reward at all (cf. Manrique and Call, 2015). Literature on innovation in chimps seems to indicate that they are reluctant to abandon a previously-rewarded response in so far as it had seemed to work: flexibility may be just what we should expect to see whenever a former response was found later to be utterly fruitless. The authors discuss the results by considering the effects of subgroup yet fail to report how factors such as age (see Manrique and Call, 2015) or hierarchy (Kendal et al., 2015 ) may influence or prevent the acquisition and/or copying of new solutions. In Manrique and Call (2015) it was shown that youngest and oldest individuals were extremely perseverative and failed to abandon old and inefficient responses once the reward contingencies were reversed. Also, another study by the same authors (Manrique and Call, 2011) showed that the oldest orangutans needed considerably more time than younger ones in order to change from the less efficient technique of dipping technique to more efficient sucking in order to drink from a juice container. Interestingly, the only chimpanzee who discovered the most efficient, straw-like technique was a juvenile male. Therefore, it would be interesting for the authors also to analyse their data by focusing on whether age influences behavioural flexibility. Furthermore, because Hopper and colleagues reported a bias towards copying by higher- ranking hierarchy members when individuals were tested in group, it is also necessary to take into account the degree of behavioural flexibility in terms of an individual’s rank: were lower ranking individuals to be those likeliest to change responses, their “innovation” could go unnoticed by conspecifics more readily than were higher-ranking individuals to hit upon the more efficient solution. In lines 328 to 339 the authors refer to the role of an expert model as a constraining factor, which reinforces the need to take into account the hierarchical structures of the two subgroups and the possibility of preferential access by higher-ranking individuals to the apparatus and/or their willingness to change behaviours. Specific comments: Lines 45-46. I am not sure that there is evidence of cumulative culture in chimpanzees at all, yet the authors’ statement implies that there is, albeit limited. Given the rarity of the phenomenon it would be convenient to explain briefly what this evidence is. In line 55 “such as reversal learning paradigms” the work by Manrique and Call (2015) should be added as they also employed a reversal learning paradigm to measure cognitive flexibility as a function of age. References used: Kendal, R., Hopper, L. M., Whiten, A., Brosnan, S. F., Lambeth, S. P., Schapiro, S. J., & Hoppitt, W. (2015). Chimpanzees copy dominant and knowledgeable individuals: implications for cultural diversity. Evolution and Human Behavior, 36(1), 65-72. DOI: 10.1016/j.evolhumbehav.2014.09.002 Manrique, H.M., Call, J. (2011). Spontaneous use of tools as straws in great apes. Animal Cognition 14, 213–226. Experimental design: The main weakness of the study stems from the design: specifically from the fact that individuals were tested in group. Were the authors to have been investigating social learning and transmission of a newly- acquired behaviour, then group testing would have been a mandatory requirement. However, because the stated aim was “to investigate the capability of chimpanzees to alter their behaviour in response to an artificial foraging task” and the method chosen was to test the flexibility of the behaviour and/or innovativeness of the individuals, it might have been preferable to test individuals in isolation and to avoid confusing individual behavioural flexibility with social learning. A more appropriate methodological approach would be first to investigate behavioural flexibility of individuals while tested in isolation with administration of the three apparatus “phases”, and then to select successful individuals and introduce them to the group in order to find out whether or not conspecifics choose the new behaviour after watching how success can be achieved. When presenting new tasks to a group, factors such as rank, social dynamics, etc., may affect an individual’s attempts to solve problems and thus confound interpretation of the results, particularly if comparisons are to be drawn with previous studies undertaken with isolated individuals. Nor yet is generalization of findings helped by using two different subgroups of chimps with different life histories. Many factors in the study (social testing, previous history, etc.) could have impinged on the observed behaviour, thereby rendering it difficult to tease apart the specific influence that each of them could exert on the solving abilities of the apes. Now (Given) that the final results of the study have been arrived at, thereby precluding any modification of the experimental procedure, the authors should go the extra mile by discussing how the variable factors mentioned above might impinge on the purported results. Validity of the findings: Statistical analyses and appropriateness of the interpretation of the results: The statistical analyses employed are suitable and the conclusions reached are derived appropriately from the data provided. I see no problems there. Notwithstanding the fact that results would have been clearer were subjects to be tested alone. Additional comments: No additional comments

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.

Title: CHIMPANZEES (PAN TROGLODYTES) DISPLAY LIMITED BEHAVIOURAL FLEXIBILITY WHEN FACED WITH A CHANGING FORAGING TASK REQUIRING TOOL USE Review round: 2 Reviewer: 1

Basic reporting: No comment. Experimental design: Dear authors, You did an excellent job of clarifying terms and concepts in your revision. Your treatment of testing in a social context and how this relates to behavioral flexibility was also well done and provides a nice base for future studies to build on. Additionally, because you now provide information on the effectiveness of each technique, I understand how you treated individual effects in your models. Since there was very little individual variation in your study, I can see why it makes sense to discuss the results in the context of the whole group rather than at the level of the individual. Validity of the findings: No comment. Additional comments: A few additional thoughts/comments came up as I read your revised manuscript (line numbers are from the tracked changes Word document): 100 - “cumulative progressions rather than unconnected innovations”. Couldn’t cumulative culture result from both cumulative progressions and unconnected innovations? The assumption would be that only those unconnected innovations that were more functional would end up being incorporated into the repertoire. 110 - “Social learning, innovation and behavioural flexibility are expected to work in concert to support cumulative culture – an individual innovates an improvement to a behaviour or tradition, and this improvement is passed on via social learning to other group members.” It’s not clear where flexibility is in this example. It seems from later sentences in this paragraph that flexibility involves the ability to choose the more functional behavior, which keeps culture adaptive? 165 - the western scrub-jay is now called the California scrub-jay…I’m not sure if you should update the name in your paper even though you are referring to the name used in the paper you discuss, but I thought I would mention it. 257 - didn’t the orangutans abandon some solutions and solve some, but not all, of the new solutions in the Manrique study? If so, I would rephrase the sentence to indicate the orangutans didn’t completely fail this task, they just performed more poorly relative to the other species. 320 - “scaffolding in this manner” Please clarify what “in this manner” means because I don’t quite know, which makes it unclear how it differs from learning through exposure to artefacts. 480 - “Note that all techniques (see Table 2) were effective in the ‘Wide Tube’ phase, in which there were few constraints upon potential solutions.” It sounds like there were no constraints in the Wide Tube phase. If there were “few constraints” list what they were. 758 - I would change “cognitive flexibility” to “behavioural flexibility” because the latter is the term used throughout the paper and it is the behavior that is measured. 761 - “and so the age of many individuals in the current study may have impaired their performance” Because most of the individuals in your study were over 27 years of age? All my best, Corina Logan University of Cambridge

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.

Title: HIGH-RESOLUTION MODELING OF THERMAL THRESHOLDS AND ENVIRONMENTAL INFLUENCES ON CORAL BLEACHING FOR LOCAL AND REGIONAL REEF MANAGEMENT Review round: 1 Reviewer: 1

Basic reporting: The manuscript “High-resolution modeling of thermal thresholds and 1 multiple environmental influences on coral bleaching
for regional and local reef managements” by Kamagai and Yamano provides a new and useful modeling approach for coral bleaching integrating citizen science, sophisticated statistical and machine algorithms and satellite data. Introduction and background shows well the context of the research. Literature is well referenced and relevant. Structure conforms to PeerJ standards, discipline norm, or improved for clarity. Figures are relevant, high quality, well labeled and described. Raw data and some codes are supplied. To improve the manuscript to be accepted authors must improve professional English language used throughout. I also recommend authors making available all R codes (including figures/maps plotting). The manuscript is relevant and may be accepted to publication after the minor modifications suggested bellow. Experimental design: The original primary research is within Scope of the journal. Research question is well defined, relevant and meaningful. It is stated how the research fills an identified knowledge gap. Rigorous investigation performed to a high technical and ethical standard. Methods described with sufficient detail and information to replicate but I suggest including all codes (including for plotting all figures). Authors chose GLM and Random Forest for modeling bleaching but not justify why these algorithms were chosen. Please add a sentence explaining the motivation for this choice. Validity of the findings: Data is robust, statistically sound and controlled. Conclusions are well stated, linked to original research question and limited to supporting results. Additional comments: Abstract: Authors refer coral reefs as corals. Corals are animals and coral reefs the environment. Material and Methods: The first paragraph of this section should be considerable shortened. In line 110 I found: “An observer who attempted to submit an observational record to the Sango Map Project was requested to provide the following information as mandatory fields for quality control”. All this information is really necessary or authors can site the monitoring program? Lines 140-146: this section should be considerable shortened Lines 215-217: It is not clear why authors used this data/information. If it is relevant for models building please add a sentence explaining. Line 233-249: Why authors chosen RF and GLM? Please add a sentence explaining the motivation for this choice. What R package was used to perform GLM, please add a citation. There are some assumptions for GLM, what about RF? Please add a sentence explaining if there are some or not. Results: Line 299: “worst” does not sound scientific for variable evaluation. Please add a more technical term such “did not explain well…”. Please see line 367 in Discussion section, this comment extends also for the term “good”. Table 3 – It is uncommon to see tables divided by letters. I suggest to reformat this table (all lines should have values/observations for each column) or to split in four tables. Discussion: Lines 385-387: I really think using RF in to model coral bleaching is very interesting and innovative, please add a sentence explaining how RF is being using for ecology modeling.

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.

Title: HIGH-RESOLUTION MODELING OF THERMAL THRESHOLDS AND ENVIRONMENTAL INFLUENCES ON CORAL BLEACHING FOR LOCAL AND REGIONAL REEF MANAGEMENT Review round: 1 Reviewer: 2

Basic reporting: Kumagai and Yamano took a bold move to challenge NOAA’s predictive model of coral bleaching. By optimizing thermal thresholds and using different environmental parameters and modeling methods, the authors describes the potential of their high-resolution bleaching predictive model to improve local reef management. This interesting insight may be very helpful for small coastal countries where potential bleaching incidents may be overlooked by general models. One concern is that the screening experiment is considered a trial and should not be emphasized in the abstract. The paper is generally easy to follow. However, it will also certainly benefit from proof reading to correct the numerous typographical and grammatical errors. Tables and figures are important and it is critical to lead your audience on how to read or use the information. Abstract: 1. Abstract can be more concise and seems to be very similar to the conclusion section of the paper. Introduction: 1. The authors need to have supporting citations even for general information. For example, in P.3, line 41: “Extreme rising sea temperature … reef-building corals (REF, REF). 2. P.4, line 78: “Observations in local areas of research interest … Database. Can the authors name some areas covered? 3. P.4, line 80: Can the authors name some areas where records are limited? 4. P.5, line 100: Figures and tables should not be mentioned in Introduction. Materials and methods 1. P.7, line 149: Table 1 is an important information. Authors should describe and introduce Table 1 appropriately in the text such as “Steps to analysed the data were summarized in Table 1”. 2. P. 10, line 212. Similarly, for table 2, authors should explain how to use and read table Conclusion: 1. Conclusion is very similar to abstract, authors should consider rephrasing either segments. Table and figures: 1. Table 1: Caption should be more refined and proper. For those without references, are those steps created by the authors? If so, please include ‘This study (2017)”. 2. Table 2: For those terminologies without references, are those terms created by the authors? If so, please include ‘This study (2017)”. Experimental design: Materials and methods 1. P.6, line 112 to 124: What about coral area surveyed? 2. P.10, line 204: Were the climatologic data from July to September obtained from 1997 to 2016? 3. P.13, line 270. Suggest to review the sentence to “In total, we evaluated 22,650 and 36,150 models … RF model respectively”. Discussion: 1. P.20, line 443-449: “Our study showed that reducing UV radiation by increasing screening significantly reduced bleaching risk as … warming”. An actual study of coal screening was not described in materials and methods. Authors should include the description of the experiment if they want to include this point. Validity of the findings: Results: 1. Results can be more qualitative than descriptive. The authors have all the numbers in tables and figures, use them to reinforce the results segment. For example, the improve scores can also be included in results segment. Additional comments: Abstract: 1. P.1, line 3: Suggest to replace “managements’ with ‘management 2. P.2, line 17: Suggest to remove ‘living’ 3. P.2, line 18-20: I don’t understand this sentence. Can the authors try to rephrase this or combine with the previous sentence? 4. P.2, line 31-32: Suggest to review the sentence to “Prediction based on the best explanatory model revealed that coral reefs in Japan are experiencing bleaching in many areas recently. A practical method to reduce bleaching frequency by screening UV radiation was also demonstrated in this paper.” Introduction: 1. P.3 line 47: Suggest to revise phrase to “Degree Heating Weeks (DHW). 2. P.3, line 50: Citing one significant paper from the author should suffice. 3. P.4, line 70-75: Suggest to revise the sentence to “Furthermore, there are potentially interacting environmental stressors such as ultraviolet (UV) radiation (Hoegh-Guldberg, 1999; West & Salm 2003; Maina et al. 2008; Yee at al., 2008) and variables such as water turbidity (REF), topography of the sea floor (REF), … that can affect coral bleaching. Materials and methods 1. P.9, line 195: Can the authors explain what is “MODIS-Aqua and Terra”? 2. P.13, line 270. Suggest to review the sentence to “In total, we evaluated 22,650 and 36,150 models … RF model respectively”. Discussion: 1. P.20, line 429: Replace “coral bleaches’ with ‘coral bleaching’.

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.

Title: HIGH-RESOLUTION MODELING OF THERMAL THRESHOLDS AND ENVIRONMENTAL INFLUENCES ON CORAL BLEACHING FOR LOCAL AND REGIONAL REEF MANAGEMENT Review round: 2 Reviewer: 1

Basic reporting: Authors had greatly improved the manuscript after revision. I recommend this manuscript for publication in PeerJ in the present form. Experimental design: no comment Validity of the findings: no comment Additional comments: no comment

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.

Title: HIGH-RESOLUTION MODELING OF THERMAL THRESHOLDS AND ENVIRONMENTAL INFLUENCES ON CORAL BLEACHING FOR LOCAL AND REGIONAL REEF MANAGEMENT Review round: 2 Reviewer: 2

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

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.

Title: SEROPREVALENCE OF HEPATITIS B VIRUS IN TAIWAN 30 YEARS AFTER THE COMMENCEMENT OF THE NATIONAL VACCINATION PROGRAM Review round: 1 Reviewer: 1

Basic reporting: In introduction section, author shew context of hepatitis B infection and prevalence globally. There are some data need to be updated. 1. Author mentioned that hepatitis B virus infection is a major cause of acute hepatitis, this is not precise because most of the acute infections become immune and the major problem is chronic infection, since majority of chronic infections are lifelong. 2. Author cited literature and said “More than 350 million people worldwide remain chronically infected with HBV”, which should be updated by the WHO new published document (Hepatitis Report 2017, WHO). Experimental design: Suggest to make close linkage between birth cohort and policies change Validity of the findings: 1. What makes difference of HBsAg prevalence is not the birth cohort, but the policies change. Therefore, author should have more discussions about the policies rather than the birth cohort. 2. The HBsAg positivity rate decreased from 9.7% among patients born before June 1994 to <1.0% among patients born after 1992. There is a cross time, please ckeck. 3. See Table 2. Author had clear criteria for age of each group, why there is an overlap for age range. Please clarify. 4. Table 1 needs to be restructured in a more standard way. 5. Figure 2, Can author provide more information and explanation why there is a stepwise decline for anti-HBs? Additional comments: This manuscript is written in simple and common English language, need more professional.

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.

Title: SEROPREVALENCE OF HEPATITIS B VIRUS IN TAIWAN 30 YEARS AFTER THE COMMENCEMENT OF THE NATIONAL VACCINATION PROGRAM Review round: 1 Reviewer: 2

Basic reporting: - Experimental design: - Validity of the findings: - Additional comments: Hu et al. report seroprevalence of hepatitis B virus (HBV) infection in Taiwan, after 30 years of the initiation of the national HBV vaccination program, since 1984. To explore the long-term efficacy of the HBV vaccination program, the investigators analyzed available data on the presence of HBV surface antigen (HBs Ag) and anti-HBs antibody in the sera of a total of 17,611 students enrolled into a Taiwanese university, during 2005-2016. I have some comments that might help to improve the manuscript, below: -The title and other places in the manuscript: the term 'hepatitis B infection' should be clearly stated as 'hepatitis B virus infection'. -The term 'patients' used in the abstract and the main text may not be accurately defined, since the subjects here are students with no diseases. -Line 67: duplicate words (that that). -Line 67-68: four- or three-dose plasma-derived vaccination? please check the number of time points for vaccination, mentioned in the sentence. -Line 74, 77, 78, and other places: "hepatitis B (HB)" should be clearly stated as 'hepatitis B virus (HBV)'. -Line 99-111: the Methods '2.1. National HBV vaccination schedule' - This section seems to be more appropriate to be incorporated in, as a part of, the introduction. -Line 130: titer or level? -Line 130: Please provide a reference for the criteria "anti-HBs Ag antibody < 10 mIU/mL is non-protective". Is it possible to have the immuno-protecitve state against HBV with the detectable anti-HBs Ab level < 10 mIU/mL? -Line 131-132: Please check the criteria for setting 'reactive' VS 'non-reactive' for anti-HBc antibody. Should 'S/CO > 1' be considered as reactive (not non-reactive nor just 1-3)? -Should not begins a sentence with number, i.e., Line 168 and 170. -Line 196: please consider to delete 'due to sampling restriction'. -Line 198-203: This paragraph, as it currently stands, is more like discussion. The APC model analysis seems to be the key information of this manuscript, so please revise this section to report clearly the facts/results (with some details). This includes brief descriptions of some key parameters used in Table 3 (perhaps as footnote), so that the readers who are not familiar with this kind of APC model analysis can follow. -Line 175-176 mentioned the HBV carrier state in males > females, and in contrast, Line 181-182 mentioned the anti-HBsAg antibody level in male < female. Since the male-to-female ratio < 1 (i.e., as shown in Table 1), what is/are reason(s) behind this paradoxical observation, in regard of gender and HBV carriers? -Line 183-186: Anti-HBc antibody can be used to discriminate the HBV protective immunity from natural infection and vaccination. The anti-HBc antibody dropped from 4.3% (in 2008) to 1.7% (in 2012) and 0.6% (in 2016). What does it mean? Rate of natural HBV infection is decreased? What about the other markers (i.e., HBsAg and anti-HBsAg) in this groups of students? -The discussion could be shortened, by for example, removing repeated statements (i.e., the first sentence of the first paragraph), and perhaps shortening/removing the statements that are considerably non-relevant to the results of the current study (i.e., Line 284-296). -Regarding the persistence of anti-HBs antibody, Cohort C (students were born during 1986-1992, and received the plasma-derived vaccine), the mean anti-HBs antibody level was observed to be higher in the 1990-92 birth year group, compared to that of the 1986-88 and 1988-90 groups. This observation can be expected, because the 1989-92 group received the vaccine in later time point than the other 2 groups. However, for Cohort D (students were born during 1992-99, and received the recombinant vaccine), I wonder why the mean anti-HBs antibody level of the 1996-99 group was observed to be lower than the students born and received the vaccine earlier (i.e., 1994-96 and 1992-94).

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.

Title: SEROPREVALENCE OF HEPATITIS B VIRUS IN TAIWAN 30 YEARS AFTER THE COMMENCEMENT OF THE NATIONAL VACCINATION PROGRAM Review round: 2 Reviewer: 1

Basic reporting: All fit, no comment. Experimental design: No additional comment. Validity of the findings: No additional comment. Additional comments: Author responsed: We have updated this text accordingly in lines 66–67 on page 3: “more than 350 million people worldwide have chronic HBV infection, with the majority of the infected people living in Africa and Asia (WHO 2017).” However, I checked The Global Hepatitis Report 2017(WHO), it says that: WHO estimates that in 2015, 257 million persons, or 3.5% of the population, were living with chronic HBV infection in the world. Hence, 257 million should uodate 350 million.

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.

Title: SEROPREVALENCE OF HEPATITIS B VIRUS IN TAIWAN 30 YEARS AFTER THE COMMENCEMENT OF THE NATIONAL VACCINATION PROGRAM Review round: 2 Reviewer: 2

Basic reporting: - Experimental design: - Validity of the findings: - Additional comments: No additional comments

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.

Title: BODY MASS INDEX INFLUENCES THE PLASMA GLUCOSE CONCENTRATION DURING IATROGENIC HYPOGLYCEMIA IN PEOPLE WITH TYPE 2 DIABETES MELLITUS: A CROSS-SECTIONAL STUDY Review round: 1 Reviewer: 1

Basic reporting: See below Experimental design: See below Validity of the findings: See below Additional comments: In this paper, the authors demonstrate that in individuals with T2DM who experience severe iatrogenic hypoglycemia, BMI influences plasma glucose levels at hospitalization. The paper is susceptible for publication, but I have some comments that need to be addressed before by the authors: 1. Since some patients are young and treated with insulin, the authors should specify how type 1 diabetes has been excluded; 2. Patients affected by any organic disease impacting on BMI must be excluded; 3. Methods for the determination of glucose, HbA1c, creatinine, and potassium should be indicated, as well as quality of the analytical performance (precision). 4. By analyzing the file data, it emerges that all continuous variables have a non-normal distribution. Thus, non parametric tests must be employed; 5. In linear regression analysis, the impact of BMI must be adjusted for other confounding factors. 6. In the discussion: line 180, “glycemic therapy” is not clear. 7. Line 204: The Authors should briefly indicate the role of fat tissue in the production of adipokines, whose role is important in insulin sensitivity and inflammation. (Waki H, Tontonoz P, Annu Rev Pathol 2007; Fasshauer M, Bluher M, Trends Pharmacol Sci, 2015). 8. Line 205 could be better expressed as follows: “Weight loss improves insulin sensitivity by decreasing free fatty acid mobilization, and by changing adipokine profile in obesity (Schenk et al., 2009; Greco M, et al, Mediators Inflamm 2014), and intentional weight loss in T2DM, correlates with lower fasting plasma glucose concentration (Wing et al., 2011)”. 9. References should be listed in alphabetical order.

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.

Title: BODY MASS INDEX INFLUENCES THE PLASMA GLUCOSE CONCENTRATION DURING IATROGENIC HYPOGLYCEMIA IN PEOPLE WITH TYPE 2 DIABETES MELLITUS: A CROSS-SECTIONAL STUDY Review round: 1 Reviewer: 2

Basic reporting: The manuscript is well written and associates BMI with the nadir of hypoglycemia upon admittance to the hospital for hypoglycemia-care. The study is observational and not an intervention, however, great care was taken to adjust for confounding variables where applicable. The main finding of this work is that individuals with lower BMI tend to have lower plasma glucose levels (30 vs 38 mg/dL) and that this relationship is quite strong (B-coefficient of 0.72). I have a few minor suggestions that may improve the presentation of the data and the discussion of the results, however, overall I find this manuscript to be of good scientific merit. Throughout the manuscript, the authors refer to “energy deficit and glycogen depletion.” It should be noted, however, that unlike rodents, humans do not experience glycogen “depletion.” In fact, even after days or weeks of fasting, glycogen is still present in the liver. Furthermore, Hendrick and Cherrington (1990, AJP) showed that in dogs, glycogen is present in the liver after a 7d fast and that when their livers were exposed to glucagon, a “normal” amount of glycogen was mobilized, despite the liver glycogen concentrations. Therefore, in the context of your conclusions, I am of the opinion that the proposed mechanism whereby “BMI is associated with chronic energy deficit and glycogen depletion” would cause “more severe hypoglycemia” is slightly inaccurate. On the other hand, in the paper by Winnick et al., that you cite, they observed that low liver glycogen, such as what you are suggesting is present with lower BMI, is associated with diminished secretion of the counterregulatory hormones glucagon and epinephrine. By reducing glucagon and epineiphrine secretion, it would be expected to lower hepatic glucose production and make the glucose nadir lower than what was occurs in the high-BMI group. I am of the opinion that in order to provide a speculative mechanism of action, this is the most consistent with your data. In the discussion, the use of the phrase “tolerance of hypoglycemia….” is of interest. Perhaps the authors mean to say “ability to counterregulate hypoglycemia….” Or perhaps “tolerance to hyperinsulinemia….” Would be a better description? Experimental design: In their statistical analysis, the authors report the relationship between the blood glucose level and age, BMI, A1C, creatinine and diabetes duration. The only variable that correlated with the blood sugar was BMI. I do not have a problem with the analysis or the presentation of the data, however, did the authors probe further to determine if a multivariate analysis would account for a greater proportion of the variance in plasma glucose? I expect that it would not, but the authors might want to add this explanation somewhere in the results section. Validity of the findings: Having diabetes at a lower body weight can often mask other illnesses an individual possesses. I comment the authors for controlling the cause of hospital admission in the cohort, but do the authors have any indication of any differences between the low- and high-BMI? For example, some of the low BMI individuals may have undergone weight loss surgery (e.g., RYGB or sleeve-gastrectomy), which can lead to “dumping” and overt, severe hypoglycemia. Do the authors know if any of the low-BMI subjects had previously undergone hypoglycemia? If the data are available, it would be helpful to report it in the results section (i.e., the number of subjects who had previously undergone weight loss surgery). Likewise, the dose of insulin and sulfonylurea each patient was on would be informative to the reader. However, I understand if they are not available. In the section where the authors note the limitations of the study, it should be included that they did not measure 1) liver glycogen or 2) counterregulatory hormones. The inclusion of these data in the manuscript would have markedly improved the merit of the manuscript. The reasons why you did not have these data, however, is understandable. Additional comments: My comments are covered by the first three sections.

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.

Title: BODY MASS INDEX INFLUENCES THE PLASMA GLUCOSE CONCENTRATION DURING IATROGENIC HYPOGLYCEMIA IN PEOPLE WITH TYPE 2 DIABETES MELLITUS: A CROSS-SECTIONAL STUDY Review round: 2 Reviewer: 1

Basic reporting: OK Experimental design: OK Validity of the findings: OK Additional comments: The authors addressed all my concerns.

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.

Title: BODY MASS INDEX INFLUENCES THE PLASMA GLUCOSE CONCENTRATION DURING IATROGENIC HYPOGLYCEMIA IN PEOPLE WITH TYPE 2 DIABETES MELLITUS: A CROSS-SECTIONAL STUDY Review round: 2 Reviewer: 2

Basic reporting: The revisions are well done, just a couple of minor things. Experimental design: Good. Validity of the findings: Good. Additional comments: In the abstract, it would be more accurate to say “This study investigates the relationship between body mass index….” Instead of “This study investigates the effect of body mass index….” At the end of the Introduction (lines 110-112), this statement is not completely accurate. A lower BMI per se does not reflect lower liver glycogen. For example, young people with lower BMI have higher liver glycogen than older people with type 2 diabetes. I think the statement “People with T2DM who have a lower BMI are also likely to have lower hepatic glycogen stores and this can diminish the secretion of glucose counterregulatory hormones during hypoglycemia.” is more accurate.

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.

Title: A NEW PYTHON LIBRARY TO ANALYSE SKELETON IMAGES CONFIRMS MALARIA PARASITE REMODELLING OF THE RED BLOOD CELL MEMBRANE SKELETON Review round: 1 Reviewer: 1

Basic reporting: Overall good: readable, very clear, well-structured and appropriately contextualized. Experimental design: I the the comparison with prior art is well designed and thoroughly explored. I wonder, is Fiji’s Analyze Skeletons plugin the only comparable software? Validity of the findings: Looks good. Additional comments: This paper was a pleasure to read. It's exciting to see another scientific application of Numba (indeed, there aren't very many yet). I appreciate the use of real experimental data and the detail-oriented comparison to existing software.

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.

Title: A NEW PYTHON LIBRARY TO ANALYSE SKELETON IMAGES CONFIRMS MALARIA PARASITE REMODELLING OF THE RED BLOOD CELL MEMBRANE SKELETON Review round: 1 Reviewer: 2

Basic reporting: Nicely written, objective, and to the point. The software is available and is licensed under a FOSS model, but the authors should also include a tutorial, for users to be able to both test their installation and learn how to use the software. I see that they have included test data, which is great. But it is useless to most users, as I will expand on below. Experimental design: PeerJ "considers articles in the Biological Sciences, Environmental Sciences, Medical Sciences, and Health Sciences", and this article, being bioinformatic in nature, makes it. But as the software package is right now, it is more of a mathematical work than something usable by the PeerJ audience. A significant flaw of this work is the complete lack of any documentation whatsoever for the software. There are no instructions on how to install or use it. No tutorial on how to use the program or its alleged GUI, no screenshots of it in action. Thus, very few, if any, biologists will use this program as it is right now. I have at least some experience programming in three languages (not Python though) and I have no clue what to do to get Skan up and running. So I didn't, and have to take the authors at their word that the program works. Because I know very little Python. Other biologists typically know even less than I do. Time is limited, people will go use Fiji instead, I am afraid. The authors say Skan is a library, with an extensive API. However, an API is not much use without documentation --don't think many people will go read your code to find out how to access your functions, what they return, etc. Validity of the findings: No comment. Additional comments: The article itself seems OK to me, although I thought the discussion was a little thin. But, OK, no use in belaboring the point if there is not more to say. What I believe the authors must do in order to avoid this apparently nice piece of software becoming yet another example of "abandonware" littering the scientific softwarescape is to write a point by point tutorial that: 1) Explains to the general biologists, who I believe are the main target user of Skan after all, how to get the program to work; 2) Explains to the general biologists how to use the program (GUI or not), by employing the test data set included (it is advisable to have also included the expected output in a directory, so the users can compare what they got to what was expected). Besides this "general user" guide, in order for the Skan API to be usable by other programmers, there must also be some documentation on how to use the API (e.g., what should be imported to begin with?) and of each of the available functions. Save the many user a significant amount of time later by spending a bit of time now and they will be very grateful to you.

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.

Title: METAGENOMIC ANALYSIS OF ORANGE COLORED PROTRUSIONS FROM THE MUSCLE OF QUEEN CONCH LOBATUS GIGAS (LINNAEUS, 1758) Review round: 1 Reviewer: 1

Basic reporting: Occasionally the writing is little hard to get through (although usually one can understand its intent). Some examples are: L30 “explaining the nature of a plausible parasite infection” - awkward. L50 overfishing would seem to be included in the detrimental human activities adduced later in the sentence. L111 “lowest common ancestor” Unsure what this means. L211 “taxonomical identification”… what other kind of identification is there? L254 to say trematodes "have been reported" in mollusks reads like a strange sort of understatement (all digenetic trematodes infect mollusks). L271-274 quite awkward. L279-280 a reference is needed for the 40 million infections mentioned, as well as the “previous studies.” L501-502. Fig 2 legend is awkwardly worded. Also, some of the nodes lack numbers, and circle size is not truly proportionate to hit numbers, as it seems the same for “no hits” (n=3000) and “not assigned” (n=900). I am not an expert, but should this conch be referred to as Lobatus gigas? Experimental design: The research gap (identity of the orange colored protrusion in conch) is well defined. However, I am puzzled by the methods chosen to address it, even if they are impressively multidisciplinary. Few macroparasite infections can be reliably identified histologically (those that can are well studied taxa in well studied hosts). So, the use here of histology as primary identification method is surprising. It is also a relatively costly in terms of sample usage, which is a concern in a case like this, when there are only a few isolates in hand (L100). As for pyrosequencing, the results speak for themselves. It does not seem surprising that the reads yield little information on the pathogen (the hits with bacteria may be of some interest, but I am not a good judge of that. However, I do find the reference to contamination for some of the more surprising bacterial hits a little understated at L249-250). Essentially, if I take a bottom-line look at the 454 results, they seem almost misleading, given the authors’ eventual conclusion: some are subject to possible contamination, and only a tiny minority are related to Trematoda. Sanger sequencing could have been a potentially valuable approach, but by choosing CO1, the authors are hoping for a very specific match. Which would be great, but is a faint hope, given the largely unknown, unsequenced nature of most marine invertebrate taxa. For assignment to higher taxa – probably the most realistic, best-case outcome here – CO1 is a poor choice, because saturation of the third codon often makes deeper phylogenetic placement unreliable. For example, the authors cite Moszczynska et al, who recommend using ribosomal markers for higher taxonomic placement. 18S could well yield something more specific than Trematoda (even if it is not a great choice for identification at the species level). Moszczynska et al also reported sequencing individual metacercariae that were very small – on par with the specimens here. Pooling the specimens (L100) is unfortunate. The analysis of the CO1 data is surprising. An NJ tree seems less appropriate that one based on character changes, such as ML, BI or MP. It is disappointing that no specimens were examined in toto, stained, mounted on slides. This could have led to a more specific identification (in addition to being less work) and would have clarified the developmental stage of the trematodes. There is a reasonable chance these are metacercariae, not sporocysts or rediae. The authors seem to be assuming the latter at L275-277. However, it is metacercaraie that are responsible for foodborne trematodiases, which are discussed at several points. Validity of the findings: The results appear valid, although as stated above, methods slightly different from those chosen might have yielded more satisfactory results (given the stated goal of the study). At L291. Not very clear to me how any particular identification would yield any kind of practical preventative or control measure. Suggest elaborating with specifics or removing. Additional comments: I don’t insist, but I feel like if the authors really want to identify this, they should sequence 18S and possibly ITS. Better chance of a more-informative near-match. Also, even if the data are left as is, NJ is not be best analytic method for the CO1 sequence.

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.

Title: METAGENOMIC ANALYSIS OF ORANGE COLORED PROTRUSIONS FROM THE MUSCLE OF QUEEN CONCH LOBATUS GIGAS (LINNAEUS, 1758) Review round: 1 Reviewer: 2

Basic reporting: The basic reporting was relatively clear; although, contextual and word usage corrections were made throughout the paper. I have made detailed corrections in my attached pdf of the article. a) L26: Please replace ‘organisms’ with ‘taxonomic groups’ as no definitive species identifications were made in this study. b) L29: Please replace ‘class Trematoda’ with ‘subclass Digenea’. c) L32: Please replace ‘meat’ with ‘muscle’. d) L45: Please add ‘marine’ after endangered and remove ‘mollusk’. e) L47-L49: The 2 conservation organizations that were cited are not named correctly. Please rewrite with the correct names as follows: ‘Convention on International Trade in Endangered Species of Wild Fauna and Flora’ ‘Red List of the International Union for Conservation of Nature’ f) L56: Please replace ‘the parasitology and microbiology of this species’ with ‘;however, the parasitological and microbial studies of this species’. g) L61: Please replace ‘phylum’ with ‘phyla’. h) L66-69: Rewrite as follows: Moreover, the etiological agent of orange-colored protrusions in the muscle of S. gigas remains unknown. These orange- colored protrusions were observed sporadically in queen conchs from the Columbian San Andres archipelago. This observation is characteristic with digenean infection found in other marine gastropods. i) L70: The phrase ‘orange/lemon-colored lesions’ is actually referring to the larval digenean stage known as sporocysts. Replace the word ‘lesions’ to ‘sporocysts’. j) L75: Please replace ‘lesions’ with ‘sprocysts’. k) L80: What is the brand of the automated DNA sequencer used? l) L82-84: Rewrite to clarify that the ‘marine samples’ are more specifically the microbiome of orange-colored protrusions found in the muscle of S. gigas. Experimental design: The experimental design was thorough with regards to the metagenomic analysis, however, this study was lacking in the morphological aspects of the digenean parasites and number of genes used for the genetic analysis with Sanger sequencing. Strombus gigas specimens could have easily been examined for the shedding of cercariae using non-destructive sampling methods by placing a live S. gigas specimen with orange-colored protrusions (sporocysts) in a container with purified seawater overnight. Morphological description of cercaria could then be compared to the other studies you cited (Stunkard, 1950; Galaltionov & Skirnisson, 2000; Werding , 1969; Hechinger & Miura, 2014). For gene sequencing a 740bp region of the mitochondrial COX1 gene was sequenced in this study. 28S rRNA gene sequence (AF023113) exist for Renicola roscovita and other Renicola species. The ITS2 region would have also been helpful in determining the taxonomic position of this unknown digenean species reported in the study. a) L89: Please clarify whether orange-colored muscle is describing an anatomical character of the queen conch or are you referring to the sporocysts. Where these three samples of orange-colored “muscle” examined from a single specimen or 3 different individuals? b) L117-118: Please clarify if you intended to write ‘100 nucleotides or amino acids’. If not, please replace with ’300 nucleotides or 100 amino acids’. c) L132: What is the brand of the automated DNA sequencer used? d) L150-151: Please explain why 22 sequencing assigned to the Trematode category is remarkable, while 19 sequences assigned to the fungi group is downplayed? e) L254: It is a stretch to suggest cestode infection just because the histological approach shows membrane consistent with tegument, especially since no mention of cestode sequence came up in the metagenomic analysis. Please remove ‘cestode’. f) L263: Please replace ‘lesion’ with ‘protrusion’. g) L523: I recommend that the cestode sequences should be removed from the Neighbor Joining tree analysis and replaced with additional Digenea sequence. The outgroup should be a specimen from the subclass Aspidobothrea, which is the sister group of Digenea. Validity of the findings: The validity of the findings with regards to evidence of Digenea infection of Strombus gigas could be much more robust with a non-destructive sampling method to recover shedding cercariae for the histological/ morphological analysis and use of additional nuclear gene sequencing if 18S, 28S, and ITS2 for the gene sequencing analysis. Additional comments: I find the title of the article somewhat misleading. Based on the title of the article, I’m expecting a parasitological study that would provide solid morphological and molecular data to show evidence of digenean infection with data on larval stages (sporocysts) within and juvenile stages (cercaria) exiting Strombus gigas. Remarkably, roughly half of the results section and half of the discussion is dedicated to bacteria. This research seems to be more in line with a metagenomic study which is focused on the microbiome of “orange-colored protrusions” found in the muscle of Strombus gigas, then a study of digenean parasites infecting Strombus gigas.

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.

Title: METAGENOMIC ANALYSIS OF ORANGE COLORED PROTRUSIONS FROM THE MUSCLE OF QUEEN CONCH LOBATUS GIGAS (LINNAEUS, 1758) Review round: 1 Reviewer: 3

Basic reporting: This study reports on the apparent presence of trematodes and bacteria in the tissues of Strombus gigas. Although the work is technically spectacular, the findings are so minor that I cannot recommend publication. The approach used has demonstrated, probably convincingly, that the conch or conchs (not many infections and the samples were pooled) had a trematode infection. However, the molecular data are so generalised that there is no real identification beyond that of "trematode". This is my problem with the paper. Ultimately, probably every marine mollusc acts as intermediate host to trematodes at some stage. Without better identification or prevalence information we are really not significantly advanced by this study. Notably, the Discussion (Lines 275-6) states that the typical outcome of trematode infections in molluscs is partial or complete castration. The authors betray their lack of familiarity with these parasites here. Castration is associated with infection as a 1st intermediate host. The current infection is consistent with infection as a second int. host and likely to be relatively insignificant in the biology of the conch. A great deal of the ms is devoted to issues associated with bacteria about which I know nothing. However, I do note that this makes the title of the paper rather misleading. According to the WoRMS database, the name Strombus gigas is outdated - it should be Lobatus gigas; this does not inspire confidence. In my view this study has not advanced knowledge of parasitism in this conch and I cannot therefor recommend publication Experimental design: As above Validity of the findings: As above Additional comments: As above

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.

Title: METAGENOMIC ANALYSIS OF ORANGE COLORED PROTRUSIONS FROM THE MUSCLE OF QUEEN CONCH LOBATUS GIGAS (LINNAEUS, 1758) Review round: 2 Reviewer: 1

Basic reporting: The English writing has improved. It is still not fluent but there is no real barrier to understanding or communication. I think the workflow used by the authors would be better represented, and their decisions more understandable, if they mention the specifics of their attempts to sequence 18S and 28S, as they do in the response (see paragraph above gel image in response), rather that making it sound like the attempt is a bad idea to begin with, as it comes across in the ms (L132-133). Also, the details of just how little tissue was available (only in the response) would be good to include in the MS proper. Experimental design: I BLASTED the CO1 sequence and I think the fact that its highest similarity (82-83%) is to Synthesium, another member of the Xiphidiata, not mentioned in the MS because (presumably) it only overlaps at about 320 bp, is also worth mentioning in support of the eventual conclusion that the lesions are caused by a digenean belonging to the Xiphidiata. Similarly, in addition to the statistical support of the clade membership, it would be relevant to state at L208-211 what ranges of similarities the sequences had with others in the tree. I think the fact that 2 different translated contigs of endonuclease-reverse transcriptase indicate the specimens belong to the Schistosomatidae needs explanation. Either the method of Monzoorul Haque et al is flawed in this, or there is some other problem. The schistosomes are very evolutionary distant from the Xiphidiata. Validity of the findings: I think the findings were, and remain valid. I think the statement that the specimens are sporocysts (L202) (rather than metacercariae) requires justification. Some discussion of the known life history of related taxa might be pertinent. Additional comments: Can the authors comment or speculate on why, if a digenetic trematode is what is causing these lesions, so many of the reads are from other taxa? If the sample's biomass is predominantly worm, than why are there few or no worm rDNA reads, but so many from fungi?

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.

Title: METAGENOMIC ANALYSIS OF ORANGE COLORED PROTRUSIONS FROM THE MUSCLE OF QUEEN CONCH LOBATUS GIGAS (LINNAEUS, 1758) Review round: 2 Reviewer: 2

Basic reporting: Since most of the corrections were made on the manuscript the basic reporting is very clear and reads well. There is one correction that need to be made in the manuscript with the tracked changes as shown below. a) L64-L67: This sentence needs to be rewritten as it is a run on sentence that is awkwardly written. Experimental design: Since most of the corrections were made on the manuscript the experimental design is more detailed and reads well. There are still a couple of corrections that either need to be made or were not addressed in my first review. The lines listed below are based on the manuscript with the tracked changes a) L89-L90: Were these three samples of orange-colored "muscle" examined from a single specimen or 3 different individual queen conch specimens? b) L122-123: "Only contig alignment lengths above 100 nucleotides or 100 amino acids were included in the assignment analysis." This still does not make sense to me as 100 amino acids are equivalent to 300 nucleotides, but this is not reflected in the text you have written in the text shown above. Validity of the findings: The validity of the finding are now acceptable with regards to evidence of Digenean infection of Strombus gigas as this is not the main focus of the paper as previously written. This is especially true since changes were made to the title of the paper. Additional comments: I'm happy to see that the authors took into to consideration the comments and corrections that I previously made. The paper now reads much better and is clear and to the point. I believe that this manuscript should be accepted with the minor revisions that I have listed in the above sections.

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.

Title: METAGENOMIC ANALYSIS OF ORANGE COLORED PROTRUSIONS FROM THE MUSCLE OF QUEEN CONCH LOBATUS GIGAS (LINNAEUS, 1758) Review round: 3 Reviewer: 1

Basic reporting: In the first review I mentioned that the writing had some problems. For the most part, these did not prevent comprehension but were distracting. I can see that the authors attempted to address this issue by making all the changes I specifically mentioned, but I’m afraid the problem remains. For publication purposes, a native speaker should be recruited to go over this closely. For what it's worth, I can sympathize: where I work the linguistic environment is not my first language, and often have to write/teach in a second language. ¡no es fácil! Other than this, I have no major comments on the ms (one minor one, below), and I commend the authors on their work. Experimental design: no comment Validity of the findings: I think the authors could explicitly state the rationale behind their opinion about the developmental stage involved. Additional comments: No additional comments

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.

Title: LIFE HISTORIES PREDICT GENETIC DIVERSITY AND POPULATION STRUCTURE WITHIN THREE SPECIES OF OCTOPUS TARGETED BY SMALL-SCALE FISHERIES IN NORTHWEST MEXICO Review round: 1 Reviewer: 1

Basic reporting: There are some areas, particularly in the Introduction where the language should be improved to make it more clear for all audiences. Some of the grammar is confusing and ambiguous and a native English speaker should double check the wording. (See my comments on the PDF) Otherwise, the references, background, figures, data, etc are clear and the paper reads well. One table (Table 1) could benefit from a delineation between the section on data and the hypotheses. Experimental design: The experimental design and methods are clearly defined and thorough. It might be beneficial to have a short section providing the reasoning behind using a subset of samples for the mitochondrial analysis. The morphological differentiation between species is stated in a slightly challenging way. Since only one individual from each species was identified through morphology, it might not even be necessary to include this; especially if the genetic information on each species already exists to indicate reproductive isolation between the three. Validity of the findings: You could also discuss the literature that suggests size at sexual maturity is extremely variable depending on food availability and temperature in multiple species (Forsythe + Hanlon, 1988 Marine Biology) Additional comments: The findings and conclusions are sound and well stated. Implications in octopus fishery management are clearly indicated and discussed. This paper adds to the growing literature on octopus fishery concerns and management recommendations.

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.

Title: LIFE HISTORIES PREDICT GENETIC DIVERSITY AND POPULATION STRUCTURE WITHIN THREE SPECIES OF OCTOPUS TARGETED BY SMALL-SCALE FISHERIES IN NORTHWEST MEXICO Review round: 1 Reviewer: 2

Basic reporting: Clear, unambiguous, professional English language used throughout. Mostly – some odd phrases and occasional wrong words – suggestions added to the pdf. Intro & background to show context. - yes Literature well referenced & relevant. - yes Structure conforms to PeerJ standards, discipline norm, or improved for clarity. - yes Figures are relevant, high quality, well labelled & described. - yes Raw data supplied (see PeerJ policy). - yes Experimental design: Original primary research within Scope of the journal. - yes Research question well defined, relevant & meaningful. It is stated how the research fills an identified knowledge gap. - yes, clearly defined in the Abstract, revisited in the Introduction. Rigorous investigation performed to a high technical & ethical standard. - not sure - see the issues raised in General Comments As only 316 individuals across 3 species, 20 localities and 5 years are used, suitable rigour could be questioned? But, because of fairly clear distinction of species by molecular typing, and the subsequent use of pooled analysis to assess general species-wide parameters, then the dataset is suitable. Methods described with sufficient detail & information to replicate. – yes – nice explanations linking hypotheses and predictions to tests employed.Two mitochondrial genes and even nuclear microsatellite loci are suitable markers for the objectives Validity of the findings: The Conclusions are clearly stated, and on the whole justified. There is some speculation, but this is identified. However, regarding whether the data are robust, statistically sound and controlled there may be a potentially major issue with the identification to species of individuals and their incorporation to subsequent analyses. What is done with the individuals in Fig. 2B that are not clearly assigned to one of the three clusters? For example, a number of individuals in the Puerto Penasco locality appear to be more assigned to O. hubbsorum rather than O. bimacularus, but this is not indicated in the species distribution map? This is acknowledged in the text (l.291-294), but the colour coding of the figure does not convey this, and so is slightly misleading. Could be rectified by cross-hatching the sample localities that contain individuals from two species? This then leads on to the question as to what was the cut-off level in the assignment to decide on which species to assign an individual to? Or was one employed? There is no mention of this in the text, but after this point the reader is presented with a series of tests that are calculated from location-based genetic data which presumes that either all individuals within a location have been assigned to a single species and pooled (which would be wrong as Fig.2B appears to indicate that many samples contain individuals that assign to species different from the one predominant in that locality), or that some individuals have been excluded from the analyses because they did not assign to the predominant species in that locality (which is not mentioned or indicated, and so cannot be presumed). This is a serious potential flaw in all subsequent analyses, because it is not clear whether some individuals that may be from a different species have been included in the within-species tests, which would introduce substantial random variance in the microsatellite genotype and allele frequencies, and so generate high and random values of statistics such as Fst (which might explain the high values in the pairwise tests – see below?). If the authors can confirm to the Editor that suitable steps were taken to identify the species assignment of each individual before subsequent analyses, and then that individuals were partitioned appropriately so that only single-species datasets were used, then the ms can be adjusted with relatively minor changes (a section in the Methods or Results to explain the ID and partitioning of individuals more thoroughly, and adjustment of Fig.2C to reflect the mixed allocations within localities). If robust ID and removal of individuals was not carried out then the dataset needs re-analysis and re-presentation. I am presuming the former for this review. Also, you might comment on what the “mixed allocation” individuals represent in Fig.2b? I’m not convinced by the values given (l.327-334) for pairwise between-locality estimates of Fst based on the 7 microsatellite loci. Many of these tests are based on sample sizes in single digits, and so will suffer from random sampling variation. I think that this section, along with the supporting Tables should be removed, as it is pushing the dataset too far and so detracts from the other better-supported sections. Additional comments: No additional comments

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.

Title: LIFE HISTORIES PREDICT GENETIC DIVERSITY AND POPULATION STRUCTURE WITHIN THREE SPECIES OF OCTOPUS TARGETED BY SMALL-SCALE FISHERIES IN NORTHWEST MEXICO Review round: 2 Reviewer: 1

Basic reporting: . Experimental design: . Validity of the findings: . Additional comments: The authors appear to have taken on board the concerns expressed and have adjusted their analyses and/or interpretation and presentation of data to account for this.

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.

Title: CODOMINANT GRASSES DIFFER IN GENE EXPRESSION UNDER EXPERIMENTAL CLIMATE EXTREMES IN NATIVE TALLGRASS PRAIRIE Review round: 1 Reviewer: 1

Basic reporting: The article was for the most part easy to understand. There are a few items that could be clarified in order to be more understandable to a broader audience. Experimental design: As the authors acknowledge, the sample size was a low and microarrays are not as detailed as an RNA seq study, but the study is important and provides an important narrative toward understanding how species may respond to climate change. I have never used microarrays, so I will defer to another reviewer on those statistics. Validity of the findings: No comment. Additional comments: Great article! We're starting an RNA-seq assisted migration study on cool-season grasses in North Dakota, so your article was of particular interest to me.

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.

Title: CODOMINANT GRASSES DIFFER IN GENE EXPRESSION UNDER EXPERIMENTAL CLIMATE EXTREMES IN NATIVE TALLGRASS PRAIRIE Review round: 1 Reviewer: 2

Basic reporting: It is well written, clearly stating the results and the implications for this field of research. Meets all the guidelines of PeerJ wrt references etc. Experimental design: Good Validity of the findings: Good Additional comments: Review of PeerJ manuscript; Codominant grasses differ in gene expression under experimental climate extremes in native tallgrass prairie. Ava M Hoffman, Meghan L Avolio, Alan K Knapp, Melinda D Smith This is a small but worthwhile analysis of the differences in gene expression between two grass species grown under environmental stress. It is well written, clearly stating the results and the implications for this field of research. I recommend acceptance and publication of this manuscript. However, I do have a number of minor comments that should be addressed. • Line 37 – Cite IPCC 2013 but there are no details in the reference list under IPCC. So add Stocker et al 2013 to the text or put the details under IPCC • Following sentence is incomplete - improving our understanding of what and there is no full stop. 52 "However, most molecular studies of plant responses to drought and heat stress are focused on 53 model organisms with limited ecological relevance (Leakey et al. 2009), although awareness and 54 sequencing costs are improving our understanding (Voesenek et al. 2014; Ellegren 2014) " • In the site description (line 99) the plot sizes are given as 3 x 6m but in the legend to Online resources Supplementary methods line 3 it states 2 x 6 m; • line 276 – 'both histone acetyltransferases were upregulated" implies only two exist in the species. Add that the two histone acetyltransferases identified as differentially expressed in A.gerardii were upregulated. I do have two comments that could be taken into account for future studies; 1. The study is limited in that only two individuals were sampled for each species under each of the treatments but I agree with the authors arguments that this is sufficient for this preliminary study. 2. Hybridisation of cDNA synthesised from leaf RNA against maize ear tissue may have limited the type of genes identified. However, I also recognise that there is a limit to the resources available for a study such as this and despite the above reservations I think these results add to the information available in this area of research.

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.

Title: BENTHIC GRAZING IN A EUTROPHIC RIVER: CASCADING EFFECTS OF ZOOBENTHIVOROUS FISH MASK DIRECT EFFECTS OF HERBIVOROUS FISH Review round: 1 Reviewer: 1

Basic reporting: More description of their study system and methods is needed. Most of these aspects should be relatively straight forward. 1. What is the drainage area of the river Nister? Drainage area is easily obtained from maps, and are much more quantitative than stream order. 2. What are the potential algivores (nace and major invertebrate grazers) in the system, how do they graze (browsing tips, clipping lawns, or scrubbing down to basal cells?) How do fish vs invertebrate grazing pressures change with substrate texture or stream velocity? In other words, tell us more about the natural history of the system, and which biota are likely to significantly affect algae. 3. I was confused about the scales over which densities were measured. Invertebrate densities were not described, and fishes were unconfined, so how do stock estimates from electroshocking relate to the densities of the nase and the invertebrate feeding fish over the scales that would influence standing crops of algae on the tiles.? 4. What taxa of algae or macrophytes were being grazed? Are they green algae, diatoms, cyanobacteria? Adnate or loosely attached? Are their natural substrates stony—were concrete blocks a good facsimile? When did the experiments occur within the seasonal algal succession and cycles of substrate colonization, vegetative growth, and sloughing that macro-algae or macrophytes show? The English is adequate, but not always completely clear. There may be too much background information and there is certainly too little description of the actual biota or the study site or the spatial and time scales of natural processes (like fish foraging ranges or seasonal succession in stream biota) that matter. Their raw data and authorizations for research all appear in order. Experimental design: I think the design is ok if 1) the concrete tiles grow periphyton that is representative of what is on the natural river bed, but you should support this. One problem, in addition to surface texture and chemistry differences, is that if you place the tiles after natural colonization periods by algal propagules, you'll not grow the periphyton that may represent the natural flora of the stream bed. 2) you can explain what factors keep fishes at (or close enough to) the densities that you estimate with electro-shocking long enough to reflect their actual impact on the food chains that influence algal biomass over your experimental periods Validity of the findings: The experiment you designed tests fish effects, not nase effects, on periphyton biomass on artificial substrates. You find that fish exclusion augments algal biomass, and infer (I suspect correctly) that invertivory may release algae from grazing invertebrates, which seem to have stronger effects than algivorous nase. If you can give us some clearer descriptions (and even better, some quantitative data) on the densities and grazing severity of grazing invertebrates versus nase, the paper would be a clearer contribution to our general understanding of which consumers can exert strong controls over producer biomass in rivers. Additional comments: Top-down effects of herbivorous fish (Chondrostoma 1 nasus L.) in a eutrophic river (#21164) The authors hypothesized that a fish they identify as the only obligate herbivorous fish in Europe, the cyprinid common nase (Chondrostoma nasus), may suppress periphyton growth in eutrophic rivers, as herbivorous fish are known to do in some midwestern North American and many tropical rivers. They tested their hypothesis with a field experiment in Rhineland-Palatinate, Germany in the river Nister, a large river enriched with human sewage and agrochemicals. They used electric fencing to exclude all fish from 40x40 cm2 concrete tiles placed on the river bed. They used natural densities that varied 8x over the first year, and in the second year, artificial stocking elevated nase densities 70x (but did the fish stay where they were stocked? See below.) The authors, however, did not find the effect they expected from nase exclusion. To their surprise, they found more algae where all fish were excluded, and concluded that benthic invertebrates were more important as grazers than fish. They offer a reasonable explanation, that invertebrates were more important grazers than nase in this system, and that excluding invertebrate-feeding fish, particularly loach, released invertebrates to graze down algae within fish exclosures. I think the large scale of the field study, the tests over a large range of free-swimming nase densities, and the lack of enclosure artifacts are all strengths of this ms, but a bit more clarification of scale and natural history is needed.

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.

Title: BENTHIC GRAZING IN A EUTROPHIC RIVER: CASCADING EFFECTS OF ZOOBENTHIVOROUS FISH MASK DIRECT EFFECTS OF HERBIVOROUS FISH Review round: 1 Reviewer: 2

Basic reporting: The basic reporting was done well. Experimental design: The experimental design was effective for testing effects of an electric field treatment on development of benthic river assemblages, and the methods were well described. But in some ways the design would not be effective for testing what was reported to have been tested, at least without further convincing by the authors (see below). Validity of the findings: The findings of these experiments are valid concerning effects of excluding a subset of grazers (and predators) from early-successional benthic communities. The focus of the paper is different to what was actually tested though. 1. I am concerned about the uncertainty of what exactly was excluded by the electric field. The authors state that all fish were excluded, so the strong focus on just one species (nase) is not warranted. Nase may be expected to be the main grazer and have the largest effect, but they were not excluded separately from other fish, so the separate effect of nase is not known. 2. Also, the possibility of some invertebrates from being excluded was not mentioned. For example, some studies have found large impacts of electricity not only on fish but also invertebrates (Brown et al. (2000) J. N. Am. Benthol. Soc. 19:176-185). Overall, the experiment can not tell if effects on periphyton are caused by exclusion of all (or some) fish, some invertebrates, or changed predation of the fish on the invertebrates. All it can answer is – what are the effects of species sensitive to an electric field on benthic assemblages? I think it is necessary to do some additional experiments to determine if any invertebrates are or are not independently affected by electricity. Or possibly the authors can find some past studies (including similar invertebrate species) that show an electric field of the same strength used in this study does not affect their abundance or behavior. 3. It is good that three experiments were done, but they are done at different times and the contexts of the experiments will differ in many ways besides just differences in nase abundance among those times. I think it is all right that the authors do include some speculation about how differences in nase abundance may contribute to differences in results among the experiments, but differences of nase density should not be overly emphasised (e.g. line 260, 314). The emphasis should be on differences among separate experiments that may differ in many ways including, but not limited to, nase density. 4. The tiles were left in the river for a total of 32-33 days, so I would think these will still be early-successional communities that have developed. If so, then the results are only applicable to these kinds of assemblages, which would need to be stated. For example, late-successional assemblages may have benthic algae that are more resistant to grazing and the results would be very different. If the natural benthos is dominated by late-successional assemblages then the results may have limited relevance. 5. The experiment did not include measurements of naturally-occurring river substrata (e.g. boulders or flat rock) so it is unknown how the colonisation of the tiles may differ to colonisation of natural substrata. For example, the surface textures may be different and affect periphyton growth. Possible differences between the natural and artificial substrata need to be discussed. If the authors have any data on what the algal and macroinvertebrate assemblages were like on surrounding natural rock surfaces they should consider including these data. 6. The opening of the abstract and introduction is about eutrophication, but the experiments are only indirectly relatable this process. I think the beginning of the introduction and abstract should be changed to be related to effects of fish, then the possible consequences for eutrophication can be mentioned. As it is, readers interested mostly in eutrophication may be confused when they realise this study it more about fish affecting the benthos. Additional comments: 1. Line 40: This should be reworded because the only comparisons of periphtyon biomass showed that there was no significant different among treatments (Line 266). The difference was in chlorophyll concentrations, which may or may not be related to biomass. 2. Line 154 – could you please include details of these preliminary experiments, perhaps as supplementary material? I would like to know details such as 1) how observations were made (were the authors certain that the nase were completely excluded during the 24hrs?), 2) were the fish starved before the trial and what kind of food were they provided near the electrified area? (if the fish were not actively foraging then they would not have any reason to go near the baited electrified area), 3) was a control area included that was not electrified in this trial? Could the authors also please include discussion about how they did not test the effectiveness of the electrified treatment on any of the many other species of fish that co-occurred with nase and which also will have affected the benthic assemblages. 3. Line 150 – did the fence chargers create a consent electric field, or one that pulsed on and off? 4. line 162 – I had trouble understanding exactly how many treatments were used. If this line means that there were 9 control tiles and 9 electrified tiles in each experiment, could the authors please make it a little clearer. 5. Line 236 – I think there is a error in this sentence 6. Line 245 – change to “weighed” 7. Line 248-249 - Can you please explain what the multiple comparisons were that needed correcting for? 8. Line 265-266 – any non-significant effect on AFDW should be mentioned in the abstract along with the significant effect on chlorophyll. 9. Line 288 – change to “There was no evidence that the environmental factors water depth, light and current velocity affected the experimental results.” 10. Line 329 - 331– the potential influence of invertebrate grazers is something that could easily have been predicted before the start of the experiment, so I think it needs to be incorporated into the hypotheses. Overall, the experiment would be made much more valuable if some more data on separate effects of invertebrates were included. 11. Line 396 – change “special” to “spatial” 12. Figure 2 – I think the Asterisks are not meant to be there.

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.

Title: BENTHIC GRAZING IN A EUTROPHIC RIVER: CASCADING EFFECTS OF ZOOBENTHIVOROUS FISH MASK DIRECT EFFECTS OF HERBIVOROUS FISH Review round: 2 Reviewer: 1

Basic reporting: no comment Experimental design: no comment Validity of the findings: no comment Additional comments: I have provided some additional minor changes. The line numbers below correspond to the line numbers on the “tracked changes manuscript”, which had line numbers that were slightly different to the reviewing PDF for some reason. Title: I would consider changing the title and expanding it with a bit more detail of the findings. The current one does not really reflect what was found in the study because there was no top-down effects of nase, while the important effect was likely from other fish eating the invertebrate grazers. Line 23-24: This sentence in the abstract seems out of place and the mention of generation times being mismatched will confuse readers. Maybe change it to something like “Although benthic invertebrate grazers reduce the growth of periphyton, this is highly context dependent”. Line 40: I may be wrong but I would guess that “benthivorous” means species that eat anything from the benthos, and this would include not only invertebrates but also algae, so maybe change to “predators of benthic invertebrates”. This may need changing throughout the MS. Line 44-50: Starting the introduction with mention of specifically invertebrate grazing is a bit confusing, especially given invertebrates are not mentioned in the title. Perhaps you could merge the 1st and 2nd paragraphs so you mention both types of grazing (invert. and fish) together. Line 82-83: I still find this ambiguous. It might mean there was one set of tiles per experiment, including 9 tiles some of which were electrified and some weren’t, or it could mean that each experiment had two sets, including 18 tiles altogether, some of which were electrified and some weren’t. This is an important piece of information, so try to be very clear, e.g. “Each separate experiment had a total of 18 tiles; half the tiles were electrified to exclude fish, and the other half were non-electrified to allow fish access” Line 319: are you certain that Standard Deviation here is meant to be a percentage? Line 335-336: Is there any reason this is in square brackets? Also, why is SD shown for the tiles but not the stone. Also, check whether you are presenting here Standard Deviation or Standard Error. Line 409: change “we have no proof” to “there is uncertainty whether” Line 413: Not sure what you mean by “quantitatively” here Line 486: add “directly” before “transferred”

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.

Title: CATCHMENT LAND USE PREDICTS BENTHIC VEGETATION IN SMALL ESTUARIES Review round: 1 Reviewer: 1

Basic reporting: The results are, in general, presented clearly; however, there is some confusion around the inclusion of chlorophyll a in their assessment. I suggest that the authors mention that (and explain why) they assessed chlorophyll a in their introduction (perhaps in final paragraph where the aim is outlined) and mention the analysis in the methods (which I’m assuming is the same as for their prediction of MA:TV). Tables 1 and 2. Please reword your Table captions. It is insufficient just to say that it is a table of results. Ideally a table should be able to be read and understood without having to read the main body. Also expand on what you mean by pr(inc) and ß as many readers will not be readily familiar with your techniques and chosen notation. Please also indicate what the abbreviations you’re adopting (or write them in full) in your table, i.e., what does “Tf” represent? When you say “Values >0.75...” please be specific about what values you’re talking about, i.e., the Bayesian variable selection. Table 3. Since you only measured 14 sites, it wouldn’t be too cumbersome, yet highly informative, if you could please show the export rates and land-use for all 14 sites rather than a summary. Experimental design: The research question is generally well identified and methods are generally clear; however, as mentioned above, the authors need to also mention that they assessed chlorophyll in their introduction and methods. Validity of the findings: No comment Additional comments: General: The authors present a study that proposes the ratio of macroalgae to vegetation (MA:TV) in South Australian estuaries as an indicator of ecological health and relate this to key catchment characteristics. A clear relationship between the % of fertilised land within a catchment and the MA:TV was identified. The manuscript is very well written and methods are appropriate for analysis. The potential factors influencing the MA:TV were selected apriori based on previous literature findings. Factors were examined for co-linearity, uninformative predictors removed and non-normal data transformed prior to analysis – all essential steps in having meaningful analysis. The results are, in general, presented clearly; however, there is some confusion around the inclusion of chlorophyll a in their assessment. I suggest that the authors mention that (and explain why) they assessed chlorophyll a in their introduction (perhaps in final paragraph where the aim is outlined) and mention the analysis in the methods (which I’m assuming is the same as for their prediction of MA:TV). Specific: Lines 46-48. Please cite the claims made in sentence beginning “Despite this, phytoplankton dynamics...” Lines 59-61. Sentence beginning “The ratio of macroalgae...”. Please provide a short sentence explaining why the ratio of seagrasses and macroalgae is sensitive to nutrient loading. Lines 65-69. Please clarify what is meant by ‘continental scale, stream-and-nested-catchment framework”. Perhaps re-word to say “catchment characteristics...” Line 71. At this point you introduce assessing chlorophyll a data yet your aims don’t mention chlorophyll a? Please expand on your aims to mention the use of chlorophyll a (i.e., that you’re using it and why) in your introduction/aims. Line 89. Please expand on the methodology used by ‘GUMLEAF’ to calculate loads and why this method is preferred to alternative methods. Line 112. Jags is an acronym so change to JAGS. Line 124. Where is the the R2 and p-value from? Is this also from heirarchical partitioning? If so then please explain the use of chlorophyll a data in your methods (and aims as mentioned above). Line 145. This could be a good point to mention how, other than increasing nutrient loading, that fertilised land can affect MA:TV. Also total area of fertilised land doesn’t take into land use type and intensity or the attenuation capacity and lag time of the vadose zone (which will differ between catchments). Figure 2 from Elwan et al (2015) shows the spatial variability in attenuation between neighbouring sub-catchments. https://www.massey.ac.nz/~flrc/workshops/15/Manuscripts/Paper_Elwan_2015.pdf Line 153. Whilst the dilution of the estuary may differ, won’t this occur of a gradient? So the areas closest to the mouth may still have high nutrient concentrations. Do you have estuary nutrient concentration data to support this claim? Line 155. Are they ‘measures’ or does the sentence need re-wording? This sentence is currently confusing but seems crucial to understanding the following list. I’m currently not entirely sure why there is a list of attributes, is these hypotheses on factors which may be influencing the MA:TV ratio? The paragraph also seems incomplete without a brief mention on why each of these factors may affect MA:TV and the likeliness that they are impacting your systems. Line 163. From Figure 1 it appears that the impact of increasing fertilised land ceases to change the MA:TV after ~20-40%, why might this be? Why doesn’t MA:TV change linearly with increasing fertilised land? Line 172. That’s an interesting finding. I’d be curious to see what kind of vegetation composed the foreign forests you compared to (no need to comment on this in manuscript). Line 187. Ecological consequences to increasing macroalgae i take it? Line 222. Please explain this interaction model in your methods. Line 229. Does MA:TV differ depending on where within the estuary it is surveyed? Or do your estimates cover the entire estuary? Tables 1 and 2. Please reword your Table captions. It is insufficient just to say that it is a table of results. Ideally a table should be able to be read and understood without having to read the main body. Also expand on what you mean by pr(inc) and ß as many readers will not be readily familiar with your techniques and chosen notation. Please also indicate what the abbreviations you’re adopting (or write them in full) in your table, i.e., what does “Tf” represent? When you say “Values >0.75...” please be specific about what values you’re talking about, i.e., the Bayesian variable selection. Table 3. Since you only measured 14 sites, it wouldn’t be too cumbersome, yet highly informative, if you could please show the export rates and land-use for all 14 sites rather than a summary.

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.

Title: CATCHMENT LAND USE PREDICTS BENTHIC VEGETATION IN SMALL ESTUARIES Review round: 1 Reviewer: 2

Basic reporting: 1. Hypotheses: I thought these could be better explained. Lines 65-69 has a dense and long sentence describing what the authors did, but there is no mention of what they expected to find. Also reiterating why this expectation might be useful from a management perspective would be helpful. Experimental design: 1. Data transformation: Please explain why the proportion data was not logit-transformed for hierarchical partitioning (see Warton, D. I. and Hui, F. K. C. 2011. The arcsine is asinine: the analysis of proportions in ecology. Ecology, 92: 3–10). 2. Statistical approaches: It would be useful if the authors described why the respective statistical methods (Bayesian variable selection and hierarchical partitioning) were used. These are appropriate, but it would be helpful for the readers to know what they do and why this is important for the data analysis of this study. For example, see Hatt et al. 2004: "This method allows identification of variables whose independent correlation with the dependent variable is strong, in contrast to variables that have little independent effect but have a high correlation with the dependent variable resulting from joint correlation with other independent variables." (Hatt et al. 2004. The influence of urban density and drainage infrastructure on the concentrations and loads of pollutants in small streams. Environmental Management, 34, 112–124.) 3. Data transformation: Please state which predictors were right-skewed, and thus log-transformed (Lines 104-105). You can refer to Tables 1-2 to save space (but see comment 1 above). 4. Site selection: It would be useful to quickly describe the selection criteria outlined in Woodland et al. (2015) here. This would help assuage any concerns that the sites had been “cherry-picked” for the non-linear response shown in Figure 1. Validity of the findings: 1. Validity of threshold response: The authors have identified a threshold of >20% of the catchment fertilized and estuarine macroalgal dominance (e.g. lines 122-123). While this seems reasonable, it would be good if this were tested objectively. Two approaches spring to mind: change-point analysis and non-linear regression ´curve´ fitting. For an example of how to use these two methods to validate an areal threshold see Burdon, F. J. et al. 2013. Habitat loss drives threshold response of benthic invertebrate communities to deposited sediment in agricultural streams. Ecological Applications, 23: 1036–1047. It should be noted that there are new ways to implement changepoint analyses in R (see Killick, R. & Eckley, I. A. 2004. Changepoint: an R package for changepoint analysis. Journal of Statistical Software 58, 1–19). Nonlinear regression fitting can make use of the "nls" and "AICc" functions in R. The latter function is in the "AICcmodavg" package. This would help describe objectively the shape of the relationship. It is important to note that the data should not be transformed for these analyses, because elucidating the actual threshold is the goal here (although OK to test a log-linear model with other candidate regression models). You can plot nonlinear regression lines a number of ways in R, one way uses "ggplot2". 2. Proximate and ultimate drivers of macroalgal cover: Although the authors discuss this issue (e.g. Lines 125-137), I wondered if a simple structural equation model (SEM) could not cast some more light on the interplay between catchment fertilization, river nitrogen loading, and estuarine macroalgae cover (keep in mind though caveats about site replication). For example, there should be indirect effects of catchment fertilization mediated through river nitrogen loading on estuarine macroalgae cover, but also a direct effect of catchment fertilization not related to river nitrogen loads (as hypothesized in Lines 156-161). SEM would be an objective way to assess causality, and its inclusion would add greater depth to the manuscript. Burdon et al. (2013) also make use of this statistical approach, but there are new R packages that can perform SEM analyses (e.g., see the "lavaan" package and the supplementary information in Grace, J. B., et al. 2014. Causal networks clarify productivity–richness interrelations, bivariate plots do not. Functional Ecology, 28: 787–798). This is important, because the “take home” message in Woodland et al. 2015 was that nitrogen load was the main driver of primary productivity in the same estuaries, but here you find that landuse (as an integrator of intensive agricultural activities) is a stronger predictor of estuarine macroalgal cover. 3. Residence times (Lines 213-214): How do the residence times of your systems compare to other estuaries around the world? It would be useful to quantify the "relatively" short duration here, and also help place your findings in the global context for the readers. 4. Mechanisms of threshold response: There is a rich literature on ecological stability and the abrupt transition from one system state to another. Although the authors do not have sufficient predictor variables or site replicates to test the underlying mechanisms of this complex system response objectively (but the simple SEM suggested above would be a move in the right direction), they could discuss their observation more with other related phenomena (e.g., state shifts to cyano-bacterial dominated algal assemblages in lakes). This would be helpful in further suggesting ways to move the science to a more predictive basis and away from description (which is useful as well - identification of thresholds have high utility for management). For a primer on this I can recommend Beisner et al. 2003. Alternative stable states in ecology. Frontiers in Ecology and the Environment 1(7): 376-382. Additional comments: 1. Lines 56-57. Is sedimentation and eutrophication of estuaries resulting from changes in catchment landuses not related to seagrass declines? Perhaps make this point a bit clearer. 2. Lines 65-69. This a long sentence. I would consider breaking it up and make the points clearer and more concise. Also see comment above under the "Basic Reporting". 3. Line 29. Delete "great". 3. Line 29. Add "...value by supporting..." 4. Line 30. Oxford comma between "...highly productive fisheries, and recreational...". Do you have a reference for these ecosystem services? 5. Line 31. "bear the brunt" is idiomatic. Consider rewording to "...estuaries are impacted by increased..." 6. Line 100. Replace "elided " with "discarded". 7: Lines 120-121. Reword to "was positively associated...".

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.

Title: CATCHMENT LAND USE PREDICTS BENTHIC VEGETATION IN SMALL ESTUARIES Review round: 2 Reviewer: 1

Basic reporting: 1. Hypotheses: The Authors have greatly improved the Introduction. Their Aims are stated unequivocally, and the utility of their approach to management clearly highlighted. Experimental design: 1. Data transformation: The Authors have explained that they did not logit-transform the proportion data because the “use of any transformation that achieves the unskewed-even spread empirically is sufficient”. There is a reasonable spread in the data which suggests this is probably true, but it would be more comforting if it were reported that the logit-transformation was attempted and did not qualitatively affect the results. 2. Statistical approaches: I have cited Ralph MacNally’s work on hierarchical partitioning, so am familiar with this contribution to the ecological literature. The example I provided previously comes from the R documentation authored by Walsh and MacNally, which I found useful when describing this method in my 2008 paper “The linkage between riparian predators and aquatic insects across a stream‐resource spectrum” (Freshwater Biology 53, 330-346). Nevertheless, it pleased me to find that the Authors have improved their descriptions of the analyses used in this manuscript. It is now clear why and how they have applied Bayesian variable selection and HP for this research. 3. Data transformation: OK, but see comments above re point 1. 4. Site selection: The Authors have provided the additional information required. Validity of the findings: 1. Validity of threshold response: The Authors have justified not objectively testing the stated threshold because “The key point here is that once catchment fertilization exceeds 20%, > 50% of the SAV is macroalgae (i.e., macroalgal dominated)”. Whilst I agree that the change in areal coverage is probably asymptotic, I would be much less confident to state that “this is just a phenomenological observation and nothing to do with a formal phase transition to another state per se”. There seems to be an element of confirmation bias in this view. Thresholds values are highly useful for management, and objective testing is not something to be dismissed out of hand. It has much less to do with “deepening our understanding”, and more with defining explicitly a value with utility for managers. I personally would find this work more useful if the threshold value were defined using changepoint analysis, as opposed to the current interpretation which is like ‘it seems to change somewhere around here’. 2. Proximate and ultimate drivers of macroalgal cover: The Authors have justified not using SEM here because of the low level of site replication. This is reasonable with data for only 14 sites. However, I would encourage them to consider using this approach in the future, given the high likelihood of complex interactions/contingencies with the stated predictor and response variables. 3. Residence times: Good stuff - references provided and a caveat issued about residence times. 4. Mechanisms of threshold response: The Authors have backed off from using “transition” in their article because it implies that the threshold elucidated is suggestive of a shift to a new ‘domain of attraction’, indicated by a much greater areal coverage of macroalgae (i.e., macroalgal dominance) in the studied estuaries. Whilst the Authors seem skeptical of such phenomena, it would seem irresponsible to discount this possibility out of hand. For one example, a stream study indicated that crossing a nutrient threshold may lead to synchronous declines in sensitive alga species with simultaneous increases in tolerant species associated with increasing enrichment (Taylor, J. M., King, R. S., Pease, A. A. and Winemiller, K. O. 2014. Nonlinear response of stream ecosystem structure to low-level phosphorus enrichment. Freshwater Biology, 59: 969–984). Additional comments: The Authors have made many changes that have improved the manuscript. However, they have been resistant to certain suggestions. The changepoint analysis might show no clear change (or a large 95% CI) because of the relatively low site replication, but that would still be a result worth reporting, because validating the threshold would enable comparison with future studies.

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.

Title: ONTOGENY OF LONG-RANGE VOCALIZATIONS IN A NEOTROPICAL FOSSORIAL RODENT: THE ANILLACO TUCO-TUCO (CTENOMYS SP.) Review round: 1 Reviewer: 1

Basic reporting: The paper is generally well-written and organized. Multiple minor issues with word choice are listed with suggestions for improvement in General Comments. A couple of broader citations would improve scope of first paragraph of intro (see General Comments). The figures are very nice. Experimental design: The study is of interest and, despite small sample sizes, definitely worthy of publication. The research questions are well-defined although the authors should consider whether their data can really address their second aim (vocal learning vs. vocal tract development). Additional information is needed in Methods (see General Comments). Validity of the findings: Overall, the findings are valid because this is primarily a descriptive study. However, the statistical tests used are not appropriate to the data (see General Comments). The Discussion is quite good but I strongly encourage the authors to consider and discuss how vocal function and the context in which vocalizations are produced change over ontogeny in their own study species and others. Additional comments: Title and throughout: The Anillaco tuco-tuco referred to as Ctenomys sp. Is this an undescribed species? If so, how is it distinguished from congeners? Some explanation that goes beyond referring readers to another publication from this research group is needed. Abstract, L304: change undistinguishable to indistinguishable Introduction L46: “vocalizations experiment an ontogeny”. Experience? A better phrase might be, “vocalizations follow a developmental trajectory” L47-51: Both citations here are for empirical papers. It would be better to have other citations to support these general opening statements. L62: change “to” to “into” L85: suggest removing “simply” L88: change “can help understand how” to “can improve understanding of how” L91: change “of” to “to” L94: change “composed by” to “composed of” L97: Not sure that abnormal is the right word. Abnormal has negative connotations for functionality whereas it sounds like these alternate vocal patterns are simply atypical/uncommon. Materials and Methods Please explain how juveniles were acoustically isolated from adults and address whether or not they were acoustically isolated from each other. Also, please provide some life history info that will place the term “juvenile” in a species-specific context: typical age at weaning (14 days seems very young), and age at sexual maturity for male and female Anillaco tuco-tucos. (Having read discussion I see that the latter is unknown; that should be stated here and at least a rough estimate could be provided based on other Ctenomys) Please provide sufficient information on the enclosure that readers can assess how the animals were maintained (e.g., group housed? Size of enclosure? Inside or outside?) and how acoustic data were collected without reading Amaya et al. 2016. This is particularly important for the “Recording of vocalizations” section. Were the animals recorded in their home enclosures or elsewhere? It sounds like they were recorded singly but this isn’t completely clear. L162-170: Please clarify what 90% means in relation to duration and bandwidth. L158-186: As I understand it, the way acoustic parameters were measured for triads and individual notes was very similar if not identical. Suggest combining the two sections to reduce redundancy in text. L188-187: Some of this is redundant with lines 148-153. L199: As above, consider changing abnormal to atypical. L215: The Spearman correlation is not appropriate for the data because repeated measures collected from the same individuals are non-independent. It’s fine to plot the data as the authors have in Fig. 5 but to test for an effect of change in age (weight) on change in acoustic variables would need repeated measures ANOVA or a GLM with individual ID as a random variable. Same goes for the Kruskal-Wallis test. L231-237: Ethics statement would be more appropriate at the end of Experimental animals and info on the stats package should go at the end of Statistical analyses. Results L243-244, 251 and elsewhere: change “were given” to “were produced” and “gave” to “produced” L266: change “lumped” to grouped or split. L271-272: This sentence is quite vague. Please be more specific as to how vocalizations achieved mature features at different developmental stages. L280: change “conformed by” to “comprised of” L282: “obviously” is subjective. A statistical test would be nice but if sample sizes make that impossible at least use numerical evidence. e.g., 7.8% is more than an order of magnitude > than 0.28% or, “abnormal” series were >25x more common in juveniles. Also, if reporting frequency of an event as a percentage should change proportion to percentage. Discussion L304-306: Need to acknowledge that, while this study did not find evidence for vocal learning, it also did not effectively test this hypothesis since the study animals were exposed to adult vocalizations for at least the first two weeks of life and it’s currently not clear whether juveniles were isolated from each other. This is addressed later in the Discussion, but if the authors want to include a statement about vocal learning in the first paragraph it should be modified. L307: Again, how do the authors know that these “abnormal” vocalizations reflect poor motor control etc? How do they know that they don’t have a function in juveniles and/or adults? Without information on the context in which different types of vocalizations are produced, can’t assume that these vocal types are “mistakes”. L332; 333-336: change “substantial genetic makeup in” to “substantial genetic contribution to”. Please clarify why the presence of series patterns in congeners supports the suggestion that there is a genetic basis to vocal patterns in the study species. L337: tuning L337-347: Again, I encourage the authors to consider how the function of vocalizations in their study species, and in other rodents, changes between birth and maturity. L361: song has not been used previously to describe this species’ vocalizations, suggest changing. L363: please clarify what “conformed only by series” means. L369: Not all researchers agree that vocal learning is completely absent in rodents. See Jarvis 2006, Ornithological Science; Arriaga et al. 2012 PLoS ONE; Arriaga and Jarvis 2012 Brain and Language and papers citing these papers for ongoing debate. L380: Listen is subjective. If the auditory meatus is open from birth then these animals can probably hear from birth. Standard ways to test for a contribution of learning to the development of adult vocalizations are complete acoustic isolation (very hard to do in mammals without deafening) and cross-fostering to a closely related species with different adult vocal patterns. L391, 393: Change presumably to presumptively; “alleged” has negative connotations re. the conclusions of Camin 2010. Consider changing. L397, 401: Georychus capensis L403: occurs L409: superficial? L411, 413: Hooper, not Hopper. Also, this citation is missing from Bibliography.

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.

Title: ONTOGENY OF LONG-RANGE VOCALIZATIONS IN A NEOTROPICAL FOSSORIAL RODENT: THE ANILLACO TUCO-TUCO (CTENOMYS SP.) Review round: 1 Reviewer: 2

Basic reporting: The manuscript is of interest, at elast for scholars and students interested in acoustic communications and rodents. It is sound, scientifically valid, well structured and celarly written. In my view, it fulfills all the criteria put on papers published in Peer J. I have only minor comments, although some of them (esp. that one concerning the age of the studied animals) must be addressed: 1) The authors state (Lines 122-130) that the captured juveniles were weaned individuals between 2-4 weeks old, and had weight of 33 g. According to Camin (2010), a paper the authors are also citing, weaning (in C. mendocinus) occus at the age of 56 d.a.b. and weight of 117 g. This discrepancy should be clarified. 2) (Lines 385-390) - It is argued that slow development in Ctenomys is due to its subterranean way of life. This is only partly true. More importantly - this is a common feature of all hystricognaths rodents! 3) Bathyergus siullius and Georinchus (line 397 and further on) - correct spelling is suillus and Georychus 4) unify writting vs - either with dot vs. or without vs 5) unify writing number and percent - either with space xx % or without xx% 6) In many cases there should be "the" after all: all the experiments, all the individuals, all the parameters etc. instead of all experiments, all individuals etc. 7) Line 46: I do not understand the sentence: Like many other aspects of biological systems, vocalizations experiment an ontogeny. (perhaps experience instead of experiment?) Experimental design: I have no comments Validity of the findings: The findings are valid Additional comments: See above

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.

Title: ONTOGENY OF LONG-RANGE VOCALIZATIONS IN A NEOTROPICAL FOSSORIAL RODENT: THE ANILLACO TUCO-TUCO (CTENOMYS SP.) Review round: 1 Reviewer: 3

Basic reporting: see below Experimental design: see below Validity of the findings: see below Additional comments: In general the manuscript present nice data showing developmental changes in the structure of long range vocalization of Anillaco Tuco Tuco. The problem with manuscript is the theoretical framework in which the author put their findings. Beside this there are some serious statistical problems. 1) Vocal learning vs. vocal maturation: The authors found no evidence for vocal learning which is not surprising because until now none of the studies describing developmental changes in rodent vocalizations found evidence of vocal learning. Their conclusion that the age related structural changes are related to maturational changes of the vocal tract is not very conclusive: First, the authors did not measure any vocal features which could describe changes related to vocal tract changes. Bandwidth and peak frequency do not describe formant structure. Insofar the authors have no measure whether changes in the vocal tract really lead to changes in the acoustic structure of these vocalizations. Further, looking at Fig. 5 makes clear that already juveniles at a weight of app. 80g have the same note structure as adults. The only difference which remains is sequence composition and number of notes. But this has nothing to do with vocal tract changes. In addition it remains unclear to which degree adults and juveniles differ in sequence composition and number of notes. The tests (L266-270) seem to be wrong. In table S3 they make correct tests, one test per subject. But in this paragraph it seems that they combine the repeated measurements of their subjects. This cannot be tested with such tests. A chance level below 0.0001 having only three females is also a good sign that something is wrong. It is possible to use a simple pairwise test comparing old juveniles and adults. 2) Abnormal series in juveniles and adults: Independent whether it makes sense to use the term abnormal for the differences in the series, the major shortcoming is that the author forgot to take the motivation of the animals into account. The possibility that juveniles are already able to produce adult like vocalization but did not do it because they have no motivation is a general problem discussing factors underlying developmental changes. It is possible that they are already able to produce adult-like series but have no motivation. 3) Development of individual notes: The author found that only three subjects produced individual notes. None of the females produce single notes although they produce otherwise same notes as males. To me the meaning of these individual notes is totally unclear. Why are they produced only by these three males? Before making any developmental story out of it (“mixed developmental mode”), the author should try to find out whether there is any communicative relation with the production of these individual notes. 4) Life-history traits and territorial vocalizations …: This paragraph is very vague. In addition I cannot see why the development of the LRV is protracted about 110-120 days. Fig. 5 shows nicely that only very young subject differ in note structure. Juvenile seem to vocalize less but this could be simple due the fact that they have no motivation. If the authors could not come up with evidence that only the adults can produce the adult like version they should skip this part of the discussion. 5) It is unclear how the authors correct for multiple testing (e.g. Table S3).

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.

Title: ONTOGENY OF LONG-RANGE VOCALIZATIONS IN A NEOTROPICAL FOSSORIAL RODENT: THE ANILLACO TUCO-TUCO (CTENOMYS SP.) Review round: 2 Reviewer: 1

Basic reporting: No comment Experimental design: No comment Validity of the findings: No comment Additional comments: The authors have done a very nice and extremely thorough job of revising this manuscript. It is significantly improved and will make a nice addition to the literature on vocal ontogeny in rodents.

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.

Title: ONTOGENY OF LONG-RANGE VOCALIZATIONS IN A NEOTROPICAL FOSSORIAL RODENT: THE ANILLACO TUCO-TUCO (CTENOMYS SP.) Review round: 2 Reviewer: 2

Basic reporting: Most parts of the revised manuscript are clear and unambiguous. The description of the different acoustic characterizations (L 199-239) is partly redundant, otherwise difficult to understand. Similar table 2: Unclear why there are no p-values for “series per vocalization. What is the meaning of “A”, “B”, “C” & “D”? Experimental design: no comment Validity of the findings: The authors modified their statistical methods. Unfortunately not all changes led to a satisfactory result: 1) The authors present only p-values (table2, Text L304-313, 333-336). This is not correct. At least they should give also test statistic and/ or total N. 2) Again, it remains unclear whether the authors adjusted for multiple testing (pairwise statistic, several acoustic parameters). 3) It is unclear how it is possible to get a p-value below 0.001 with two subjects (females) using Friedman test. Additional comments: No additional comments

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.

Title: DIFFERENT INTENSITIES OF BASKETBALL DRILLS AFFECT JUMP SHOT ACCURACY OF EXPERT AND JUNIOR PLAYERS Review round: 1 Reviewer: 1

Basic reporting: No comment Experimental design: The authors have not defined ‘fatigue’ as either peripheral or central, so accordingly, cannot postulate that fatigue has actually been induced. Yes, the player’s heart rate and perceived exertion may have increased, but this is not because of heightened levels of fatigue – reinforced by the fact that the expert players jump height actually increased after the high fatigue protocol! Given this, I am almost certain neuromuscular fatigue was not induced, making the entirety of their results and discussion misguided. The protocols used to ‘fatigue’ the players appeared nonsensical, and lacked construct validity. Why did the authors not use the protocols described by Scanlan et al. (2012 – The development of the basketball exercise simulation test)? This test was comprehensively developed, using local positioning system data extracted from game-play to inform its construct. Had the authors used this, it is likely they would have incurred ‘fatigue’. Validity of the findings: The authors note a decline in performance of the junior group following the high fatigue protocol, citing the kinematics of the upper body being the confounding factor given the maintenance of jump height (again, showing the lack of fatigue actually induced). However, given no kinematic analysis was done, how can this be the author’s conclusion? More directly, I feel that the decline in shooting performance was more of a reflection of the attention shift participants are likely to have encountered given the perception of being ‘fatigued’ (see Maarten et al., 2005 – Effects of mental fatigue on attention: An ERP study). Surely the expert players possessed a superior level of physiological fitness relative to the junior players? So, why did the authors not extract this data at the start and then modify the protocols to the relative physiological fitness of player groups? More directly, the ‘fatiguing’ protocol for the expert group could have simply been a warm up given the likely superior fitness they possess relative to the junior players, who are likely to have struggled more so with this protocol. Thus, are you not comparing apples with oranges? Additional comments: The concept of fatigue and its impact upon jump shot accuracy in expert and junior basketball players is interesting. However, given the above points, I feel the study has just missed the mark here. In addition to the more major commentary listed above, there are multiple minor points of concern throughout that the authors need to consider prior to re-submission. Abstract • The first sentence is nonsensical – what is conditioning and related fatigue? Introduction • The physiological parameters presented in Lines 39 and 40 hardly warrant the use of “Very severe”…. This is where I would be more inclined to focus on the movement demands of the players, as these are what would have impacted neuromuscular fatigue – making more sense for your experimental protocols. • No use of paragraphs throughout? Results • Lines 122 – 123 – again, how can the authors state that fatigue has been induced? Jump height has maintained and actually increased slightly for the expert group! Further, the expert / junior differences are merely a reflection of training age, no? General • Reference inconsistencies / Figure and Table captions on different pages.

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.

Title: DIFFERENT INTENSITIES OF BASKETBALL DRILLS AFFECT JUMP SHOT ACCURACY OF EXPERT AND JUNIOR PLAYERS Review round: 1 Reviewer: 2

Basic reporting: There are a number of grammatical errors throughout the paper. I propose that the following changes be made for this paper to be accepted. Abstract, Line 17- include a comma after basketball. Change to "In basketball, conditioning and related fatigue affect performance." Abstract Line 17- include comma after moreover and remove "a". Change to "Moreover, maximum accuracy is required while shooting." Abstract, Line 18- include "The" and change second "study" to investigate. Change to "The aim of the study was to investigate the effect of three different levels of fatigue on jump shot...". Introduction, Line 38- I would suggest to change severe to specific. Introduction, Line 41- remove "a" before maximum. Change to "Together with a high level of fitness, maximum accuracy is required..." Introduction, Line 46- change "Similarly, it has been showed a detriment...' to "similarly, it has been found that a detriment...". Introduction, Line 48- change "3 points-shooting" to "3 point-shooting". Keep consistent throughout the rest of the article. Introduction, Line 52- change worsening to "reduction in accuracy". Introduction, Line 55- change "considering" to "during". Introduction, Line 56&57- change "indices" to "scores". Introduction, Line 56- you have misinterpreted the results of the repeated-sprint study. There was no difference reported between total sprint time, after the warm up and after the game. Only difference reported was sprint at half-time. Introduction, Line 59- change "showed" to "shown" Introduction, Line 59- include training in between sport-specific and methods. Change to "...sport-specific training methods..." . Keep consistent throughout the rest of the article. Introduction, Line 68&69- Include the jump shot in this sentence. "Our hypothesis was that fatigue could induce in both groups a decrease of the accuracy and jump height as exertion is increased during the jump shot." Introduction, Line 70- change "with respect to" to "compared with" Experimental Procedure, Line 86- change "minutes" to "minute" and "consisting in" to "consisting of". Experimental Procedure, Line 87- change "free shots" to "free throw shots". Keep consistent throughout the rest of the article. Experimental Procedure, Line 90- change "proved" to "moved". Experimental Procedure, Line 92- change "Then he had to run..." to "The participant ran..." Experimental Procedure, Line 94- change "he" to "they". Experimental Procedure, Line 94- include a comma, change to "After reaching the cone, they performed a cutting manoeuver..." Experimental Procedure, Line 102- change "always on that for all the trials" to "the same for every trial." Experimental Procedure, Line 106- change "fly time" to "flight time". Experimental Procedure, Line 110- change "prior the tests" to Prior to the tests." Experimental Procedure, Line 115- include significance instead of statistically or write both e.g. "If the statistical significance..."/ "If the significance...". Results, Line 122- change “set’ to “sets”. Discussion, Line 155- change “contribute” to contributor”. Discussion, Line 177- I would suggest changing “proposed” to “implemented”. Discussion, Line 203- change “experts” to “expert”. Experimental design: No comment. procedure is satisfactory. Validity of the findings: No comment. Validity of findings seemed satisfactory. Additional comments: I think the procedure used was scientifically sound. It was a good approach to investigating the effect of fatigue on shooting accuracy and a well thought out study design. I agree with the implications for skill training in basketball provided in the comments.

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.

Title: DIFFERENT INTENSITIES OF BASKETBALL DRILLS AFFECT JUMP SHOT ACCURACY OF EXPERT AND JUNIOR PLAYERS Review round: 2 Reviewer: 1

Basic reporting: No comment Experimental design: No comment Validity of the findings: No comment Additional comments: The authors should be congratulated for addressing both reviewer comments with respect. Their rebuttal was sound and where necessary, they addressed the reviewer commentary in a sound way - well done. I have no further commentary and wish the authors luck for their future research ambitions.

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.

Title: FACTORS ASSOCIATED WITH ELEVATED BLOOD PRESSURE OR HYPERTENSION IN AFRO-CARIBBEAN YOUTH: A CROSS-SECTIONAL STUDY Review round: 1 Reviewer: 1

Basic reporting: No comment Experimental design: No comment Validity of the findings: No comment Additional comments: The authors report an interesting cross-sectional study on factors associated with prehypertension in 898 young adults (mean age, 18.8 years). All subjects were born between September and October 1986, then similar in terms of age. The study describes the burden of metabolic disorders such as obesity, high glucose and triglycerides in this large cohort of young Afro Caribbean adults. Authors show that metabolic disorders and socioeconomic status are associated with prehypertension a clear risk factor of hypertension development. Gender analysis is also interesting and discloses differences in prehypertension associated factors. The study results may be able to support public health policy option to decrease the prevalence of metabolic disorders in young Afro Caribbean adults. I have only minor concerns 1) In Table 3: I think that the 3 stars associated with “Binge Drinking” should be deleted. 2) In Table 4: The factor “Parental Occupation” may be deleted from the table since no association with prehypertension in multivariate analysis is shown. 3) I suggest that authors could propose that the results of their study may support a public health policy that focused on metabolic disorders decrease in childhood and in young adults.

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.

Title: FACTORS ASSOCIATED WITH ELEVATED BLOOD PRESSURE OR HYPERTENSION IN AFRO-CARIBBEAN YOUTH: A CROSS-SECTIONAL STUDY Review round: 1 Reviewer: 2

Basic reporting: This paper is presented in a clear, unambiguous, and professional manner, it conforms to professional standards of courtesy and expression. The authors have done a reasonable job and citing the most up to date references, although they have neglected to report on the CVD outcomes from the Modeling the Epidemiologic Study, a large cohort study currently following young adults (25-45yrs) in Jamaica, and 4 other African-origin adults e.g. Cardiovascular risk status of Afro-origin populations across the spectrum of economic development: findings from the Modeling the Epidemiologic Transition Study. Dugas LR, Forrester TE, Plange-Rhule J, Bovet P, Lambert EV, Durazo-Arvizu RA, Cao G, Cooper RS, Khatib R, Tonino L, Riesen W, Korte W, Kliethermes S, Luke A. BMC Public Health. 2017 May 12;17(1):438. And Elevated hypertension risk for African-origin populations in biracial societies: modeling the Epidemiologic Transition Study. Cooper RS, Forrester TE, Plage-Rhule J, Bovet P, Lambert EV, Dugas LR, Cargill KE, Durazo-Arvizu RA, Shoham DA, Tong L, Cao G, Luke A.J Hypertens. 2015 Mar;33(3):473-80; discussion 480-1. The current study should be discussed in relation to these findings. Furthermore, many of the methods are not referenced (e.g. Physical activity questionnaire?) and some of the sentences are incomplete: e.g. sentence 88: where do estimates range from 2-19%, and were are estimates ranging from 12-45%? The authors also present prevalence data for Jamaica: lines 107-111, however prevalence may be changing as a result of increased screening, it would be helpful to know incidence data. Perhaps increases are simply as a result of more people undergoing screening. The authors are inconsistent throughout the manuscript with the use of abbreviations. Sometimes they use the abbreviation before the word is defined, other times they present the whole word, and then only abbreviate later. This reviewer also feels that there are too many tables (especially supplemental tables), representing models that do not change the outcome of the paper, or fail to reach statistical significance. The authors have submitted a paper which was rejected by another journal, and not removed the edits or formatting requested by that journal. It is recommended that the authors submit a clean version of this manuscript, fulling PEERJ’s formatting style. Experimental design: While the overall aims, and research question are well presented and the paper does present with some novel findings there are several issues for this reviewer. 1) It is not clearly stated that participants were overnight fasted 2) How is the WHR defined? 3) HOMA-IR used fasted insulin and glucose, which is presented in the paper, why not calculate it? 4) No reference for the physical activity questionnaire 5) No references for SES questionnaires 6) The authors imputed biochemical data, this is a serious weakness in the current data. There is no data presented to show how the associations changed with or without the imputed data? Also up to a quarter of some of the variables were missing: Family history of HTN. This would seem to be a major flaw if HTN data is missing? 7) The authors did not adjust their models for smoking/ganja, this seems as a major flaw for predicting future risk for HTN. Validity of the findings: This paper addresses a unique population for early diagnoses of HTN among young adults. However, this reviewer has several issues with the statistical analyses (lack of adjusting for smoking), and imputation of missing variables (how do outcomes change with or without imputation?). The paper also does not include several references, see basic reporting section. Throughout the paper, it is not clearly stated who comparisons are being compared to, e.g line 326-327. This reviewer suggests cutting down on the tables, particularly those representing models that fail to reach statistical significance. The authors have complied with the data sharing policy. Additional comments: Overall this is a well written paper presenting novel findings in an under-studied age group. This reviewer suggests that the authors be given the opportunity to address the comments, and particularly the analyses and then resubmit their work.

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.

Title: FACTORS ASSOCIATED WITH ELEVATED BLOOD PRESSURE OR HYPERTENSION IN AFRO-CARIBBEAN YOUTH: A CROSS-SECTIONAL STUDY Review round: 1 Reviewer: 3

Basic reporting: No comment Experimental design: The study is a retrospective case control study with cases defined as Afro-Caribeean youth having elevated blood pressure (either pre-hypertension or hypertension) The reviewer congratulates the research team in recognising the important contribution that pre-hypertension plays as a cardiovascular risk factor The study seeks to fill an important evidence gap pertaining to elevated blood pressure in youth from a specific ethnic group. My concern with the study design is the lack of a subset analysis looking at hypertension (preferably stratified into Type I and Type II hypertension). The reason for this is two fold. Firstly, from a public health perspective understanding the risk factors for youth with established hypertension as opposed to just pre-hypertension is important as it assists in prioritising preventive action. The other reason is that readers less familiar with the concept of pre-hypertension may be misled by the combination of cases being defined as elevated hypertension. By reporting the results categorically, and combined it will better inform readers and inform practice. I appreciate that the prevalence of hypertension is low which may preclude this sort of analysis however this should be mentioned explicitly if the authors believe this is the cas.e The association between increased ACR and hypertension is not mentioned in the results - despite this data being available. I would like to see this finding mentioned. As an early marker of renal impairment it would be interesting to know if it contributes to elevated BP in this group. The research question is well defined and appropriate methodology and statistical analysis is used. (5) Ethical clearance for the article was evidenced. Validity of the findings: (1) In the discussion I would like to see further comparison with other studies of elevated BP in youth. Eg the gender difference that was found here has been found among Australian Indigenous youth. (2) The limitations of the study are appropriately delineated. (3) Further exploration of the public health implications of the study would be beneficial Additional comments: No additional comments

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.

Title: FACTORS ASSOCIATED WITH ELEVATED BLOOD PRESSURE OR HYPERTENSION IN AFRO-CARIBBEAN YOUTH: A CROSS-SECTIONAL STUDY Review round: 2 Reviewer: 1

Basic reporting: no comment Experimental design: no comment Validity of the findings: no comment Additional comments: Author's answers are appropriate with my requests. I have no more comments Thank You

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.

Title: CALIBRATION ADJUSTMENTS TO ADDRESS BIAS IN MORTALITY ANALYSES DUE TO INFORMATIVE SAMPLING—A CENSUS-LINKED SURVEY ANALYSIS IN SWITZERLAND Review round: 1 Reviewer: 1

Basic reporting: Clear and unambiguous english is used for the most part making the manuscript comprehensible. Some editorial revisions including the suggestions to the author below would improve clarity. Experimental design: The authors effectively demonstrate how a survey-based census system without consideration for differential non-response, such as that adopted in Switzerland, will impact the validity of survival and/or mortality analyses. They do so by comparing mortality rates and life expectancy derived from survey weights with those derived from inverse probability weights using survival data from the country’s Vital Stats Registry and taking into consideration survey non-response data. The analysis is adequate and understandable, with appropriate tables and figures, provided table 1 is modified. The findings and conclusions are accurate and of importance. Validity of the findings: While the overall findings are valid and important and the conclusion is well stated, the general context of this research question is not discussed especially the practical implications of these findings (IMPACT). Moreover the baseline data of STATPOP could be better described. For the rest, the data seems robust , statistically sound and controlled. Additional comments: I read the manuscript by Moser et al. with great interest. The authors effectively demonstrate how a survey-based census system without consideration for differential non-response, such as that adopted in Switzerland, will impact the validity of survival and/or mortality analyses. They do so by comparing mortality rates and life expectancy derived from survey weights with those derived from inverse probability weights using survival data from the country’s Vital Stats Registry and taking into consideration survey non-response data. The analysis is adequate and understandable, with clear, appropriate tables and figures. The findings and conclusions are accurate and of importance. Some concerns are as follows: Major concerns: • While the manuscript shows that estimates based on survey weights will be underestimated (MR) and overestimated (LE), it falls short of explaining the impact or significance of this concern. For population-based studies on vital statistics, one could always fall back on the STATPOP file; thus, it is important for the authors to convey what the consequences of this difference in estimates might be in practice, ideally providing concrete examples. • It would be advantageous to provide the regional European context. Is this a local problem, or are other countries reverting to the same census plans? • Survival Concerns: Please discuss the completeness of mortality records for linkage with STATPOP. Regarding the mortality records of non-Swiss populations (roughly 20% according to Table 1), what is the “lost to follow-up” rate? How is vital status ascertained? (death certificate alone? Regular collection of “state income or pension” anywhere in the world? Etc.) What about people moving to warmer geographies or to their countries of origin and dying there (some with the authors’ exact characteristic of interest - poor health status)? How would these aspects affect the survival used for the IP weights? Furthermore, due to the overlap with poor health status, how would it affect the estimates of the current study? At minimum, these concerns could be addressed in the limitations section. • Non-Swiss populations have significantly lower odds of response to the survey, but the effect of that was not discussed. Please also clarify if cross-border workers to cities like Geneva and Basel are included in STATPOP –as part of the Swiss population - and/or the survey? Minor suggestions: • The word “informative” may come across as positive to the less informed reader. The text should be modified so that “informative” is clearly portrayed as an unwanted characteristic. • Please check the order of the Figures. Currently starts at 3. • Lines 129-131: Is the survival time individually updated as per some sort of contact with the subject or is survival time measured throughout the full period presuming the subject is alive in the absence of a death record? • Line 144: Does the OR=4 come from Pizzi et al. as well? If not, please substantiate your choice. • Line 149: The sentence “The overall percentage of deaths was set to 10% and 25%” needs to be clarified with information regarding which group or data subset is involved. • Lines 262-263: This sentence is best suited for the Introduction. • Lines 303-305: This statement is an overreach and possibly wishful thinking. Readers will understand that resource shortages are driving countries towards novel approaches to counting their populations. Yet, as researchers, we know that there is no real substitute for a Full Enumeration Census (albeit also imperfect). To suggest that surveys and statistical estimates could ever replace an actual total count is bold at the least, and surely contentious, unless Switzerland is unique and there is a total absence of undocumented persons, the “lost-to-follow-up” rate is zero, and the borders are fully controlled. I would strongly consider modifying this segment of text. Minor language/word choice concerns: While the manuscript is comprehensible, some editorial revisions including the following would improve clarity. 1-The use of the word “register” is awkward 2-The use of the word “consistent” -it often seems like the authors actually mean accurate or valid 3- “Despite” is not used correctly; sentences using it should be modified. 4- The use of future tense in some sentences is odd/unusual. 5- Other awkward phrases:  true underlying population estimates (need a better word for “true”)  they address for the sampling  because of privacy preservation  a bad health status  studies including Switzerland  state-of-the-art nowadays  provided almost In addition, table 1 is confusing and should be modified, possibly with horizontal lines.

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.

Title: CALIBRATION ADJUSTMENTS TO ADDRESS BIAS IN MORTALITY ANALYSES DUE TO INFORMATIVE SAMPLING—A CENSUS-LINKED SURVEY ANALYSIS IN SWITZERLAND Review round: 1 Reviewer: 2

Basic reporting: 1. Throughout the article, the switch from a full census to a survey-based micro-census is provided as justification for the work. Presumably, however, full censuses also have non-response and the same conclusions could apply (i.e. inverse probability weights would still improve the longitudinal validity, despite their not being a sampling probability). Please clarify the generalizability of your findings, and if they are generalizable beyond this micro-census scenario, perhaps use a different motivation to justify your study. 2. Abstract: Define a registry-based census. Be consistent with calling it either a registry-based or register-based census. 3. Line 35: Describe who the 6.5 million individuals are (i.e., all persons included in the registry-based census) 4. Line 37: Clarify “aimed to be sampled”. Presumably 3.5% were sampled, but not all responded? Perhaps remove “aimed to” 5. Line 74: “the statistical analyses” is vague – what statistical analyses? 6. Lines 80/81: This sentence is very general and therefore confusing. I would differentiate between what your aim was (specific, mortality rates) and its implication (potentially broader, any time to event data) 7. Line 94: Remove “will” 8. Lines 111, 121: English language editing needed. 9. Line 136: Figures should be numbered in the order they appear in the text 10. Lines 140, 242, Figure 3: Replace “a bad health” with “poor health status” throughout. 11. Line 185, Table 1: I may be ignorant given that this is not my area of expertise, but are the mean CS and IP weights informative to the reader? I am not sure how to interpret these in Table 1 and wonder whether there is use in them being there? 12. Figure 2: Suggest making the x-axis categorical with the different methods across the x-axis. Could also consolidate to one graph. Experimental design: 1. The simulation study seems like a bit of an afterthought, both in the presentation and the interpretation of the results. I suggest either fully justifying the usefulness and implications of the simulation study, or leaving it out altogether. Validity of the findings: No comment. Additional comments: Overall, I think this is a well-executed and thorough study that is well described and has valid findings. Some English language editing is needed and some further clarification of the generalizability and implications of the results would improve the paper, but on the whole it seems to be a quality piece of work worthy of publication.

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.

Title: THE STATE OF OA: A LARGE-SCALE ANALYSIS OF THE PREVALENCE AND IMPACT OF OPEN ACCESS ARTICLES Review round: 1 Reviewer: 1

Basic reporting: This article is well and clearly written, and is characterized by (to the extent possible, given the subject matter) an admirable avoidance of jargon. It is well organized, with clear and logically-arranged sections. However, the authors do need to review their references: in at least one case, they cite an article in support of a point not addressed in that article, but rather in another one by the same author that is uncited in this piece. All data sets, including the source code for the tool under examination, are made publicly available. Experimental design: Given that PeerJ "considers articles in the Biological Sciences, Medical Sciences, and Health Sciences" and "does not publish in the Physical Sciences, the Mathematical Sciences, the Social Sciences, or the Humanities (except where articles in those areas have clear applicability to the core areas of Biological, Medical or Health sciences)," it is not clear to me that this article is strictly in-scope. This strikes me as a piece that would fall within the category of the social sciences. However, the tool under discussion certainly has application to publications in biology, medicine, and the health sciences, so PeerJ's editors will have to decide whether the subject connection is strong enough to merit inclusion. The research methodology described in the article strikes me as perfectly sound, and the authors' interpretation of the results seem reasonable to me. Validity of the findings: The findings strike me as sound. Not everyone will necessarily be driven to the exact same conclusions from these data as those arrived at by the authors, but since the data are provided openly, there's no reason why those who disagree can't come to their own conclusions. This article adds a valuable and (I think) important piece of the puzzle in our ongoing quest to understand the OA publishing ecosystem. The article's most significant problem is not related to its content, but rather to the fact that its authors have (unless I missed the disclosure somewhere) failed to disclose a serious conflict of interest. Nowhere in the article, that I can determine, is it revealed that both unpaywall and oaDOI are products of Impactstory -- the company of which the paper's first two authors are founders and principals. In fact, at several points in the paper (notably the final paragraph of its Discussion and Conclusion section, which states "this paper clearly shows the potential of the oaDOI service for future research"), it begins feeling like an infomercial for Impactstory's products. A particularly attentive reader might notice that the links to source data for the study lead to Impactstory domains, but this doesn't seem sufficient: instead, the lead authors should say right at the beginning of the paper that they are principals in and cofounders of the company that produces the tool the performance and potential of which are under examination in this article. Additional comments: No additional comments

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.

Title: THE STATE OF OA: A LARGE-SCALE ANALYSIS OF THE PREVALENCE AND IMPACT OF OPEN ACCESS ARTICLES Review round: 1 Reviewer: 2

Basic reporting: Overall the article is well written and structured. There are some minor formatting issues with citations that should be reviewed and cleaned up (e.g. see first paragraph of lit review). I was surprised that Walt Crawford's extensive work on OA Journals wasn't referred to, but that may have been deemed out of scope. The figures do not translate well to black and white and minor revision to make that more clear is recommended. The bar charts were incredibly difficult to understand without the color. This also made it unclear if the keys and the charts aligned. A couple of typos scattered throughout (e.g. under definition of ASNs "we we" Formatting of the definitions of OA vary a lot -- citations bounce all over the entries. Please update for consistency. Raw data was available. Thank you for the very clear dictionary. Experimental design: On Page 8 the authors mention using a broader date window than the Archambault sample -- was this only for the WOS portion? Please clarify. On the top of page 11 where the authors describe the article assignment to discipline. It was unclear how the authors determined which journals were multidisciplinary and how articles were then further assigned. Was this by hand? Validity of the findings: no comment Additional comments: Overall I really enjoyed reading this paper. I made comments as I went through and found nearly all of these addressed later in the paper.

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.

Title: THE STATE OF OA: A LARGE-SCALE ANALYSIS OF THE PREVALENCE AND IMPACT OF OPEN ACCESS ARTICLES Review round: 1 Reviewer: 3

Basic reporting: A comprehensive description of oaDOI would be helpful earlier in the introduction. I was expecting more information about oaDOI in line 81, consider moving some of the language in line 230 to better frame the role of oaDOI in 'the state of OA' Regarding the raw data and analysis available at the DOI provided, you might consider including a manifest with data and article DOIs as well as a more complete codebook or at least definitions of all variables and codes in dataset (ie, 999 for missing data). This is a valuable dataset for the community and is somewhat difficult to interpret given the current documentation. In lines 307-308 the authors assert that Scopus and WoS are known to underrepresent segments of the literature. The article would benefit from a reference for this assertion. There is a grammatical error on line 498 'this paper aimed at answering...' Several references are formatted inconsistently, ie line 689 Experimental design: It would be helpful for the reader to clarify which ASNs were excluded from the analysis - all ASNs or only commercial ASNs? For example, would articles shared in the Humanities Commons be excluded? Validity of the findings: It would be useful to address the potential for self-selection among users of the Unpaywall extension and the possibility that this might impact the Unpaywall sample. In section 1.5 of the results, the conclusions are not well-stated. Consider a comparison of disciplines based on either the percentage of open papers or the percentage of gated papers. A combination of both is confusing for the reader. In the discussion of Bronze OA (line 527), you state that it 'seems likely' for Bronze to be disproportionately non-peer-reviewed. Why does this seem likely? Additional comments: I appreciated the opportunity to review this paper, this is a fascinating and very important analysis of open access scholarly literature. I am looking forward to seeing what additional research emerges from this, especially in the areas of citation advantage for Gold OA and the impact of Bronze OA.

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.

Title: THE STATE OF OA: A LARGE-SCALE ANALYSIS OF THE PREVALENCE AND IMPACT OF OPEN ACCESS ARTICLES Review round: 1 Reviewer: 4

Basic reporting: No comment. Experimental design: No comment Validity of the findings: No comment. Additional comments: Wonderfully accessible and well framed for understanding by multiple audiences. It would be interesting to see what could be done about parsing out the shadow of the green OA, since the availability of that content is likely more stable, and less subject to the whims of publishers than bronze (and some Gold, esp. in the hybrid case). Speaking of... the community would definitely welcome further research on the bronze OA concept, so I'm thrilled to see that you plan to develop that further. Thank you for an open article about openness that uses open data!

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.

Title: THE STATE OF OA: A LARGE-SCALE ANALYSIS OF THE PREVALENCE AND IMPACT OF OPEN ACCESS ARTICLES Review round: 2 Reviewer: 1

Basic reporting: Line 69 contains a reference to a piece by Anderson ("The Forbidden Forecast") that isn't relevant to the point under discussion (current Big Deal cancelations). The authors may have confused that piece with this one: https://scholarlykitchen.sspnet.org/2017/05/01/wolf-finally-arrives-big-deal-cancelations-north-american-libraries/ Later in the paper the "Forbidden Forecast" piece is cited in the context of a more relevant point. Experimental design: No change to previous comments Validity of the findings: No change to previous comments Additional comments: No change to previous comments

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.

Title: THE STATE OF OA: A LARGE-SCALE ANALYSIS OF THE PREVALENCE AND IMPACT OF OPEN ACCESS ARTICLES Review round: 2 Reviewer: 2

Basic reporting: No comment Experimental design: No Comment Validity of the findings: No Comment Additional comments: Thank you for reviewing the edits suggested before and making updates.

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.

Title: THE STATE OF OA: A LARGE-SCALE ANALYSIS OF THE PREVALENCE AND IMPACT OF OPEN ACCESS ARTICLES Review round: 2 Reviewer: 3

Basic reporting: Thank you for your revisions and response. I maintain that the underlying data provided at http://doi.org/10.5281/zenodo.837902 could benefit from more documentation, including a manifest with data and article DOIs as well as a more complete codebook or at least definitions of all variables and codes in dataset. However, I believe that this revised manuscript meets the PeerJ criteria and am recommending that it be accepted as is. Experimental design: No comment Validity of the findings: No comment Additional comments: No additional comments

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.

Title: FREQUENCY AND DEVELOPMENTAL TIMING OF LINEAR ENAMEL HYPOPLASIA DEFECTS IN EARLY ARCHAIC TEXAN HUNTER-GATHERERS Review round: 1 Reviewer: 1

Basic reporting: - The paper is well written and in this context it do not need any changes. - The literature is correctly selected, although you can delete the oldest quotes (e.g., Sarnat 1941, 1942). - The structure of manuscript is very confused.In paragraph "Methods" the authors write about materials. It is not known why they gave an additional sub-section "Study population" (line 72). In the subsection "materials" they described using methods (line 103). -some tables are illegible (e table 2) - a column with a number of teeth was introduced, but it is not clear why there are so many rows. Experimental design: -The aim of the study was not clear stated. -The teeth with strong wear were excluded (line 115).But there are not any information about the method for estimate the stages of dental wear. -There is no information about the age of individuals. But in the discussion the age category ("juvenis") was introduced (line 170). - The authors mention about deciduous teeth, but the Dean and Reid method applies only to permanent teeth ( line 144, 149). So it does not really make sense to write about decidous teeth in this context. - In the paragraph "results" the authors compare the Bucheye Knoll population with the other groups (line 160). This is a mistake, because such a comparison should be transferred to the discussion. - The authors mention about the weaning stress in the context of LEH. However, we know that the weaning stress must be assess according to isotopic studies (nitrogen), and LEH can be used only as a indirectly be used for this purpose. - In literature (line 280) Larson - it should be Larsen. - In literature (line 328) Wood - it is not found in the text. Validity of the findings: No comment Additional comments: The material used for the study is very interesting.But the results are quite poorly presented in this paper.

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.

Title: FREQUENCY AND DEVELOPMENTAL TIMING OF LINEAR ENAMEL HYPOPLASIA DEFECTS IN EARLY ARCHAIC TEXAN HUNTER-GATHERERS Review round: 1 Reviewer: 2

Basic reporting: I suggest the authors start the Introduction with hypoplasia (lines 44-58), then give the information on the population studied (lines 32-40) and conclude with the third subsection (59-70). The aims and purpose are clearly stated in the sentence (lines 41-43) ''Here, we infer nonspecific nutritional and developmental stresses via the developmental timing and frequency of linear enamel hypoplasia defects (LEH) in the canines using photogrammetric methods.'', and it would be better if the Introduction finished with it. Experimental design: No comment Validity of the findings: The conclusions are connected to the original question investigated, which should be more cleary stated in the Introduction section, as suggested above. Additional comments: No additional comments

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.

Title: THE EFFECT OF SUPRAGINGIVAL GLYCINE AIR POLISHING ON PERIODONTITIS DURING MAINTENANCE THERAPY: A RANDOMIZED CONTROLLED TRIAL Review round: 1 Reviewer: 1

Basic reporting: No comments Experimental design: No comments Validity of the findings: No comments Additional comments: There is adequate literature on use of glycine air powder for non-surgical periodontal therapy and its comparison with ultrasonic debridement. The authors have reviewed some of it in relevant sections of the manuscript. It is standard of care to disrupt subgingival biofilm during periodontal maintenance and proposing to modify that well accepted treatment methodology will require strong scientific support. Perhaps for a convincing argument to be made in favor of supragingival debridement alone, a long-term comparison of clinical and microbiological parameters with subgingival debridement will be required. Glycine air powder is restricted in its ability to disrupt calculus deposits and an ultrasonic debridement for those areas would be standard of care. It is interesting to note that patients in this particular study did not have any calculus deposits during their maintenance phase (an assumption based on lack of mention of this in the manuscript). Authors’ idea about patient comfort and time and cost-effective nature of supragingival plaque control that may have crossover effect on subgingival biofilm is the strongest hitherto largely unexplored question in this area. However, it is possible that the time and cost effectiveness of supragingival debridement alone would be diluted if cost of purchase, maintenance and training on both air-powder and ultrasonic instruments are taken in to account. No discussion was found on this aspect in the manuscript. Overall, the manuscript needs significant revision from a grammatical and spelling standpoint. At multiple places throughout the manuscript, it was somewhat difficult to interpret statements. Based on the overall deficiency in use of proper language and grammar, redundancy of already available data, development of clear rationale and lack of support for it restricts the utility of the manuscript in its current format.

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.

Title: THE EFFECT OF SUPRAGINGIVAL GLYCINE AIR POLISHING ON PERIODONTITIS DURING MAINTENANCE THERAPY: A RANDOMIZED CONTROLLED TRIAL Review round: 1 Reviewer: 2

Basic reporting: I think that this manuscript would benefit from a review and thorough evaluation of English grammar and structure . There are spelling and grammar errors throughout the article, for example: Lines 72-73 (introduction) "And A.a. was less frequent than ultrasonic debridement group. Line 213 (results) "there was approximately significant difference between baseline and 12 weeks after treatment". Line 320 (discussion) I would replace "serious periodontitis" with "severe periodontitis". Improper use of some references. For example: Loe's study (line 43) showed that dental plaque can cause gingivitis, not periodontitis. Experimental design: Inadequate information on the randomization method. Please provide more details regarding the methods or software used to distribute the right or half of the mouth to the two study groups. Were all right quadrants assigned to the test group whereas the left ones to the control? If yes, can you please provide the rationale for this decision. As mentioned in the discussion, being left- or right-handed can have an effect on the performed oral hygiene. Were all patients right handed or left handed? Other than that I think that is a well designed study. Validity of the findings: I think the main limitation of the study is that it does not take into account the possible presence of calculus in the the periodontal patients and how this can affect the effectiveness of either of the two methods applied in this study. A main advantage of the ultrasonics, is the ability to remove calculus, and ability that air polishing is lacking as discussed in one of the references included (Moene et al. 2010). A 3-month period, is a long enough interval for plaque to become mineralized, opposite to what is stated in the discussion where White's paper is cited. There is a number of papers supporting that mineralization of plaque starts within a few days rather than months. The rate of calculus formation varies considerably between individuals. Taking these factors into consideration, I think that sections of the paper should be revisited and as well as the conclusion (the recommendation for 3-month maintenance interval is based at an extend on the aforementioned parameters). Additional comments: Overall I would say that the experimental design of the study was very good with the exception of the lack of details on the randomization methods. Major revisions are recommended to address the issued discussed in the previous sections. Thank you.

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.

Title: THE EFFECT OF SUPRAGINGIVAL GLYCINE AIR POLISHING ON PERIODONTITIS DURING MAINTENANCE THERAPY: A RANDOMIZED CONTROLLED TRIAL Review round: 2 Reviewer: 1

Basic reporting: Okay Experimental design: Okay Validity of the findings: Okay Additional comments: There are still minor grammatical errors in the manuscript.

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.

Title: THE EFFECT OF SUPRAGINGIVAL GLYCINE AIR POLISHING ON PERIODONTITIS DURING MAINTENANCE THERAPY: A RANDOMIZED CONTROLLED TRIAL Review round: 2 Reviewer: 2

Basic reporting: There are minor grammar and spelling errors that could be addressed. For example: Line 302: I would write "In the present study" instead of "In present study". Line 341: "spilt-mouth" instead of "split-mouth". Line 378: "remov1e" instead of "remove" Experimental design: Well designed RCT, details provided on the randomization method, power analysis was performed. Validity of the findings: Although clearly stated in the discussion, I would add in the conclusion section that the comparison is only valid for soft deposits and not calculus. When calculus is present, additional intervention is needed. Additional comments: Dear authors, Thank you for addressing the majority of the recommendations from the first review. I think at this point, there are only minor editing changes to be made. The manuscript describes a sound methodological approach and valid conclusions. Thank you

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.

Title: GENOMIC ANALYSIS OF MORPHOMETRIC TRAITS IN BIGHORN SHEEP USING THE OVINE INFINIUM® HD SNP BEADCHIP Review round: 1 Reviewer: 1

Basic reporting: In this study, Miller et al. analyze the genetic basis of three sexually selected traits in a population of bighorn sheep that has been monitored for a long time. The authors use an Ovine Infinium BeadChip and morphologic data to perform genome wide association studies (GWAS) and identify SNPs that could be associated to these traits. The authors find a single SNP showing a low association with body length, and argue that the lack of association suggest that the traits should be controlled by many loci of low effect, instead of single loci of strong effect. While the objective of the manuscripts is interesting, and the long term monitoring is very valuable and unique, I think that the authors could analyze with more depth the long-term dataset that they have. The main focus of the study is centered on the GWAS aspect of the results, even though they do not find any significant results. The authors argue that the lack of association is probably an effect of the phenotypic traits being regulated by many loci of small effect instead of single loci of strong effect. However, it is also possible that the lack of associations can be related to a low coverage of SNPs. I know that it can be difficult to have large amount of genomic data, and I do not believe this is a main problem in the manuscript. Given the lack of significant results, I think that this paper would be more interesting if they analyzed with more depth the genomics of populations of these individuals, including all the demographic information they have (genetic diversity, paternity analyses, etc…). In addition I would develop more the phenotypic analyses, perhaps also considering the demographic data they have. The authors have a very interesting set of data that could be incorporated into the analyses that would greatly improve the paper, instead of focusing only in the genomic part. In this regard, I have the feeling that in order to have more information, the authors perform LD analyzes and simulations to test for the power of their analyses. While these results are interesting, all this information is supporting the main results and not part of the objectives. I think analyzing with more detail the genomics of this population, and moving figures 2 and 3 to supporting information would make more sense. I addition I have a few minor comments: Lines 41-42: “For example by overdominance…..2013)”: The authors do not test or comment any of these examples in the discussion. I think this sentence should be removed. Line 49: “Lek paradox”: The authors should explain what is the lek paradox, and how would the lek paradox apply for horns. Lines 54-61: “The genetic basis … (Ovis aries)”: The authors mention that the genetic basis have been studied in this system. Then it is mentioned that breeders have been interested in removing the horns, and finally the authors explain other examples of horns. However the genetic information is explained later. I think it would be more logic to move this sentence to the part where the authors explain the studies that have analyzed the genetic basis in line 62. Line 71: though should it be through? Lines 97-99: “Found 21 regions …. (Kardos et al. 2015)”: Genomic studies on horns have already been done. I think it is important to here explain what is missing and why their study could be important. Mention that other traits remain to be analyzed? Lines 106-107: “we contribute to knowledge on the genetic basis of complex quantitative traits”: I’m not sure this is true, since they only find one SNP with low association. As I mention before, I think it would be more interesting to also analyze the genomic diversity of the population, and focus more on the phenotypic aspect of the manuscript. If not, at least explain how they contribute to this knowledge because it is not clear for me. METHODS: Line: 113: “Most individuals are marked … known age”: I think this is very valuable and could be analyzed with more detail. Maybe test if consanguinity changes between generations, or something of this kind. Also comparing morphologic data between generations could be interesting. Exploiting this information could be valuable for the manuscript and build upon the genomic analyses. Lines 151- 152: “ We also estimated ….BLUPS)”: what is individual breeding values? The authors use this to select the individuals that are genotyped, but for somebody who is not familiar with the concept it would be important to explain it. Line 167-168: The authors explain which SNPs are discarded, but it would be convenient to also mention the final number of SNPs, so the readers know the amount since the methods and not wait until the results. Lines 178-183: The authors mention two steps, but they never explain whether the two steps are compared, connected or what is the point of having two steps. Is the first step used to control for the second step? RESULTS: Line 191: “used to quality filter loci” odd sentence, the authors should change it. The authors remove SNPs based on missing data and MAF: What happens if they include some of the discarded SNPs. Maybe it is worth testing the same analyses using other SNPs in the genome. These analyses could go in supporting information, but might increase the power. Line 201: ”genomic inflation”. Can the authors explain this? Line 204: “examined” should be examine the Figure 2 and lines: 204-215: This LD analyses are interesting, but I do not think that the result presented in figure 2 is a main conclusion or result. It is part of the methods and should go in supporting information. I would recommend rather putting a figure showing summary statistics or presenting the phenotypic data in another way. Lines 226-228: Two genes….not see an immediate connection with body mass”: I think this sentence should go in the discussion and that they should discuss this further. Explain why there is not a connection with body mass, and also explain why they found this association then. Discussion: Line 230: “several”, It is only three characteristics, this is not several. Lines 233-234: “We found 1…. Poissant et al. (2012)”: It is striking that they authors do not find any SNPs within the regions found by those described by Poissant. SNPs should have a larger coverage of the autosomes. I think this needs to be addressed with more detail. Is it possible to map the candidate regions of Poissant and see if any SNP is found nearby? If so, all the candidate regions of Poissant could be false positives. Please develop further this result. Lines 243-245: “However, based on … horns region”: The authors mention that they did not find a SNP in the region of RXFP. Maybe this is because they lost many SNPs that did not pass their filters. Could the authors verify if any of the SNPs from the chip appear in this region and analyze what happens if they include them in the analyses (Even if they are not in HW, or have a lot of missing data)? As they mention later, it is also probable that some SNPs are fixed in this population. Maybe it would be interesting if the analyze this. The sentence in lines 262-268 could be moved to this part. Lines 247- 261: As with the LD analyses, the power analysis is not the main focus of the paper. This is interesting but not related to their objectives. These results could be moved to supporting information. Also, it would be important to explain better how they did the analyses, and explain better the parameters changed, because it is not very clear. Experimental design: As I explain above, I think that it would be valuable if the authors develop more the genomics of populations and the phenotypic analyses. Also it would be interesting to include analyses that consider explicitly the long term study. Validity of the findings: As I mention above, I think that the paper is too focused on the GWAS analyses, and that I would be more valuable to include other genomic analyses. Additional comments: No additional comments

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.

Title: GENOMIC ANALYSIS OF MORPHOMETRIC TRAITS IN BIGHORN SHEEP USING THE OVINE INFINIUM® HD SNP BEADCHIP Review round: 1 Reviewer: 2

Basic reporting: No comment Experimental design: No comment Validity of the findings: No comment Additional comments: In this paper the authors analyzed the genetic basis of three phenotypic features of bighorn sheep. They collected measures of horns and body mass from several individuals. Then, 95 individuals (76 used) were genotyped using a commercial SNP chip. The results showed no association for loci and phenotype (except one). The authors suggested that the results could be due to low sample/loci number or selective sweeps. The conclusions were referred to the need to increase the sample size as well as loci number. Despite the negative results, I found this manuscript relevant and also well written. Although I have not expertise on QTL analyzes, I found the Methods well explained and in general understandable. However, the authors focused on the negative results, thus leaving aside interesting results. -They showed the importance of the number of markers (lines 216-218) -They actually found a locus having significant association, although without GO (lines 203-228) -They suggested that there could be a selective sweep event that led to the lack of variation on the previous reported loci (line 262) Considering the above mentioned, I suggest the following: -There should be carried out tests of selection. This could give insights about the lack of variation found. If a signal is founded, it could be associated with sexual selection and/or hunting pressures, both of them also influenced by population demographics affected y anthropogenic factors. Please check this paper for a compilation of methods of cattle breeds (Table 1) Gutiérrez-Gil B, Arranz JJ and Wiener P (2015) An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds. Front. Genet. 6:167. doi: 10.3389/fgene.2015.00167 -The paper should be complemented with a discussion about the biological factors that could lead to the observed results (as sexual and artificial selection, genetic bottlenecks, etc.), and not rely only in the assumption of the lack of samples/loci. -Also there should be included reasons why the locus OAR9_91647990 could not be annotated. It was because a lack of well annotated genome? Or the body mass could be affected by regulatory regions that are unknown? The locus in question could have strong linkage with other locus? Are there reports of this? -Finally, the title is ambiguous. I suggest that it should include something like "..the lack of association of phenotypic and genetic variation...". Specific comments: Some parts of the Results section should be moved to Methods. Lines [192-193] (VIPER Software) Lines [200] (Manhattan plots, add an explanation of how they were generated) Lines [204-213] (PLINK Software) Fig 1 Indicate the meaning of red and blue lines Fig 2 Add an explanation for the gray scale

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.

Title: GENOMIC ANALYSIS OF MORPHOMETRIC TRAITS IN BIGHORN SHEEP USING THE OVINE INFINIUM® HD SNP BEADCHIP Review round: 1 Reviewer: 3

Basic reporting: The article is interesting as the authors examined three sexually selected traits in bighorn sheeps using a SNP chip designed for domestic sheep and try to idendify candidate genes associated to these traits. I commend the authors for their extensive morphological data set, compiled over many years of field work.The paper is written in clear and professional English, nevertheless there are a few typos that need to be checked and corrected (see detailes below). The literature reference provide sufficient field background. The introduction is clear, but there are a few concepts that should be explained for clarity such as lek paradox (line 49) and polled morphotype (line 69). The article has a professional article structure, figures and tables. Raw data is shared. Nevertheless, supplemental materials needs more descriptive metadata identifiers to be useful to future readers. Overal, the article is interesting. My main concern is that when using cross-species application of SNP chips, ascertainment bias and coverage have important effects in summary statistics, analysis of genetic structure and selection tests that reduce the power of selection tests and increase type I and type II error (see Lachance and Tishkoff, 2013 Bioessays 35:780-786). Therefore, the analysis and discussion of results should address if ascertainment bias was measured and corrected. In addition, there are a few aspects on the biology of the species and methods used that should be included in the discussion (see below). Experimental design: This article shows original primary research with a well defined question, which is relevant and meaningful. In addition, it is stated how research fills an identified knowledge gap. The investigation is interesting, but as mentioned above, when using cross-species application of SNP chips, ascertainment bias and coverage reduce the power of selection tests and increase type I and type II error. Therefore, these issues should be addressed properly before acceptance. In general, methods are well described. Nevertheless, there are a few aspects that should be described with more detail: In the methods section (line 166) the authors mention that "Genotypes were then exported to PLINK version 1.07 (Purcell et al., 2007) for additional filtering". Please explain more thoroughly what type of filtering was used and the parameters. There are a couple of paragraphs (lines 204 - 213 and lines 223 - 225) in the results section that describe methods and should be moved to the methods section. Validity of the findings: The discussion should include perspectives on how to perform a better analysis, either by focusing in amplifying the region of the RXFP2 gene (previously identified candidate for horn morphology) or increase genome coverage by using other massive sequencing approach such as RAD-seq. Also, I think it is important to consider if including available data from domestic sheep will help assess asceirtanment data or even analyse if alleles fixed in the bighorn sheep population correlation with adaptive traits. In the Method section the authors mentioned that the studied bighorn sheep population is isolated and philopatric. These characteristics of the population would result in high inbreeding coefficient and low genetic variation, therefore explaining fixed alleles in the population. I consider that it is important to include such aspects of the population and its effects on the analysis in the discussion. The authors discuss that the traits they analyzed might be of polygenic inheritance. Nevertheless, this conclusion is speculative and it is importat to propose the kind of analysis needed to test this hypothesis. Another point that should be addressed in the discussion is the effect of different selection regimes on the results, when there is strong sexual selection towards horn size in males, but not so in females. Finally, I would recommend that the authors discuss briefly on the utility of SNP chips designed for domestic species in the study of wildlife. Additional comments: Please check the following lines: Line 187: "in in R version 3.2.4". Please remove one "in". Line 204: "We were interested to examined gene annotations". Should it be "We were interested to examine...". Line 215: "It interesting to note". Please change for "It is interesting...". Line 249: "R script developed by (Minikel, 2012)". Please check for the position of parenthesis.

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.

Title: GENOMIC ANALYSIS OF MORPHOMETRIC TRAITS IN BIGHORN SHEEP USING THE OVINE INFINIUM® HD SNP BEADCHIP Review round: 2 Reviewer: 1

Basic reporting: no comments Experimental design: no comments Validity of the findings: no comments Additional comments: Dear Dr. Eguiarte, I have now read the new version of the manuscript entitled “Genomic analyses of morphometric traits in bighorn sheep using the Ovine Infinium HD SNP BeadChip” by Miller et al. I think the authors have addressed well the comments made my editor and the rest of the reviewers. I have three suggestions or concerns that should be attended. Lines 122-123: Is there a justification of why they measured these three traits and not others. A simple justification about their importance or why they were chosen for this paper would be nice. Line 218-219: The authors mention that they keep 76 out of the 94 individuals that have measures. Maybe there is something I did not understand well, but they mention in the materials and methods that they chose individuals based on their individual breeding values. Having individual breeding does not mean that you have measures? Maybe there needs to be a better explanation. Line 229: “candidate markers”: isn’t it only one? In line 224 the authors only mention one candidate locus.

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.

Title: GENOMIC ANALYSIS OF MORPHOMETRIC TRAITS IN BIGHORN SHEEP USING THE OVINE INFINIUM® HD SNP BEADCHIP Review round: 2 Reviewer: 2

Basic reporting: no comment Experimental design: no comment Validity of the findings: no comment Additional comments: I found this new version pleasant to read. Also, I consider that all suggestions/comments were answered properly. Therefore, I suggest that this paper should be accepted for publication.

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.

Title: GENOMIC ANALYSIS OF MORPHOMETRIC TRAITS IN BIGHORN SHEEP USING THE OVINE INFINIUM® HD SNP BEADCHIP Review round: 2 Reviewer: 3

Basic reporting: As I mentioned in my previous review, the article is interesting and the paper is written in clear and professional English. I think the authors made a good work addressing my previous comments. I only have minor corrections that should be addressed upon acceptance. Experimental design: Ok Validity of the findings: Ok Additional comments: I think the authors made a good work addressing my previous comments. I only have minor corrections that should be addressed upon acceptance. Lines 219 – 222. Report the correlation values published in Poissant et al. 2012. Line 229 and 231. Indicate the threshold used as breeding value. Define what refers to highest and lowest breeding values. Line 240. Individual within loci does not makes sense to me. Please revise this. Line 302. 3,777 instead of 3777. Line 373. Parenthesis in italics.

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.

Title: A BIBLIOMETRIC ANALYSIS IN GENE RESEARCH OF MYOCARDIAL INFARCTION FROM 2001 TO 2015 Review round: 1 Reviewer: 1

Basic reporting: Zhou et al aimed to evaluate the Global scientific output of gene research of MI and explore their hotspots and frontiers from 2001 to 2015, using bibliometric methods. This is an interesting paper based on a different concept of research articles. The use of English language is adequate throughout the manuscript. Literature references could still be improved, by mentioning and discussing more works related to this field. Article structure and data are satisfactorily presented. Results and outcomes are relevant. Experimental design: The methods are appropriate. Search strategies have well been illustrated. Validity of the findings: Data is sound. Conclusion is adequate. However, addition of other relevant points could improve the significance of the conclusion. Additional comments: Even if the quality of language is adequate, due to some minor language issue, further polishing of language will improve the quality of the paper.

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.

Title: A BIBLIOMETRIC ANALYSIS IN GENE RESEARCH OF MYOCARDIAL INFARCTION FROM 2001 TO 2015 Review round: 1 Reviewer: 2

Basic reporting: Overall the article is well-written, organized, and includes sufficient content. This review primarily suggests ways in which the authors can improve the writing and thoroughness of the paper but there are no suggested changes for methods or analysis. 1. It is suggested that in the introduction section that a paragraph be added to address other bibliometric studies that have been conducted on MI research or conducted on genetic research. This will provide the rationale for your study and indicate to the reader what this particular analysis is adding to the literature. For example: Bibliometric Analysis of the Top 100 Cited Cardiovascular Articles ;The American Journal of Cardiology ; Volume 115, Issue 7, 1 April 2015, Pages 972-981 Cardiovascular disease research activity in the Middle East: a bibliometric analysis S Al-Kindi, T Al-Juhaishi, F Haddad Disparities in Cardiovascular Research Output and Citations From 52 African Countries: A Time‐Trend, Bibliometric Analysis (1999–2008) GS Bloomfield, A Baldridge, A Agarwal Global Cardiovascular Research Output, Citations, and Collaborations: An Ecologic, Time-Trend, Bibliometric Analysis (1999-2008) MD Huffman, A Baldridge, GS Bloomfield… - 2013 - Am Heart Assoc 2. The article has a large number of figures and supplementary material, all of which are useful. However, the figures alone are not very informative. One option would be to see whether the figure can be expanded in order to view which label is near to which network/cluster. The other option is to show one or two figures but the remainder of data switch the figure to the supplement and the table to the paper. Experimental design: The research question is clearly stated and the methods of mapping are highly technical. If you refer to this website: https://sites.google.com/site/citespace101/design-rationale/how-should-i-cite-citespace You can provide more details about the strength of this methodology and include all of the relevant citations. Validity of the findings: The major threat to the validity of this study is the search. The authors should add a few sentences to the methods section to explain why they chose to search only in this search engine as oppose to using multiple search engines. The evidence for adequate coverage in the search strategy should be stated. The major weakness of the paper is the discussion and conclusion. The current discussion largely focuses on a more detailed explanation of the results with some repetition. The revised discussion should highlight the findings and compare these findings with the other bibliometric studies (e.g. are they in alignment regarding productivity by region or by institution, by journal etc.?). Also, one unique component of CiteSpace is the analysis of burst keywords. The results of this analysis and particularly the relevance and implication of the identified areas should be discussed. Conclusion should be revised in order to state what exactly is the future direction of research indicated as a result of this study. Additional comments: The remaining items are very minor line 49: "genetic mystery" either explain what you mean by this term or remove it. line 76: "simplily" is a typo but the term can be removed line 96: "more likely"....I think that this statement is not supported by your evidence. Either add evidence/reference or revise it. line 99: change American to North American so that it is clear that you are referring to the continent and not the country.

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.

Title: A BIBLIOMETRIC ANALYSIS IN GENE RESEARCH OF MYOCARDIAL INFARCTION FROM 2001 TO 2015 Review round: 1 Reviewer: 3

Basic reporting: A well written article reviewing the literature related to myocardial infarction. According to me article is acceptable for publication after corrections are made (Minor revision) Experimental design: Bibliyometric analysis (literature analysis) with co-citation analysis Validity of the findings: The validity of the findings was examined by using the documents the authors uploaded in the supplementary materials. The findings are valid. Additional comments: Analyzed in detail and given important findings on the subject but the following should be taken into consideration. 1) Authors should write a limitation of the study because the analysis were performed only with publications in the wos index (pubmed scopus et al. are not included). 2) Maps do not look nice and difficult for readers to understand. So this study was carried with the VOSviewer could have been better. Authors should read and cite the following study for corrections; “Ozsoy, Z. & Demir, E. The Evolution of Bariatric Surgery Publications and Global Productivity: A Bibliometric Analysis, OBES SURG (2017). https://doi.org/10.1007/s11695-017-2982-1” 3) If descriptive footnotes are added to the figures, readers can understand more easily

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.

Title: AN OBSERVATIONAL STUDY ON RISK OF SECONDARY CANCERS IN CHRONIC MYELOID LEUKEMIA PATIENTS IN THE TKI ERA IN THE UNITED STATES Review round: 1 Reviewer: 1

Basic reporting: In this article ' A long term observational study on risk of secondary cancers in chronic myeloid leukemia patients in the TKI era in the United States' by Kumar et al., the authors used the updated SEER database, which released the chemotherapy treatment status of CML patients in April 2017. They systematically compared the SIR of secondary cancers status of these CML patients with the general population. They concluded that the CML patients have enhanced risk for SR, and indicated that TKI may not play a role in inducing the SRs. The paper clearly laid out the background information, their study design and nicely discussed the recent literatures in this field. Moreover, the limitations of this study in clearly stated in the discussion, which help better interpret the results and compare it with other studies. The raw data shared is very clear, however, the two major figures of the paper are pretty small and blurry, which make it hard to read/comment on. The authors should improve the quality of these two figures. One minor issue is the use of abreviations in the paper, i.e. SIR is not spelled out in its first appreance but the full name is spelled out more than once later on. Experimental design: The main objective of this study is not clearly stated. As there are many previous studies that have already investigated the SR risks in CML patients, and some of these studies actually use the SEER database, the authors emphasize that one advantage of their analysis is that they included the chemotherapy treatment data for these patients. As these data are collected in the post TKI era, the authors stated their data could partially reflect whether TKI usage will affect SR development. However, the authors never state whether the aim of the study is to determine the impact of TKI on SR for CML patients. And if not, the authors should better explain what makes their study stand out compared to previous studies, i.e. what knowledge gap does this study fills in. As the authors already mentioned in the discussion, their dataset only indicated whether patients were treated with chemotherapy or not. One does not know if the chemotherapy means TKI and should be caustious when making such assumptions, although TKI is one of the main chemo drugs used for CML in recent years. The authors should bring this explaination to introduction instead of mentioning them at the very end of discussion, to help readers understand the setup of the study from very begining. If the authors would like to study the impact of TKI on SR development, a better way to analyze the data is to compare the SIR of SR rates between CML patients from pre-TKI era vs. those from post-TKI era, rather than comparing cancer patients data with the general population. This pre vs. post TKI comparion could eliminate factors such as the impact of genetic mutations due to CML on SR development. Validity of the findings: The statistical analysis of this study is good in general. However, there are some issues that could be improved to better validate the findings. 1. In the patient selection criteria part, it is unclear why the authors exclude 141 patients since they developed 6 SRs. This has to be better explained. 2. It is not stated in the text how the authors get the SIR data of secondary cancer development in the general population. 3. The authors just compared the SIR of different groups but did not calculate the p-value of SIR to determine if the differences are statistically meaningful. The authors need to explain why p-value is not calculated. Additional comments: No additional comments

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.

Title: AN OBSERVATIONAL STUDY ON RISK OF SECONDARY CANCERS IN CHRONIC MYELOID LEUKEMIA PATIENTS IN THE TKI ERA IN THE UNITED STATES Review round: 1 Reviewer: 2

Basic reporting: I think the title uses the term “long-term observation study” but which was not well defined in the manuscript. One would also question if the follow-up duration for this group of patients with CML can be considered long enough to be called long term. I suggest the authors define the term accurately in the text and reconsider if this descriptive term is appropriate. Experimental design: Cancers diagnosed in the period 2-12 months after the diagnosis of CML more likely could be a late presentation or remaining an overt characteristics of a synchronous double primary cancer. This period typically in an epidemiological study would be excluded from the calculation of secondary cancer. Therefore, I would like to see more likely "true" secondary cancer after the first follow-up year. Line 116~117: The rationale to exclude this subgroup of patients seems not so justifiable. After line 121: A subsection with a subheading of “Follow-up of Participants” or equivalent would be better to let readers understand the follow-up details. Validity of the findings: Line 120 to 121: The authors stated that “A sensitivity analysis was conducted after excluding SCs which were diagnosed during the first year after diagnosis of CML to adjust for the surveillance bias.” Nevertheless, there are no ensuing results presented. I think it would be nice if a new figure 3 showing these results can be presented before acceptance. Additional comments: The occurrence of chronic myeloid leukemia and chronic lymphocytic leukemia in the same patient is considered to be a rare event. However, this paper nicely quantitates the frequency of CLL after CML as 16/9200 = 0.17%, which, in my opinion, has added a contribution to the literature. Interestingly, case reports of CLL after CML also occurs in women, unlike the all-male result in this manuscript. Table 1: Ethnicity: Would it be helpful to separate non-White into Black, Latin American and Asian-Pacific islanders? Line 293 and line 265-266: In the Discussion, I think the authors can give us an idea of the estimated frequency of HSCT (which should be spelled out when first appears in the text) in patients with CML in the TKI era in the US.

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.

Title: AN OBSERVATIONAL STUDY ON RISK OF SECONDARY CANCERS IN CHRONIC MYELOID LEUKEMIA PATIENTS IN THE TKI ERA IN THE UNITED STATES Review round: 1 Reviewer: 3

Basic reporting: Overall, the manuscript is very-well written with relevant introduction/references. It would be great if the authors could improve the quality of text in Fg. 1 & Fig. 2 as the current format is blurred/difficult to read. Experimental design: The overall research question is very well defined and has clinical relevance. Validity of the findings: The authors have extensively discussed the present study and compared with previous similar studies. The authors may want to add to the discussion as in what could potentially contribute to elevated risk for secondary cancers in CML in the TKI era. Additional comments: Please see above.

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.

Title: AN OBSERVATIONAL STUDY ON RISK OF SECONDARY CANCERS IN CHRONIC MYELOID LEUKEMIA PATIENTS IN THE TKI ERA IN THE UNITED STATES Review round: 2 Reviewer: 1

Basic reporting: The authors did a great job revising the manuscript. I have no further concerns and would recommend the publication of this work. Experimental design: The authors did a great job revising the manuscript. I have no further concerns and would recommend the publication of this work. Validity of the findings: The authors did a great job revising the manuscript. I have no further concerns and would recommend the publication of this work. Additional comments: The authors did a great job revising the manuscript. I have no further concerns and would recommend the publication of this work.

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.

Title: AN OBSERVATIONAL STUDY ON RISK OF SECONDARY CANCERS IN CHRONIC MYELOID LEUKEMIA PATIENTS IN THE TKI ERA IN THE UNITED STATES Review round: 2 Reviewer: 2

Basic reporting: This study, at least from the results in the presented Tables and Figures, does not investigate the impact of TKIs on the development of SCs. Please revise line 95, 96 to "This study aimed to analyze the development of SCs among patients with CML in the TKI era in the United States." Experimental design: No comment Validity of the findings: No comment Additional comments: I think the Discussion Section has room to improve to make it more relevant and concise.

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.

Title: DESICCATION RESISTANCE: EFFECT OF CUTICULAR HYDROCARBONS AND WATER CONTENT IN DROSOPHILA MELANOGASTER ADULTS Review round: 1 Reviewer: 1

Basic reporting: In this work, Ferveur and collaborators study desiccation resistance in Drosophila by analyzing cuticular hydrocarbon composition and its relationship with water content and with survival. For this, the authors compared wild type strains, artificially selected desiccation resistance flies, transgenic lines with reduced desaturase expression, which should affect cuticular hydrocarbon composition and hence desiccation resistance, and mutant flies with reduced cuticular hydrocarbon levels. Experimental design: The authors clearly explain how they carried out their experiments, and include important controls like differences between males and females, and they discard the possibility of unavertedly selecting other traits that would ameliorate desiccation resistance like seize, and biases for the generation of males versus females in the offspring of different genetic backgrounds. Validity of the findings: The conclusions of this work are valid, limited to and supported by the data provided. The authors show that desiccation resistance can be acquired and fixed in a population after only few generations, which persist without further selection through several generations. The work highlights the complex relationship between desiccation survival and the variables measured in the study. According to the data, it seems that the resistance cannot be easily narrowed down to one or two variables, and this is already apparent in the different cuticular hybrocarbon composition of different strains, for instance, Zimbabwe and Dijon2000. Additional comments: No additional comments

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.

Title: DESICCATION RESISTANCE: EFFECT OF CUTICULAR HYDROCARBONS AND WATER CONTENT IN DROSOPHILA MELANOGASTER ADULTS Review round: 1 Reviewer: 2

Basic reporting: The manuscript includes sufficient background. It shows clearly the context. The structure of the article is according to the required format by PeerJ. Figures are appropriately labelled and described. Experimental design: Although the research question is well defined and relevant, the results found seem be very preliminary. The experimental design incorporates many variables so the results are very difficult to interpret and to make precise conclusions. Validity of the findings: The representation and statistic analysis of the data are appropriate. The conclusions are very general and are not completely consistent with the results found. Additional comments: The manuscript entitled “ Desiccation resistance: effect of cuticular hydrocarbons and water content in Drosophila melanogaster adults” by Ferveur et al. addresses a very interesting topic. The authors studied the possible relationship between desiccation resistance, cuticular hydrocarbons (CHs) content and relative water content. Ferveur et al. found that an increased proportion of desaturated cuticular hydrocarbons, but not the total amount, is associated with an increased desiccation resistance. Also, authors found that transgenic flies with a high proportion of water showed the lowest levels of resistance. They conclude that desiccation resistance and the proportion of desaturated CHs are tightly linked while a high water content negatively affect desiccation resistance, at least when a low level of desaturated CHs are presented. Although this work provides some interesting data, I consider that the results are very preliminary for publication leading to complex and confusing interpretations. For example, they found that lines 77S shown increased desiccation resistance respect to the control, it increased resistance was no significantly different between these lines but the ratio desaturated CHs: linear saturated CHs (D:L) was significantly different. Authors say that these results suggest that CH composition and desiccation resistance are not identical (manuscript lines 235-236) however they conclude that increased resistance was linked with increased ratios D:L (manuscript lines 382-383). In my opinion, the results do not show a consistent relationship between these two characteristics (desiccation resistance and ratio D:L). In experiments using the UAS-desat1-RNAi transgene, authors said: “Knocking down desat1 in all relevant tissues induced a reduction of both desiccation resistance and the ratio D:L. However, selective targeting of desat1 expression in oenocytes strongly decreased the ratio D:L, but did not affect desiccation resistance or water content” (lines 336-340). Again, these observations are not consistent with what the authors propose regarding to a relationship between desiccation resistance and the ratio D:L. The results regarding water content and desiccation resistance are not convincing enough. In experiments using RNAi lines it is desirable to use more than one RNAi line to avoid off-target effects and include some RNAi control line like GFP RNAi. Minor comment: In manuscript line 119. Change “homozygous” to “heteroallelic”.

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.

Title: DESICCATION RESISTANCE: EFFECT OF CUTICULAR HYDROCARBONS AND WATER CONTENT IN DROSOPHILA MELANOGASTER ADULTS Review round: 2 Reviewer: 1

Basic reporting: The authors have modified the text in a way that further strengthens its readability. They explain what their results imply regarding desiccation tolerance in flies, and they clarify the use of their fly lines according to findings reported in previous publications. Experimental design: No comments. Validity of the findings: No comments. Additional comments: No additional comments

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.

Title: DESICCATION RESISTANCE: EFFECT OF CUTICULAR HYDROCARBONS AND WATER CONTENT IN DROSOPHILA MELANOGASTER ADULTS Review round: 2 Reviewer: 2

Basic reporting: No comments Experimental design: No comments Validity of the findings: No comments Additional comments: The authors have adequately modified the conclusions doing these more consistent with the results found. Although I consider that the results are somewhat preliminary, these are interesting and provide of information for future studies about the relationship of desiccation resistance with cuticular hydrocarbons and water content in insects.

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.

Title: SMARTPHONE-BASED REMINDER SYSTEM TO PROMOTE PELVIC FLOOR MUSCLE TRAINING FOR THE MANAGEMENT OF POSTNATAL URINARY INCONTINENCE: HISTORICAL CONTROL STUDY WITH PROPENSITY SCORE-MATCHED ANALYSIS Review round: 1 Reviewer: 1

Basic reporting: a. Line 16 the reference is listed as 1, and the rest of the paper is using author last names. b. Clear/English i. Line 43, I think you're trying to compare postpartum women to postmenopausal women? It may be more clear to state the group you are comparing them with. After all, postpartum women are non-pregnant women. ii. Line 86, I suggest "All data" instead of "All the data" iii. Line 113, Should it say "this data is not published"? iv. Line 118/119, I think you could say "The participant who agree to participate answered a similar initial questionnaire to the experimental group for background characteristics and current UI status." v. Line 185, the "two and 16" is confusing. Are these the participant numbers? If so, it isn't necessary and you could just state that two participants were excluded and the reason. c. References/sufficient background and context-Yes d. Raw data shared-Yes, I am able to open and view this file. Experimental design: a. Original-Yes b. Aime and scope-The focused aim for this study is a strength. c. Question well defined and meaningful-Yes, I believe it is interesting and meaningful research. d. Identified knowledge gap-There is a clear gap between the knowledge and the action of the women with UI. This study looks at this gap. e. Method described in detail-Yes, I believe this study could be replicated based on the description in the article. Validity of the findings: Impact of this study was assessed. I believe this study could be replicated based on the description in the article. Conclusion is well stated and linked to the original research question. Additional comments: a. In line 114, I think it would be nice to either have the same exclusion criteria or list the exclusion criteria for the control group so the reader knows there wasn't bias toward one group over the other.

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.

Title: SMARTPHONE-BASED REMINDER SYSTEM TO PROMOTE PELVIC FLOOR MUSCLE TRAINING FOR THE MANAGEMENT OF POSTNATAL URINARY INCONTINENCE: HISTORICAL CONTROL STUDY WITH PROPENSITY SCORE-MATCHED ANALYSIS Review round: 1 Reviewer: 2

Basic reporting: Thank you for the opportunity to review this article. The article provides sound findings regarding the effectiveness of the smartphone-based reminder system to enhance PFMT adherence and to manage UI in postpartum women. However, there are some issues that need improvement. These issues are outlined below: Major Revision I wonder about the withdrawal. You describe that the smartphone-based reminder system excel as a simple free way to assist postpartum women in performing PFMT in their free time. But sixteen women in the smartphone group did not record their current UI status after 8 weeks. It is 32.7% of enrollments. Why did not you discuss this point. Minor Revisions 1. Line 16 loss of urine.”1) In a population 　　 Please delete 1). 2. Line 56-58 I could not understand this sentence. Why do you put a parentheses. 3. Line 79 Is ICI a mistake of ICS? 4. Line 101 Who is a midwife? Does the midwife belong to the clinic? 5. Figure 2 Historical control group and Smartphone group are assigned from a beginning in this research. I think that you should show a group name the upper part of the figure. 6. Figure 2, Follow-Up section In the Historical control group, A parenthesis is not written. Experimental design: Please provide more information about the exclusion criteria in the control group in the Materials & Methods section. You describe that it is similar to those in the smartphone group. It isn’t same. Please explain what is different. Validity of the findings: no comment Additional comments: no comment

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.

Title: SMARTPHONE-BASED REMINDER SYSTEM TO PROMOTE PELVIC FLOOR MUSCLE TRAINING FOR THE MANAGEMENT OF POSTNATAL URINARY INCONTINENCE: HISTORICAL CONTROL STUDY WITH PROPENSITY SCORE-MATCHED ANALYSIS Review round: 2 Reviewer: 1

Basic reporting: Line 91, I think the parenthesis within the parenthesis should be brackets. Experimental design: No comment. Validity of the findings: No comment. Additional comments: This version of your manuscript is more clear and concise. Thank you for the opportunity to review your work.

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.

Title: USE AND MISUSE OF TEMPERATURE NORMALISATION IN META-ANALYSES OF THERMAL RESPONSES OF BIOLOGICAL TRAITS Review round: 1 Reviewer: 1

Basic reporting: The article is generally well written in unambiguous language, sufficient introduction material and background with additional provision of theoretical context which greatly enhances readability for non-expert audience. In my opinion, the article would benefit from consistent use of the terms ‘traits’ or ‘rates’, which I have highlighted throughout in the PDF and ‘general comments’ section of the review. In additional some restructing in the introduction is suggested in the ‘considerations’ and additional points to consider which I think are essential for the discussion are also highlighted in the ‘considerations’ section of my peer review. There is no statement of submission of data to a public archive, and the data in the supporting information did not download with correct formatting for me to adequately re-use or comment on suitability for re-use (perhaps a problem with a file conversion through the peer-review process). Other than these comments, I have no major problems with the basic reporting of the article. Experimental design: A clearly defined, and well tested, research question is explored throughout the manuscript which is undertaken to an impressive technical standard. Lines 97-100 should clarify further the conditions for inclusion of these data in the article, additional a sentence describing ‘Biotraits’ on line 114 would be useful. Clarification is needed as to the software and packages used throughout the manuscript for full replication. Validity of the findings: The general validity of these findings is likely to be high based on the robust analytical techniques and extensive database used, I believe the simulations are well designed an appropriately analysed and interpreted. Additional comments: Thank you for providing an insightful and thought-provoking piece of work exploring the parameterisation of thermal performance curves and the consequent inflation of standardised performance estimates to review. It is clear the analyses are carefully orchestrated and undertaken with rigor and the resulting article is an interesting read. It is testament to the research that the article raises interesting questions which could be answered, I believe, within this piece if work – however I would consider these suggestions are at the authors discretion as the analyses are, in my opinion, sufficient in their current state. These suggestions are presented below with ‘considerations’ and ‘line-by-line’ points identified. I believe I have identified some necessary revisions to the manuscripts figures and additional points of discussion that should be addressed. Considerations: The article generally ignores discussing another key assumption that “a simpler version of the full model that ignores low-temperature enzyme inactivation is most often use” other than to acknowledge it. This assumption could be more strongly criticised than the assumption that Th is greater than Tref. While I don’t think it would be necessary for this particular publication that this assumption is explored (although it would be interesting and add to the paper), I think at least a discussion of the potential implications of this additional assumption should be included in the discussion, given that a seemingly more minor assumption of the model is explored in such detail throughout. Additionally, the analysis initially raised my concerns that a temperature of 0°C was chosen at Tref where I assume enzyme activity will be very low – while the assumption discussed here isn’t the main point of the article it would be better to acknowledge and discuss the implications of this assumption explicitly to avoid potential criticism that the analyses presented here ignores a potentially more important key assumption. I light of the above comment, I think the analysis in “Identification of conditions that lead to a severely overestimated B0” would benefit from separating ‘cold adapted’ and ‘warm adapted’ species such that the assumption that enzymes are active at 0°C does not apply to the warm adapted species (i.e., set Tref to different values for these two groups? Or apply 0°C and 15°C Tref to both) – I think that the assumption that enzymes operate above 50% activity at 0°C for a tropical poikilothermic species is very weak, and the authors have a large dataset to choose to further test these ideas and assumptions. The analyses using real thermal performance rate variation across temperature gradients may be strengthened by comparisons with simulations. For example, in the analysis “Inflation of trait value at reference temperature (B0)” a simple simulation coupled with the analysis of real data would provide an interesting comparison and be less biases by available data. Additionally, the behaviour of the simulation would be independent of biological heterogeneity. A comparison of expectations based on theory (simulation) with the resulting inflation of B0 in real traits would provide further insight to the magnitude of real inflation compared to potential for inflation (simulation) (i.e., is this as large a problem in real data as it could be?). In the analysis “Implications of the inflation for investigations of thermal adaptation” the choice of Tref has been demonstrated as important in the previous analysis but is given as a fixed value here. Given that this is a simulation it would be relatively trivial to re-run over multiple values of Tref to explore the interaction between Tref and the negative relationship between Tpk and B(Tref) – I think this is important as currently I think the support for an ‘artificial’ relationship between Tpk and B(Tref), and thus false identification of MCA, is quite weak given the strength of the correlation. Furthermore, it would be better to justify where the choice of 7°C arises, other than it is below the minimum Tpk A second suggestion for the analysis of “Implications of the inflation for investigations of thermal adaptation” that would support the take-home message of the paper, is to definitively show that MCA is not falsely detected when using the alternative approaches/models put forward by the authors. This should also be relatively simple given the simulation approach taken but would strengthen the authors argument that the Sharpe-Schoolfield model may falsely identify MCA but other types of models will not make the same error, and that therefore this is due to the assumption of the SS model. Figure 2 isn’t as clear as it could be, although the information is fundamental to the paper. First, I think the equation defining the y-axis may be incorrectly printed as if B0 or Ppk is greater than B(Tref) then the equation suggests we take the log of a negative number? Second, I think the differences between B0 and B(Tref) should be presented in both absolute and proportional terms (relative to initial value and maximum rate – thus creating a 4-panel plot) because a doubling of a rate from 0.01 to 0.02 when the maximum value of the rate is 200 could be interpreted as less of a ‘problem’ compared to a lower proportional rate inflation of 10 to 15 which has a much larger absolute change. Second, the y-axis is very confusing and a value of ‘0’ to define when changes are non-negligible seems odd to me, it would be better if this were transformed such that data at 0 is a negligible change in B0 from B(Tref), and differences get larger with increasingly positive y-axis. Perhaps even a log(response ratio) may be useful here for proportional comparisons between B0 and B(Tref)? On line 122-123 I’m not completely convinced that applying a cut off whereby rates = 0 at B0 were removed is valid, many species are likely to have performance rates at 0 for certain values of B0 depending on the thermal environment the species is adapted to. Can it be demonstrated this does not bias results, or that this cut-off was relevant for a small proportion of species (i.e., n=2). Consistency in the use of ‘rates’ and ‘traits’ would be conceptually tighter. I personally would consider most TPCs to be derived from rates, rather than traits, and that the term ‘rates’ is more specific. My supporting data files didn’t download properly, and a conversion from text to data in excel did not produce a dataset with standardised columns. Perhaps this is from transfer between the journal but may be worth double checking the files. Line-by-line considerations: 4: This is a funding body/PhD program rather than an address? 26-32: I’m not convinced that the introduction benefits from this paragraph greatly. I think the work presented here is more broadly applicable to accurately understanding thermal variation in traits and comparative thermal physiology, which has relevance for climate change, but climate change shouldn’t lead the introduction in my opinion as your research is more fundamental and climate change isn’t relevant to later discussions. 24: Suggest changing keywords ‘model’ and ‘trait’ , ‘rate’ as very broad. 26-32: Given that the main importance the article highlights of accurately estimating B0 I would consider introducing metabolic cold adaptation early in the introduction 29: Garcia et al. 2014 isn’t relevant here. 30: Suggest changing ‘biological traits’ to ‘biological rates’ 33: Suggest changing ‘are unimodal’ to ‘are generally unimodal’. Suggest changing ‘trait-value’ to ‘biological rate’ 34: Suggest changing ‘data’ to ‘relationships’. 39-41: In my opinion, the introduction would benefit from a broader discussion of how the parameters are used in comparative physiology (not just MCA), with an emphasis that detection of MCA is an example of where inaccurate parameterisation of models can lead to false-positive results (I’m sure however there are many others too, but obviously MCA is useful to mention as the analysis investigates this effect later). 42: “the traits value” sounds odd. Which trait? ‘a cellular, organismal or population rate’s value’? 58: Could the ending of this sentence please be more explicit by defining ‘to data’. (e.g. to thermal performance rates). 42-56: In my opinion, this paragraph could benefit from a brief sentence describing the explicit consequences of overestimating B0 and how overestimation could alter current understanding of metabolic cold adaptation. 60: rates 79-82: Is this list of references is necessary given Table A1? 96-97: This statement on first reading appears contradictory to the result presented in figure 1A this is because the y axis on figure 1 is very non-intuitive and could be improved. Based on this statement, I initially thought why at the minimum difference between Th and Tref is the deviation of B0 from B(Tref) at a minimum too, if I misinterpreted this with I’m sure others will too. Consider rescaling such that the difference between B0 and B(Tref) is minimal at 0 on the y-axis. 104-105: Ensure the number of rejected vs. potential TPCs is recorded in the manuscript based on these cut-offs. 105: I would be interested to know that the results do not depend on the R2 cut off. 111-114: Please be specific about the machine learning approach used on first mention. 116-119: I do not follow the logic of using a Tref that = 0°C to obtain “reliable estimates of B0” when the argument put forward in the article is that “when non-negligible loss of enzyme activity occurs at Tref – e.g., due to denaturation or inactivation of some other component of the metabolic pathway – B0 overestimates the real value of the trait at that temperature (B(Tref))”. I may be wrong but I cannot imagine that >50% enzymes would be active at 0°C, I think this would be valid if the aim of this is to artificially inflate B0? It isn’t clear to me if this is the aim here. See ‘Considerations’. 122-123: I’m not completely convinced this cut off couldn’t bias your results. See ‘Considerations’. 124-136: In my opinion, the precise aim of this analysis should be introduced in more detail prior to describing the modelling process with a conditional inference tree. It is not clear in this paragraph what the ‘predictor’ variables are, and found it difficult to follow the paragraph and its relevance as a consequence. 134: ‘assess overfitting’ 164: Your data are larger than your simulation of 1,000 TPCs, so this isn’t a valid justification (although I support the use of a simulation here). 164: consider rephrasing difficult to read. 167-168: How was ‘negative skew’ was assessed. 175-176: Is there a reference which justifies that species <15°C Tpk are ‘cold’ adapted? 201-203: The low value of the correlation coefficient should be emphasised here as it is in the legend of Figure 4. 210-211: This sentence would benefit from emphasising whether this is a novel finding of the study. 212-213: The first sentence here could be more clearly articulated. The word ‘this’ is used twice and thus the meaning of the sentence is lost, consider rephrasing. For example, “We determined that the discrepancy between real trait performance and estimated trait performance at B0 arises under the conditions that…” 216-217: This paragraph would benefit from some assessment as to whether most of the literature would suffer from this error, I would assume this is the case in a few studies of cold adapted species. 223-225: Is there a way to build the ML model such that the inappropriate use of Tref can be assessed by the parameters available in the literature? 232: ‘ones’ sounds informal. 233-234: Consider rephrasing as meaning is not initially clear to me. Is this sentence saying there may still be a small amount of bias in B0? 235: Unsure if this sentence is necessary? 238: A further useful suggestion could be to use a Tref appropriate based on the metabolic group such that a Tref of 25°C is not used for stenothermic polar species (for example). 261: This feels like it should be in the ‘recommendations’ section rather than a stand-alone header. 265-266: This sentence suggests there would only be a single temperature at which enzyme activity is at 100%, is this the case? 277-279: In my opinion, this sentence slightly overstates the implications of the results. I don’t think the patterns demonstrated in this analysis justify a ‘strong exaggeration’ of temperature-normalised trait-estimates and the correlation coefficient in figure 4 is quite low and, as such, the consequences of this rate estimate exaggeration appear to be relatively minimal. 284-285: Is there a NERC funding grant no. attached to each DTP?

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.

Title: USE AND MISUSE OF TEMPERATURE NORMALISATION IN META-ANALYSES OF THERMAL RESPONSES OF BIOLOGICAL TRAITS Review round: 1 Reviewer: 2

Basic reporting: The basic reporting meets most of the criteria. However, they seem to be missing some key citations (see specific comments) from the literature. Experimental design: The authors achieved their research goal and provided an answer to their question. However, they left out a few key talking points (see specific comments). Validity of the findings: The authors demonstrated some problems with the Sharpe-Schoolfield model, but need to consider enzyme and whole-organism performance separately. Thus, I don't find the results particularly interesting and even a little misleading at times. Additional comments: General comments: Here the authors evaluate the use of the Sharpe-Schoolfield equation to normalize data for making comparisons of organismal performance. Overall, the authors make a sound argument that the Sharpe-Schoolfield model generates biased estimates of temperature normalized performance when key assumptions are violated. However, the results are underwhelming and I have reservations as to why anyone would use such a model for whole-organism or population data. See papers (below) by Andy Clarke which explain why such models should never be confused with a description of the mechanisms underlying performance, which are undoubtedly fare more complex than a rate-limiting enzyme or even enzymes alone. Thus, the model’s parameters can only be interpreted at the enzyme level, rather than at the organismal level. At the very least the authors should address this issue in their discussion. Furthermore, the authors discuss and seem to promote the use of the Arrhenius equation as an alternative method. However, Andy Clarke (2004; 2006) provides good arguments against molecular interpretations of the Arrhenius equation when fit to the metabolic rates of organisms. This leads me to question the relevance of the study in general. Organismal biologists will likely not find this paper very useful as one should not draw conclusions about enzyme performance from whole-organism performance. Perhaps a more specialized journal (e.g., comparative and evolutionary biochemistry) would be more appropriate than PeerJ. Clarke, A. (2004) Is there a Universal Temperature Dependence of metabolism? Functional Ecology, 18, 252-256. Clarke, A. (2006) Temperature and the metabolic theory of ecology. Functional Ecology, 20, 405-412. Specific comments: Lines 35-37: This is an unconventional way of describing a thermal performance curve and I’m not aware of any ecologists that actually quantify these four values. The only citation provided for use of these values is a self-citation, which makes me even more skeptical. For example, optimal temperature (To) is the common term here, not “the temperature where the performance peaks (Tpk)”. I don’t much care for acronyms, and trying to introduce a new version of an existing acronym is unnecessary and confusing to the field. Ecologists are also concerned with the more common terms “performance breadth” and “critical thermal limits” (e.g., CTmin and CTmax). Lines 218-220: It seems odd that this point (a single sentence) needs to be its own paragraph. Either elaborate on the point or work it into another paragraph. Lines 242-244: Why should these other models be considered? Provide a sentence or two describing the validity of their application here. Lines 247-249: I don’t agree with this statement as numerous studies (almost all?) that measure performance curves measure performance below and above optimal temperatures. After all, that is how optimal temperature is determined. See: Angilletta (2006) Estimating and comparing thermal performance curves. Vickers et al. (2011) Extending the cost-benefit model of thermoregulation: high-temperature environments. Williams et al. (2016) Biological impacts of thermal extremesL mechanisms and costs of functional responses matter. Lines 261-273: This is the most common, and most appropriate, approach researchers use when studying whole-organism performance.

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.

Title: USE AND MISUSE OF TEMPERATURE NORMALISATION IN META-ANALYSES OF THERMAL RESPONSES OF BIOLOGICAL TRAITS Review round: 2 Reviewer: 1

Basic reporting: I thank the authors for including MCA in the introduction, but feel it's definition is too vague and little introductory information is provided on MCA. At least a specific definition of MCA would improve the introduction, particularly now that the paper is more focussed on this topic. In my opinion the “Theoretical Context” section hangs awkwardly between the introduction and the methods, moving to the methods may improve the flow of the article. The discussion does a good job in suggesting solutions to help compare temperature normalised rates, but would benefit from some specific examples of MCA 'false positives' based on incorrect parameterisation of TPCs, there is a broad literature, emphasised in Appendix A. The discussion would be more thorough and constructive if these references were used to place the results relating to MCA false detection in a richer context. Experimental design: Including an equation of how the beta-distribution is parameterised would be necessary to understand how the ‘final curve height’ and ‘final curve width’ of the Table 1 are used. I cannot see how these are used in the parameterisation of the beta distribution. Subscripts i, j, and k, are not explained in the text or table 1. Validity of the findings: No comment. Additional comments: Thank you for your thoughtful and detailed responses to each of my comments. I think the updated manuscript is much improved and have only minor comments in the PeerJ review, and a few detailed points below. Line by line considerations: 69: Reword to contain example in parenthesis within sentence for clarity, “aforementioned and other analyses” sounds vague. 134: Is the text for this subheading intentionally smaller? 140: unintentional double space 141: Unnecessary - “again using a large empirical dataset” 143: What is the total sample size of individual TPCs including training and test sets? 148: Would be beneficial to see a summary table of the taxonomic coverage/trait coverage in the SOM. Bacteria, macroalgae and terrestrial plants seems an odd choice of organismal diversity to choose to emphasise Biotraits scope. 169: Was this a subset of the Biotraits/literature. The sentence sounds like this was a separate dataset at the moment? Data subset? 184: Unnecessary 189: Please specify that the alpha and beta parameters are parameters of the Beta distribution. 200: Consider rephrasing this paragraph as I find it surprisingly difficult to understand despite the relative simplicity of the procedure. 209: The results start with a statement to direct the reader to a figure rather than a statement of the result with the relevant figure in parenthesis. 210: Could this be stated in terms of interpretation of the parameter differences rather than the parameters themselves? The reader currently has to juggle how the parameter equations relate to concepts and then to results in one go. Figure 2. Could the Figure 2 axis y label be phrased in words rather than equations, with equations in brackets perhaps? (i.e., Deviation of B0 from B(Tref), Deviation of optimum performance from B(Tref)). I feel like this figures requires a lot of work from the reader and axis simplification would remove on component of the complexity.

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.

Title: USE AND MISUSE OF TEMPERATURE NORMALISATION IN META-ANALYSES OF THERMAL RESPONSES OF BIOLOGICAL TRAITS Review round: 2 Reviewer: 2

Basic reporting: No new comments Experimental design: No new comments Validity of the findings: No new comments Additional comments: I appreciate the authors’ responses to my comments and the addition of some additional references to strengthen their arguments. This is a much improved version of the manuscript. The only concern I have at this point is the author’s interpretation of optimal temperature. I think they are oversimplifying the measure and actually just describing it with their new proposed acronym (point at which the performance curve peaks). I feel that this is unnecessary and confusing to new readers in the field of thermal biology, but shouldn’t prevent the paper from being published. Readers can decide to follow this new acronym or not. Specifically, I’m not sure how the authors are interpreting “optimal temperature”, but my understanding is that it is the temperature at which “optimal performance” is experienced produces the “highest peak” of a performance curve for that given trait. They could use their modified definition to simply describe what optimal temperature (a much better known term) is. I agree that where some performances are optimal (i.e., highest peak) does not automatically mean the “organism’s fitness is maximal”. In fact, the only times that is possibly correct is when the performance curve is specifically measuring fitness or a given trait’s optimal temperature overlaps with the temperature that produces maximal fitness. However, this is rarely the cased as most performance curves are more specific than “fitness” (or measure different proxies for fitness) and measure a single trait such as sprint speed, digestion rate, or enzyme reaction rates. Yes, organisms often experience temperatures below optimal temperatures as these temperatures are energetically costly and unnecessary at all times. For example, an animal has no need to be at optimal temperature for digestion when it has an empty stomach. It makes ecological sense to be below the optimal temperature for digestion when without food in order to conserve energy. Furthermore, this is why there are often different optimal temperatures (or performance peaks) for different traits (e.g., sprint speed vs assimilation rate). And finally, according to a brief literature search through Google Scholar, “the temperature where the curve peaks” did not produce any direct hits whereas “optimal performance” produced hundreds if not thousands of hits.

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.

Title: ANTITUMOR ACTIVITY OF CHLORELLA SOROKINIANA AND SCENEDESMUS SP. MICROALGAE NATIVE OF NUEVO LEÓN STATE, MÉXICO Review round: 1 Reviewer: 1

Basic reporting: The introduction is too brief. The results for DNA degradation in 2% agarose gel electrophoresis are not found in the text or Figure. Experimental design: In the abstract the authors reported that The extracts were shown to induce tumor cell death by the mechanism of apoptosis. However, only one experiment was conducted (AOPI staining) to prove apoptosis (a cell death pathway). There were no experiments done to show the mechanism of apoptosis such as caspase activity and gene expression study. Validity of the findings: Not enough data to prove the cytotoxic activity of the C. sorokiniana and Scenedesmus sp. methanol extracts. The results for DNA fragmentation is missing. Apoptosis should be supported by other assays such as cell cycle, Annexin 5, Mitochondrial membrane potential, caspase activity and apoptotic gene expression using qpcr. The IC50 values of the extracts were not reported. Additional comments: Not enough data to support the conclusion from the study. Hence, the results are inconclusive. The experimental designs should be expanded to provide supporting results to justify the research question.

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.

Title: ANTITUMOR ACTIVITY OF CHLORELLA SOROKINIANA AND SCENEDESMUS SP. MICROALGAE NATIVE OF NUEVO LEÓN STATE, MÉXICO Review round: 1 Reviewer: 2

Basic reporting: 1. English writing needs improvements. 2. In the discussion, need to cite and comment on recent paper showing that C. sorokiniana extract inhibits lung cancer in vitro and in vivo (BMC Complement Altern Med. 2017 Feb 1;17(1):88). 3. Should provide a representative image of cells stained with AO/EB and indicate apoptotic and necrotic examples in Fig. 3. 4. The methods mention DNA laddering/smear but this figure is not presented. This is very important to provide further confidence that the extracts are working through apoptosis (laddering) more than necrosis (smear), as suggested by AO/EB results in Fig. 3. In methods line 163, should state DNA smear not scan. Experimental design: 1. Appears to be original in that they obtained organisms from local river, However, there is one very recent but more complete paper mentioned above that uses C. sorokiniana extract in lung cancer. 2. Methods for isolation, growth, and preparation of extracts is well described. There are some issues in methods described in general comments. Validity of the findings: 1. AO/EB results would benefit from a representative image. 2. DNA laddering result is not shown and is essential before acceptance. Additional comments: The authors obtained water samples from a local river in Nuevo Leon Mexico and isolated two strains of micoalgae, Chlorella sorokiniana and Scenedesmus. They present details on the methods of growing and confirming the identity of these organisms by 18S PCR. Methanol extracts (250-500 ug/ml) of dried mass obtained from bioreactors was used for testing anti-cancer efficacy in mouse lymphoma L5178Y-R cells. An acridine orange/ethidium bromide (AO/EB) staining assay was used to determine effects on apoptosis and necrosis. These extracts had less cytotoxic effects on non-cancer mouse thymocyes. In general, this paper provides some interesting information on utilizing a local micoalgae organism for testing anti-cancer activity. However, there are several issues that need to be addressed. 1. Should provide a representative image of cells stained with AO/EB and indicate apoptotic and necrotic examples in Fig. 3. 2. The methods mention DNA laddering/smear but this figure is not presented. This is very important to provide further confidence that the extracts are working through apoptosis (laddering) more than necrosis (smear), as suggested by AO/EB results in Fig. 3. In methods line 163, should state DNA smear not scan. 3. In the discussion, need to cite and comment on recent paper showing that C. sorokiniana extract inhibits lung cancer in vitro and in vivo (BMC Complement Altern Med. 2017 Feb 1;17(1):88). 4. Sentence in lines 247-249 needs to be revised. It is assumed what is meant is that extracts have low cytotoxicity in non-cancer cells but higher in cancer. 5. English writing needs improvements. 6. Fig. 1, why after 18d Scenedesmus biomass much greater vs S. sorokiniana? Does not correspond to numbers given. 7. Several issues in methods section: a) more information of 18S PCR to identify strains; b) “Tumor cytotoxicity and apoptosis assay” subheading is misplaced and should be moved to line 120; c) how is the concentration of the extract measured? It is given as 1 mg/ml; d) more information on microscope source, wavelength used for analysis; e) there is mention of vincristine as positive anti-cancer drug but actinomycin D is used in Fig. 3.

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.

Title: ANTITUMOR ACTIVITY OF CHLORELLA SOROKINIANA AND SCENEDESMUS SP. MICROALGAE NATIVE OF NUEVO LEÓN STATE, MÉXICO Review round: 4 Reviewer: 1

Basic reporting: No comment Experimental design: No comment Validity of the findings: No comment Additional comments: Some modifications have been made in the revised manuscript. I have attached the pdf file of the edited manuscript.

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.

Title: ANTITUMOR ACTIVITY OF CHLORELLA SOROKINIANA AND SCENEDESMUS SP. MICROALGAE NATIVE OF NUEVO LEÓN STATE, MÉXICO Review round: 4 Reviewer: 2

Basic reporting: 1. Line 282--- misspelled ladder (“latter”). 2. Line 290-291---revise to read “…resulting in up to 26% and 19% toxicity with the highest extract concentration (500 g/ml) (Fig. 4). In L5178Y-R tumor cells, 500 g/ml of extract resulted in 62-75% toxicity (Fig. 2)." Experimental design: Acceptable. Validity of the findings: Acceptable. Additional comments: Minor writing changes. Paper is improved and is now acceptable.

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.

Title: EVOLUTION OF THE SCHOLARLY MEGA-JOURNAL, 2006–2017 Review round: 1 Reviewer: 1

Basic reporting: The paper is well written and meets all journal standards for clarity etc. Some minor points: Lines 224-225. “In a separate on-going study together with Mikael Laakso, we’ve estimated that there were 327,000 such articles in Scopus in 2016.” It’s not clear to me from the preceding paragraph what “such articles” refers to. The number seems too high to be mega-journal articles. Please clarify. On line 181 the reference is a number, rather than the author name. Lines 230-232. “Taking that as a rather conservative estimate for the current APC-funded article share, the estimate for articles for which APCs were paid is around 160,000 articles. These estimates are presented in table 4. Around 2,9 % of articles were published in mega-journals.” It took me a couple of reads to realise that the "2.9% of articles" referred to ALL articles published, and not of articles for which an APC was paid (which is what the previous sentence refers to). I think this paragraph could be restructured to make it clearer. I think all of the Tables would benefit from some additional thought regarding layout: In Table 1, for completeness the SUM row should include the data from 2006-2008. I think Table 2 would be clearer if it showed the increases as percentages rather than factors. In Table 3, the Chinese share of all mega-journal articles (%) is shown in the far right hand columns, under the raw numbers – why not put them in the left hand columns under the other percentages? I find the layout of Table 4 a little strange – I’m not sure why different (untitled) columns are used for the various article counts. I think this could helpfully be compacted. Experimental design: I have two significant concerns. The first is the decision to class RSC Advances and Palgrave Communication as mega-journals. RSC Advances has the following criteria for publication on their website (http://www.rsc.org/journals-books-databases/about-journals/rsc-advances/): “The criteria for publication are that the work must be high quality, well conducted and advance the development of the field. Articles submitted to the journal are evaluated by international referees for the overall quality and accuracy of the science presented.” Similarly, Palgrave Communications state the following as their aims and scope (https://www.nature.com/palcomms/about): “The journal editors are dedicated to publishing high-quality original scholarship. Actively welcomed for submission is research on agenda-setting issues, grand societal challenges and emerging areas of thinking, irrespective of the field of study. This also includes research that reflects on, or seeks to inform, policymaking of all types. Palgrave Communications additionally welcomes interdisciplinary research that makes an explicit and valuable contribution to the advancement of the humanities and/or social sciences.” While I would agree that in both cases the term “quality” leaves some room for interpretation, neither journal explicitly states (as all the other journals on your mega-journal list do) that they review solely for scientific soundness. I therefore see no difference between RSC Advances and other large, broad scope, OA journals such as Nature Communications, Science Advances, or eLife. My view is that either these two journals should be excluded from the analysis (which I think is preferable), or instead explicit discussion of their peer review processes should be included in the paper, along with clear justification for their being considered mega-journals. My second issue is with the method used to obtain data relating to the proportion of Chinese authors. The method states that “The share of Chinese authors in some of the journals was estimated by picking 100 sequentially ordered articles published in the summer of 2017 or 2013, and by visually identifying articles were [sic] all the leading authors were Chinese in the tables of contents.” I think this needs clarification, as there seem to be a number of questions left unanswered. Why was summer chosen as the sampling period? Was only the nationality of the lead author considered? How was the nationality of the author determined (just based on name? Institutional affiliation?). I also have an issue with the sample size, particularly in the case of PLOS ONE and Scientific Reports. Given the publishing volume of these journals, the sample required to estimate a proportion with a reasonable degree of confidence is significantly higher than 100. Given this it’s unclear to me why this sampling method was favoured over the use of a bibliometric database (e.g. Scopus, which was used for data collection later in the paper, and was used by Wakeling et al. to generate the 2015 figures you include in the table). Using Scopus would have allowed you to obtain true figures rather than estimates. Out of curiosity I ran several such searches in Scopus, and in some cases found quite different results to the ones presented in the paper. e.g. For 2013, Scopus shows 18.5% of PLOS ONE articles having an author affiliated with a Chinese institution (paper suggests 12%). For Scientific Reports the figure is 29% (compared to 25%). For AIP Advances Scopus shows 32% (compared to 44%). To be clear I suspect that were the full analysis done in Scopus, the conclusions would be broadly similar. But the Scopus approach is much more technically sound. Validity of the findings: I am confused by some of the data presented in Table 1. The outputs of RSC Advances and Medicine prior to their conversion are shown as 99 each year. I suspect these figures may be place-holders that have not been updated – RSC Advances published many thousands of articles in those years, while Medicine published fewer than 99 each year prior to 2014. The potential link between JIF and submission rates is interesting, but as the author notes, establishing cause and effect here is difficult. Almost all mega-journals (PLOS ONE being the notable exception) show year-on-year growth between 2011 and 2016. I think therefore that if the paper wishes to provide evidence of a potential link between Impact Factor and submission rates, it needs to put post-JIF submission increases in context (i.e. identify whether post-JIF growth is at a faster rate to pre-JIF growth). To illustrate this it is interesting to note that the data presented in Table 1 shows the one and two year increases in PLOS ONE articles following their receiving a JIF in 2010 (2.05 & 3.48) and almost identical to the increases in the two years following 2007 (2.16 & 3.50). Indeed PeerJ actually grew more slowly in the years after it got an Impact Factor (1.67 & 1.82) than it in the two years after 2013 (2.03 & 3.34). I suspect that if post-JIF increases are viewed in context it may be possible to identify more clearly those journals which were most effected by the JIF. I was also left wondering whether the author might have drilled deeper into the geographic factors he alludes to on line 181. We know that in some countries (China being the most obvious, Spain another example) publication in journals with JIFs is formally incentivised. I wonder if analysing submission rates for these countries pre- and post-JIF might reveal something? Given the peer review instructions I feel obliged to point out that the second half of the following sentence in the conclusion is not really supported by evidence in the paper: "its also evident from the numbers, that mega-journals have established a definite niche for themselves, based on benefits to authors in combination with the reasonable brand recognition they provide in CVs" Since the paper does not examine why authors submit to mega-journals, it is probably necessary to make it clear that the proposed reasons are based on the literature or speculation. Additional comments: It is helpful to see updated mega-journal publication data, and there are some interesting findings in the paper. I do feel though that some changes to the data collection are necessary to make this paper methodologically sound.

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.

Title: EVOLUTION OF THE SCHOLARLY MEGA-JOURNAL, 2006–2017 Review round: 1 Reviewer: 2

Basic reporting: No comment Experimental design: Identification of Chinese authors needs more detail. What is leading author – first author, corresponding author? And is this the only author looked at in order to identify the article as Chinese one? And what is “visually identifying”? Is that checking the relevant author’s affiliation, or whether the author name looks Chinese? – In the latter case, Chinese working in non-Chinese institutions will be lumped with authors working in China, which is quite another matter. Author behaviour will be influenced by institutional surroundings, not by nationality or ethnicity per se. A sample of 100 seems to me, intuitively, to be a bit small for the large-volume journals – could this number be expanded to 200 for some journals and years, to make the numbers more reliable? The 2017 numbers in Table 1 are 2 times the actual numbers end of June. Finding numbers by end of September and calculating on that basis could (should?) give more reliable numbers. If it could be without delaying publication much, I would advise this be done. No comments on other aspects. Validity of the findings: No comment Additional comments: Some comments on minor points, referring to line numbers in brackets: [12] [which authors pay for the dissemination services] I think you should enlarge on this - as it stands, it could be read as that you are of the opinion there is nothing done in the pre-dissemination phase, that authors need pay for. Which I cannot think is your opinion, based on your previous publications. (Might be I misinterpret your use of the term “dissemination” here?) [17] Can any comparable number for Chinese authors in general in OA or TA journals be found? [51] A tentative percentage would make this a better read. [65] No Björk 2016 in the literature list? [87] [5] looks like a literature reference, but according to another standard. Should it be [2017]? [133-134] a. for [as], substitute [a] b. No, no different font in Table 1, but suspicious-looking rows of 99’s for both converted journals. [158] For [of], substitute [or] [228 ff] The percentage of OA articles published with APC payment is problematic. Crawford (who, alas, publishes himself and does not submit his works to peer scrutiny) found that for 2014 that 57 per cent of articles in OA journals were paid for through APC. (See https://scholarlykitchen.sspnet.org/2015/08/26/do-most-oa-journals-not-charge-an-apc-sort-of-it-depends/). Despite lack of peer review, Crawford’s numbers generally can be trusted. Crawford analysed the whole set of DOAJ journals, while you limit your analysis to Scopus. I take for granted that what is missing in Scopus generally is small OA journals which tend to be non-commercial. That means the APC payment rate in your data should be even higher than Crawford suggest, at least 60 per cent. This is, however, not a major point of your manuscript. I hope you follow up later with some analysis of the background for, and possible consequences, of the large influx of Chinese authors in mega-journals, and compare this to the more standard journals. Also, why only to some of the journals?