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

Input:
Title: EXPLORING THE ROLE OF INDIVIDUAL LEARNING IN ANIMAL TOOL-USE
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1.	Is the review of broad and cross-disciplinary interest and within the scope of the journal?
Yes, the review is relevant to researchers from a variety of disciplines studying social and individual learning in animals, the origins of (non-) human culture, cultural evolution, and innovation. The review is within the scope of PeerJ, as its topic relates to a number of previously published papers in PeerJ.

2.	Has the field been reviewed recently? If so, is there a good reason for this review (different point of view, accessible to a different audience, etc.)?
To my knowledge, a review bringing together data on individually learned tool-use behaviours in animals has not been done yet. There is a slight overlap to a recently published review on innovation in chimpanzees (Bandini & Harrison, 2020), but the two reviews have clearly different foci and unique contributions to the literature.

3.	Does the Introduction adequately introduce the subject and make it clear who the audience is/what the motivation is?
The introduction is well-written, provides sufficient background information on the current state of the field and clearly describes the motivation for the current review.
Experimental design: 1.	Is the Survey Methodology consistent with a comprehensive, unbiased coverage of the subject? If not, what is missing?
Yes, the authors made sure to carry out the literature search in an unbiased manner.

2.	Are sources adequately cited? Quoted or paraphrased as appropriate?
Sources are adequately cited/quoted.

Is the review organized logically into coherent paragraphs/subsections?
Yes, the review is organized logically. However, it would be helpful if the sources in Table 1 were sorted alphabetically within each species.
Validity of the findings: 1.	Is there a well developed and supported argument that meets the goals set out in the Introduction?
The review meets the goal set out in the introduction (to provide a dataset with cases of individually learned tool-use behaviours) and shows that, as argued in the introduction, the role of individual reinnovations for the emergence of tool-use behaviours is probably larger than some researchers have suggested.

2.	Does the Conclusion identify unresolved questions / gaps / future directions?
Yes, e.g., research into the role of genetics for the emergence of tool-use behaviours and the role of individual and social learning in other domains, such as social behaviours and gestures.
Additional comments: This is a very well-written manuscript which provides an overview which will be very useful for many researchers of several disciplines. I only have 2 points, which will be stated first, and the rest is just minor points. I am looking forward to seeing this work published soon and being discussed in the wider research community.

Table 1: Looking at the authors’ interpretation column, I get the impression that not that many papers make a strong claim for copying social learning to play a role in the findings of their respective studies. Many papers just seem to give a neutral description or actually acknowledge the possibility of individual learning. It would be quite insightful to try to classify the interpretations of the authors to see the proportion of interpretations in favour of the social learning hypothesis, those that stay neutral, and those that are compatible with the ZLS account. This can help identify whether the dominance of the social learning hypothesis is actually due to many researchers supporting it or whether it is more due to a few very influential researchers representing the social learning hypothesis. If the latter is the case, and it turns out that the social learning hypothesis is not that prevalent in the explanations given in the cited papers of the current review, this might actually support the case of the ZLS hypothesis and the arguments presented in the current review. This is not to say that the authors are wrong are in stating that there is a bias in the field towards the social learning hypothesis, this is probably the case. Yet, if the authors could show that the studies they found do not necessarily rely on the social learning hypothesis to interpret their findings, this could help shift readers’ perception of the field, which might encourage them to engage with the claims of the ZLS hypothesis and to more critically question the assumptions of the social learning hypothesis.

Discussion: The manuscript discusses the potential role of the environment, genetics, and the knowledge of pre-existing techniques. However, one crucial factor seems to be missing, which is other cognitive factors. This is especially important as the abstract and introduction introduce the focus on the mechanisms behind tool use behaviours. Of course, the focus of the current review is on individual and social learning, but they are only one part of the potential (cognitive) mechanisms involved. For example, previous literature has discussed the role of information processing and recombination, the motivation for object manipulation, physical cognition and causal reasoning, sensorimotor abilities, and executive functions (especially working memory), see references below. The review should, if not briefly discuss, at least point towards these other potentially crucial mechanisms underlying the acquisition and maintenance of tool-use behaviours.
References:
Call, J. (2013). Three ingredients for becoming a creative tool user. Tool use in animals. Cognition and Ecology, Crickette M. Sanz, Josep Call, & Christoph Boesch (eds.), Cambridge University Press.
Seed, A. & Byrne, R. (2010). Animal tool-use. Current Biology, 20, R1032-R1039.
Read, D. W. (2017). Quantitative Differences Between the Working Memory of Chimpanzees and Humans Give Rise to Qualitative Differences: Subitizing and Cranial Development.
Read, D. W. (2008).Working Memory: A Cognitive Limit to Non-Human Primate Recursive Thinking Prior to Hominid Evolution. Evolutionary Psychology. 6(4), 676-714. UCLA: Human Complex Systems. Retrieved from https://escholarship.org/uc/item/5d06v437

Minor points:

Lines 83-85: “A large number of non-human animal species (henceforth: animals) use tools (e.g., Finn, Tregenza, & Norman, 2009; Kenward et al., 2011; Krützen et al., 2005; Ottoni & Mannu, 2001; Robbins et al., 2016; Whiten et al., 1999).” The manuscript should here also refer to the comprehensive and fairly recent review of animal tool use by Shumaker et al. (2011), also because this review contains the currently widely accepted definition of tool use, which is not given in the current manuscript.
Reference:
Shumaker, R. W., Walkup, K. R., & Beck, B. B. (2011). Animal Tool Behavior. The Use and Manufacture of Tools by Animals. Revised and updated edition. The Johns Hopkins University Press.

Lines 83-85: “A large number of non-human animal species (henceforth: animals) use tools (e.g., Finn, Tregenza, & Norman, 2009; Kenward et al., 2011; Krützen et al., 2005; Ottoni & Mannu, 2001; Robbins et al., 2016; Whiten et al., 1999). Yet it is still unclear how these animals acquire and sustain their tool-use repertoires.” It seems like there is a sentence missing here linking the first and the second sentence: The first sentence makes a broad statement about tool use in any kind of animal species; the second sentence, by using the term “tool-use repertoires”, suggests that the narrower focus is on flexible tool behaviour and on those animals that have a repertoire of tool behaviours and not just a single, stereotyped tool use behaviour. Therefore, the use of “these animals” in the second sentence is not entirely correct – the question how the tool-use repertoires are acquired and sustained is probably not intended to apply to all tool-using animals, but to those capable of flexible tool behaviour. As Hunt et al. (2013) describe, there seem to be two classes of tool-use behaviour: 1) Stereotyped tool behaviour, which often occurs in a highly specific context with only little variation between individuals (often seen in fish and invertebrates, but see the octopus for a possible exception) and 2) flexible tool-use behaviour, which requires individual learning, is often not shown by all members of the population, and which is cognitively more demanding (tool use in birds and mammals). A brief addition to the text should be included explaining that the interesting explanandum are the mechanisms behind this latter class of tool-use behaviours.
Reference:
Hunt, G. R., Gray, R. D., & Taylor, A. H. (2013). Why is tool use rare in animals? In Crickette M. Sanz, Josep Call, & Christophe Boesch (eds.), Tool Use in Animals. Cognition and Ecology, 89-118.

Line 86: Extra space before “Early”, should be deleted.

Line 114: the term “behavioural forms” is a rather novel, technical term and should be defined here. Why behavioural forms instead of just behaviour?

Lines 113-115: “The ZLS proposes that many animal (and sometimes human) tool-use behavioural forms are within the ‘Zone of Latent Solutions’ of the species, and can be acquired through individual learning.” The manuscript provides no definition for the “Zone of Latent Solutions”. An easy solution could be to change the sentence to: “…, i.e., can be acquired through individual learning.”

Table 1: Searching the table would be a bit easier for the reader if within each species references were sorted alphabetically. I would suggest doing so, unless there was another factor the sources were sorted by (this should then be stated).

Table 1, first page, source Marshall-Pescini & Whiten (2008): 1. The comma after Marshall-Pescini should be replaced by a “&”. 2., and more importantly, it is unclear why this case was included. Even if it remains to be confirmed that Mawa had been living in deprived conditions, the authors suggested that he had already been familiar with nut cracking. So it is unclear on what basis this case is still included? This should be explained.
Similarly, why is Biro et al. (2013) included if there is the possibility that the chimpanzee had prior experience?

Table 1: Headings, “Author’s interpretation” – maybe change to “Authors’ interpretation”, as in most cases the papers are authored by more than a single person?

Throughout the document: maybe consider replacing the term “man-made” by a gender-neutral term, e.g., artificial, non-natural, human-made.

Line 289: “Wolfgang Köhler (1914-1920) spent many years investigating …” The dates in parentheses are misplaced, as their current position behind the name suggest them to be related to the lifetime. However, the dates are meant to specify the “many years” and so should be placed after years.

Line 294: “use sticks to retrieve honey from inside bee’s nests”. Apostrophe needs to be changed to “use sticks to retrieve honey from inside bees’ nests”.

Footnote 2: “could be taken to imply a sole, or primary, role of genetics in the emergence of a behaviour However, it is more” Full stop missing after “behaviour”.

Line 313, line 391, line 433: “Zimmerman, (2015),” “However, Zuberbühler et al., (1996)”, “ Kenward et al., (2005, 121)” – in all, remove comma before parentheses.

Line 464: “the authors argue that their “observations provethat innovative tool-related problem-solving” – add space to “provethat”

Lines 467-470: “Similarly, when naïve pigeons solved a task inspired by Köhler’s (1925) work with chimpanzees, in which the pigeons had to use boxes to reach a banana hanging outside their enclosure, the authors conclude that that they “have on hand an instance of insightful problem solving” (Epstein, 1985, 62).” Two issues: 1) Change “the authors” to “the author”; 2) remove one “that” from “conclude that that they”.

Line 545: “unlikely that the captivity effect enhances animal’s cognition” – apostrophe misplaced, should be “animals’ cognition”.

Line 583: “and, dolphin sponging behaviour” – remove comma after “and”.

Line 632: “Gruber et al.s’ work (2009)” change to “Gruber et al.’s (2009) work”

Line 653: “can be individual learnt” – change to “can be learnt individually”?

Line 668: “alongside recognising the equifinality of behaviours” – the role of the equifinality of behaviours for the reinnovation of a behaviour needs to be explained briefly.


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

Input:
Title: EXPLORING THE ROLE OF INDIVIDUAL LEARNING IN ANIMAL TOOL-USE
Review round: 1
Reviewer: 2

Output:
Basic reporting: This review of the role of individual learning in animal tool use will be of broad interest to those in animal cognition, comparative psychology and beyond. The review provides a comprehensive resource documenting tool uses in many animals, with the authors focusing on the role that individual, rather cultural processes may play in animals discoveries of tool uses. Overall, this will be a great addition to the literature, and it is clear that the authors put a lot of work into the article, reviewing over 200 papers!

I would like to see a few changes that should help introduce the subject matter to readers unfamiliar with animal tool use and the social learning literature:

1) Please define animal 'tool use'. There are many definitions in the literature and it would be helpful to include a short sentence detailing what criteria the authors are using. For example, does social and arbitrary tool use count, does tool use need to be goal directed etc?

2) Please define the social learning mechanisms included in the MS. For example, many readers will not know what stimulus or local enhancement mean. Perhaps include a table of definitions if necessary. Related to this, personally I find 'non-copying social learning' and 'copying social learning' a little confusing, especially as social learning mechanisms have been clearly defined in numerous reviews (e.g, Hoppitt and Laland). Perhaps it is best to refrain from introducing new terminology to an already quite complex area. Otherwise, I would like the authors to delineate which social learning mechanisms they see as falling under their two umbrella terms (e.g., is copying social learning just another term for 'imitation', and 'non-copying social learning' a term for all other social learning processes, and if so could this be renamed 'observational learning' or something else).

Minor points for the introduction:

L83. Perhaps cite Bentley-Condit & Smith 2010 and Beck 1980 as they also provide extensive reviews or catalogs of animal tool use.

L88. Could the authors note where the figure of 20 came from? General social information use is almost, if not ubiquitous in the animal kingdom, used even by solitary living animals (see papers by Dall/Giraldeau for examples of widespread social information use, and the behavioral ecology literature more broadly). Or is the 20 just relating to social learning of just 'tool use behaviors' - please clarify.

L97, Is 'copying' referring to 'imitation' here?

L87-97. The background given for academics interest in social learning, and in particular the role imitation plays in the emergence of animal behaviors, may need teasing out a little further. The authors suggest that research first looked at individual learning, then because some 'non-copying' social learning was documented, researchers hypothesized non-human animals may imitate like humans. I believe the background is a little more nuanced, where the first intimations of animal cultures received backlash since there were few direct examples of social learning in animals, despite regional variation in wild populations. More specifically, authors suggested that even if animals had cultures, they were incapable of the 'complex mechanisms' responsible for human cultures (e.g., Galef, 1992; see Kendal, 2008; Laland & Galef, 2009). This then drove the push to investigate whether animals transmitted information socially (it was already clear that individual learning occurs), whether traditions emerge in this way, as well as if other animals use mechanisms homologous to humans (the role of imitation).

L102-105. Please provide the references to back up the statement quoted below. Many studies actually find the opposite, documenting the propagation of novel behaviors within groups of primates and other animals via social processes. Unless the authors are using 'copy' to mean 'imitate behavior patterns' in which case the evidence is indeed more limited ( his again highlights the need for clear definitions of the terminology used in this paper).
"Experimental approaches that explicitly examined the ability to copy behaviours in unenculturated primates (i.e., animals who have not been exposed to extensive human contact and/or training; see also Henrich & Tennie, 2017) were unable to find spontaneous copying abilities in their subjects"

L100-L107. I'm not sure many researchers, if any, would suggest that learning tool use behaviors strictly requires imitation (or indeed that imitation is required at all). Rather, accounts of tool use often highlight the need for certain socioecological conditions e.g.,  the right ecology, motor control, mental capacity and social conditions  (see van Schaik, Deaner & Merrill, 1999). Thus I'm not sure emphasis on individual and social learning is an 'alternative' view.

L104-105. Please explicitly define what is meant by enculturated and unenculturated here (or in the method section). This is particularly important as the methodology excludes enculturated animals from their survey. Do animals have to be hand reared to be enculturated, do they have to live in human environments, are zoo animals enculturated as they have extensive human contact and training? What about reserach facilities were animals can be tested many many times? Also why are the chimps at Yerkes considered enculturated (the Pope imitation study) and those at similar facilities not?  I'm also unclear why the Paquette (1992) study (and indeed Kanzi) are discussed along with findings from unenculturated chimps (L292-297) when the Paquette  paper notes their “chimpanzees were separated from their respective mothers very soon after birth, and were never again in the presence of adults of their species, they may be considered as good subjects for observation because they never experienced restrictive captivity conditions such as social isolation (see Menzel, Davenport & Rogers 1970). On the contrary, they evolved together in an environment rich in stimulations, benefiting from the care and attention of human surrogate mothers fulfilling their need for security.” Adding more detail concerning the criteria used would be very helpful.

L139. Perhaps remove "suggesting that animal individual learning abilities may have been underestimated in the current literature" given that the survey finds over 100 papers in which the authors state individual learning occurs. This seems quite a few.
Experimental design: No comment
Validity of the findings: The method is appropriate and the authors offer a well developed argument that meets the goals set out in the introduction.

Minor points:

Some of the statements made seem a little presumptuous and not necessarily supported by the literature they cite. For example, L243 notes "the authors interpret this 'instantaneous reinnovation' as evidence that the chimpanzee must have copied the behaviour by watching others beforehand". It is tricky to assert that this is a case of 'instantaneous reinvention' as the chimpanzees witnessed others perform the act before they themselves did so. Thus, it could be reinvention, socially learned, or a mix of both. It would probably be better to just state "the authors interpret this as evidence that.....". There are similar examples throughout the MS.

L244-246. Please note that if there is a lack of evidence with small samples and few studies testing an ability, it does not need to indicate that the ability is not present (lack of evidence does not equate to evidence of lack). Also, maybe address the conflicting evidence (e.g., Horner & Whiten, 2005) that showed copying causally irrelevant actions only when an opaque box was presented suggesting action ‘copying’ could be at play in wild born sanctuary chimps. (there are probably more examples).

L294-296. But don't wild chimps show hierarchical structuring of tool sequences (see Sanz and Morgan & Boesch papers), using 3-5 tool elements sets for extraction (tools serve different functions) and regional variation in this? I do not think that this complexity and tool behavior has been reproduced in naïve chimps, as far as I am aware. I think it would be nice if the authors balanced their argument by acknowledging this.

L300-307. Would focusing on some of the other examples tell a different story, for example, the authors recent study found that naive chimps could not reinvent nut cracking tool use behaviors that are evident in wild populations?

L315-316. Please provide a reference for ecological explanations for the variation seen in chimps ant-dipping. I believe Humle and Matsuzawa, 2002 is being referred to but since then more sophisticated analyses suggested there are both individual and socially learned elements (see Humle 2006; Mobuis et al., 2008; Schning et al., 2008).

L354-356. Were the capuchins in Westergaard & Suomi (1994) unenculturated? It may be worth making it clear to the reader that Kanzi is enculturated bonobo.

L423-425. I thought Hunt & Gray (2003) originally proposed cultural transmission may be important, and even went as far to suggest the NCC behavior as a potential case of cumulative cultural evolution.

L503. In saying "this review does not therefore suggest that non-coping social learning plays no role..." the authors are ruling out 'copying'. Does the review discount this as a possible mechanism? Perhaps change to "suggest that social learning plays no role..."

L521-523. There are also studies that do show an effect of model on the acquisition of tool behaviors (e.g., Whiten et 2005; Hopper studies with the Panpipes, among others), and their occurring faster than in groups that were not shown the tool use method. Perhaps direct the reader to some of these so they are aware of some alternative findings.

L547. As previously mentioned, please outline why these chimps (Pope et al., 2017) are enculturated and others with similar backgrounds are not.

L670-671. As the authors note, there is a role for social learning in tool use behaviors in addition to individual learning, and many of the studies in their Table 1 show evidence for both (social and asocial learning). So it seems a little strong saying 'this review suggests instead that it is perhaps time to include individual learning as a serious alternative" as this suggests discounting evidence for social learning as individual learning also occurs. Perhaps the review suggests that the role of individual learning needs to be taken more seriously, or that researchers should acknowledge it is often a mix of the two processes that are important.
Additional comments: No additional comments


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

Input:
Title: GENOME-WIDE ANALYSIS OF PRR GENE FAMILY UNCOVERS THEIR ROLES IN CIRCADIAN RHYTHMIC CHANGES AND RESPONSE TO DROUGHT STRESS IN GOSSYPIUM HIRSUTUM L.
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors analyzed cotton PRR genes, regarding to circadian rhythm and drought stress responses. This is the first report of PRR genes in cotton. Although I have comments on the manuscript, I feel this paper add significance of importance of PRR family in circadian clock in cotton.

Major comment
Gene expression analysis in Figure 5.
Proper controls of PEG treatment are required. In other word, the experiment should contain non-PEG treated samples at 1h, 3h, and 6h. I could not distinguish whether PEG treatment or time-of-day affect PRR genes expression, in this layout. For example, GhPRR3c was unregulated at PEG 6h, suggesting that either PEG treatment, the clock, or both induce GhPRR3c.

Minor comments
Line 49. I recommend to add a paper describing TOC1 cloning as reference (DOI: 10.1126/science.289.5480.768).

Line 54. The N-terminal of PRR is PR (Pseudo reciever) domain, not REC (Response regulator reciever) (DOI: 10.1093/pcp/41.6.791). REC is involved in the His-Asp phosphorelay signal transduction, whereas PR is not (DOI: 10.1093/pcp/41.6.791).  Instead, PR domain of PRR family is crucial for protein-protein interactions (doi: 10.1074/jbc.M803471200,  doi: 10.1105/tpc.107.053033). It is possible to find PRR proteins using homology search using REC and CTT; however, precise description of domain name of PRR is essential to avoid misinterpretation by readers.

Line 59. In addition to binding to CO, CCT motif of PRR proteins are required for association with target gene promoter such as CCA1 and LHY (doi: 10.1073/pnas.1205156109, DOI: 10.1073/pnas.1200355109). The PRRs repress expression of CDF genes that encode transcriptional repressor of CO and FT (doi: 10.1073/pnas.1205156109, DOI: 10.1126/science.1219644).

Line 71. PRR genes function in wheat was reported by other workers (doi: 10.1007/s00122-007-0603-4).

Line 83. In addition to TOC1, triple mutants of prr9 prr7 prr5 confers drought stress tolerance by upregulation of DREB1 (CBF) genes in Arabidopsis (doi: 10.1093/pcp/pcp004). Arabidopsis DREB1 genes are regulated by the circadian clock (doi: 10.1104/pp.104.058354).

Please cite proper papers in addition to above recommendation. For example, Farre and Kay 2005 paper found in the introduction is not cited in reference section.
Experimental design: Gene expression analysis in Figure 5.
Proper controls of PEG treatment are required. In other word, the experiment should contain non-PEG treated samples at 1h, 3h, and 6h. I could not distinguish whether PEG treatment or time-of-day affect PRR genes expression, in this layout. For example, GhPRR3c was unregulated at PEG 6h, suggesting that either PEG treatment, the clock, or both induce GhPRR3c.
Validity of the findings: I have no comment.
Additional comments: The authors analyzed cotton PRR genes, regarding to circadian rhythm and drought stress responses. This is the first report of PRR genes in cotton. Although I have comments on the manuscript, I feel this paper add significance of importance of PRR family in circadian clock in cotton.

Major comment
Gene expression analysis in Figure 5.
Proper controls of PEG treatment are required. In other word, the experiment should contain non-PEG treated samples at 1h, 3h, and 6h. I could not distinguish whether PEG treatment or time-of-day affect PRR genes expression, in this layout. For example, GhPRR3c was unregulated at PEG 6h, suggesting that either PEG treatment, the clock, or both induce GhPRR3c.

Minor comments
Line 49. I recommend to add a paper describing TOC1 cloning as reference (DOI: 10.1126/science.289.5480.768).

Line 54. The N-terminal of PRR is PR (Pseudo reciever) domain, not REC (Response regulator reciever) (DOI: 10.1093/pcp/41.6.791). REC is involved in the His-Asp phosphorelay signal transduction, whereas PR is not (DOI: 10.1093/pcp/41.6.791).  Instead, PR domain of PRR family is crucial for protein-protein interactions (doi: 10.1074/jbc.M803471200,  doi: 10.1105/tpc.107.053033). It is possible to find PRR proteins using homology search using REC and CTT; however, precise description of domain name of PRR is essential to avoid misinterpretation by readers.

Line 59. In addition to binding to CO, CCT motif of PRR proteins are required for association with target gene promoter such as CCA1 and LHY (doi: 10.1073/pnas.1205156109, DOI: 10.1073/pnas.1200355109). The PRRs repress expression of CDF genes that encode transcriptional repressor of CO and FT (doi: 10.1073/pnas.1205156109, DOI: 10.1126/science.1219644).

Line 71. PRR genes function in wheat was reported by other workers (doi: 10.1007/s00122-007-0603-4).

Line 83. In addition to TOC1, triple mutants of prr9 prr7 prr5 confers drought stress tolerance by upregulation of DREB1 (CBF) genes in Arabidopsis (doi: 10.1093/pcp/pcp004). Arabidopsis DREB1 genes are regulated by the circadian clock (doi: 10.1104/pp.104.058354).

Please cite proper papers in addition to above recommendation. For example, Farre and Kay 2005 paper found in the introduction is not cited in reference section.


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

Input:
Title: GENOME-WIDE ANALYSIS OF PRR GENE FAMILY UNCOVERS THEIR ROLES IN CIRCADIAN RHYTHMIC CHANGES AND RESPONSE TO DROUGHT STRESS IN GOSSYPIUM HIRSUTUM L.
Review round: 1
Reviewer: 2

Output:
Basic reporting: The introduction is well supported. The materials and methods, and figures legends are not properly described so it is difficult to understand the information presented.

For a better understanding of the data presented, the authors should improve the legends of the figures. These must contain all the necessary to understand the information presented. In addition, it is recommended to improve the text quality used in the figures.

Figure 1: Check the letters of the panels. The phylogenetic tree is represented by letter B but on the legend is indicated as A.

Figure 2: In panel A, for a better understanding of the information presented, it is recommended that authors indicate which figures correspond to each analysis, ex: Genetic structure (right side). In panel B, for a better understanding of the figure, I suggest indicating the X's axis the coordinates of the regulatory elements respect to the transcription start site (ex -50). In addition, the color assigned to flavonoid biosynthetic genes regulation is missing.

Figure 3: To understand the results obtained, it is recommended to include more information, including What mean the black and white bars showed on X-axis? What represent the error bars showed?

Figure 4: It is necessary to indicate the values used as filters to consider the differentially expressed genes (p-value, FDR, fold change, etc). What means "count"?
Experimental design: The information shown in the materials and methods is incomplete and not clear, it is necessary that this part be substantially improved to support the results showed.

It is unclear how they identified the PRR candidate genes. The strategy shown is confusing and more details need to be included. I suggest checking the wording, indicate the databases used, and add the e-value used as cut-off on the blast analysis.

About biological replicates, more information on experimental design should be included, how many plants for each experiment were used? How many plants by biological replicate were used?

It is necessary that the authors describe in more detail Why LMY19 and TM-1 varieties/accessions were used.

150-157: It is necessary to check the expression patterns and pathway enrichment analysis of PRR members. The reference showed (Zhang et al., 2015) does not correspond to the BioProject (PRJNA490626) and SRA accession numbers shown. These accession numbers correspond to the work reported by Hu et al., 2019 (doi: 10.1038 / s41588-019-0371-5), and they were registered on September 13, 2018, in the NCBI (https: //www.ncbi.nlm. nih.gov/bioproject/?term=PRJNA490626). Additionally, to understand how these data are related to the work reported here, it is necessary to include more information about the transcriptome data set used, including the description of the experiment, description of each sample (treatments and control), etc. In this sense, the SRA accession number of the control sample is missing.

To support the results obtained, the authors should describe in more detail the methodology used for the analysis of the transcriptome data set, including filtering of reads by quality, mapping to the reference, quantification of the expression levels, the filters used to define differentially expressed genes (p-value, FDR, fold change), etc. To enrichment analysis of KEGG, which data set was used as reference to identify the pathways enriched?

Please, explain why do you use the "mpoly" to identify differentially expressed genes instead of DEGSeq2, which was used by Hu et al., 2019 (where the data used comes from).
Validity of the findings: It is necessary to show the homology evidence of PRR sequences in the comparison with Arabidopsis, I suggest including the E-value, identity percentage, and query coverage percentage obtained for each comparison showed on Table S2.

The authors performed a search of motifs in the PRR sequences, they have found clear differences between the sequences, it is necessary to describe the possible biological importance of the presence or absence of these motifs.

Regarding the search for regulatory elements in the promoters of PRR genes, it is necessary to present the analysis and discussion of how many genes have response elements to light, abscisic acid, and drought stress.

In the expression patterns analysis of PRR genes under diurnal change, the authors claim that "the GhPRR genes have obvious circadian waves during 24 hours", however, the results as presented do not clearly support this conclusion. Some ideas are not clear, for example, the authors claim that “GhPRR genes reached the peak every 3 h after 6 h of light condition…” However, as figure 3 showed, it seems that the GhPRR7a, 7b, 9a, 7c, 7d, and 9b genes presented the maximum peak after 6h of darkness. While, the GhPRR3a, 5a, 5b, 3c, 5c, and 5d genes the maximum peak is observed after 9h of darkness. Please, verify the information showed on the figure and explain this part in more detail. It is necessary to improve de legend of this figure.

The authors only show the enrichment analysis of the KEGG pathways for the 6h treatment, please, explain why the other times were not analyzed. It is recommended to show the complete analysis of PEG treatment, for both induced and repressed genes.

The authors mention that "... genes under PEG treatment showed that these six members have the same expression trend and high expression level at 6 h ..." (228-231). To support this idea, it is necessary to carry-out a hierarchical clustering of genes based on their expression patterns, this will help to confirm if these genes have similar expression patterns.

233-234: The authors claim that "All PRR genes displayed almost the similar expression changes compared with transcriptome data sets". To support this, it is necessary to show a graph with the gene expression levels obtained in the transcriptome vs qRT-PCR analyzes or the correlation value between both analyzes.

258-275: In this part, the authors give a good description of the reports on the circadian clock in plants and the role of the PRR proteins in this molecular mechanism, however, it is not completely clear what is the contribution of the results reported here to this area. It is necessary that the results obtained must be compared and discussed in greater depth.
Additional comments: 93-94 the idea is not clear. Please, explain it. I suggest checking the wording.

102-103 the idea is not clear, what the authors mean with “Finally, the whole genome sequence of Arabidopsis thaliana (Initiative et al., 2000), Cocoa (Theobroma cacao) (Argout et al., 2011) and rice (Oryza sativa) (Yu et al., 2005) were loaded from the Arabidopsis database TAIR10 (https://www.arabidopsis.org/), the plant genome database Phytozome 12 (http://phytozome.jgi.doe.gov/pz /portal.html) and EnsemblPlants (http://plants.ensembl.org/index.html), respectively ” Please, explain it. I suggest change the word "loaded" by "download".

Check the use of the word “respectively”, in some cases it is unnecessary, for example, line 136. It should say "after treatment".

It is necessary to homogenize the writing style, the difference between the introduction and materials and methods is remarkable.

136: It is necessary to include the polymerization degree of the PEG used.

164-166: In this part, it is not clear which genome is tetraploid and which diploids. Please, check it.

168: The amino acid and isoelectric point numbers showed in the text do not correspond to those indicated in table S3. Please, check it.

209: For a better understanding, I suggest indicating the names of the products of the GhFT, GhCO, GhLHY, and GhCCA1 genes.

285-286: It is not clear what the authors mean with "... expression of GhPRR follows the expression of GhLHY". Please, explain it.

288: Arabidopsis thaliana should be in italics.


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

Input:
Title: GENOME-WIDE ANALYSIS OF PRR GENE FAMILY UNCOVERS THEIR ROLES IN CIRCADIAN RHYTHMIC CHANGES AND RESPONSE TO DROUGHT STRESS IN GOSSYPIUM HIRSUTUM L.
Review round: 2
Reviewer: 1

Output:
Basic reporting: The revised manuscript was improved. Especially, the authors added new experiment to dissect drought and clock effects on PRR genes expression.
I appreciate the authors’s effort, but I have still comments as below.

1. Jang et al., EMBO J 2008 nor Makino et al., PCP 2000, did not show function of the CCT domain of PRR proteins. The CCT domain of PRR proteins were studied well by Gendron et al., PNAS 2012 and Nakamichi et al., PNAS 2012 as the authors wrote.

2. ‘Periodic expression’, ’rhythmic expression’, ‘cyclic expression’, ‘circadian’ and  ‘oscillation’  are generally used if researchers analyzed samples at least 2-days and found 2-peaks or 2-troughs of interested biological activities. The authors analyzed expression of genes in 1 day (Figure 3), I recommend that these words are not used to explain expression patterns of the genes (‘periodic’ in Line 429, ‘circadian rhythm’ in Line 439, ‘circadian waves’ in Line 449).

3. It was unclear how the authors choose two samples to get DEG in Figure 4A. Did the authors compare transcriptome of PEG_6h and that of untreated_0h to identify DEG in PEG_6h columns? I also request the information when (time-of-day) the authors started to treat plants with PEG.

4. While the authors wrote that ‘The expression of the above mentioned genes (GhPRR5a-d, GhPRR3a and GhPRR3c) at the sixth hour after PEG6000 treatment was significantly higher than that of the blank control’, I found that GhPRR5b expression at 6h-CK and 6h-PEG are similar.
Experimental design: It was unclear how the authors choose two samples to get DEG in Figure 4A. Did the authors compare transcriptome of PEG_6h and that of untreated_0h to identify DEG in PEG_6h columns? I also request the information when (time-of-day) the authors started to treat plants with PEG.
Validity of the findings: well documented.
Additional comments: No additional comments


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

Input:
Title: THE MECHANISM AND DETECTION OF ALTERNATIVE SPLICING EVENTS IN CIRCULAR RNAS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The review is well structured, however I recommend that a native English speaker is consulted as there are several occasions where a wrong word is used. The review shows a comprehensive and adequate literature review. The review might be interesting for scientists studying alternative splicing within circRNAs however there has been a recent review paper in Briefings in Bioinformatics (Chen et al. Feb. 2020: The bioinformatics toolbox for circRNA discovery and analysis) summarizing even more tools and resources for circRNAs. Li at al has a slightly stronger focus on alternative splicing and mentions only two programs Chen et al. do not mention.
Experimental design: The review mentions many programs for alternative splicing in circRNAs, however it would be good if they had also compared advantages and disadvantages of the programs or tried to run selected programs to give the reader advice on which tool to use for which type of data.
Validity of the findings: Li et al. nicely highlights the drawbacks of short read sequencing when trying to reconstruct full length circRNAs.
Additional comments: The review nicely summarizes the current field and might be a good starting point for further reading.


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

Input:
Title: THE MECHANISM AND DETECTION OF ALTERNATIVE SPLICING EVENTS IN CIRCULAR RNAS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors have compiled an informative and insightful review of the mechanism and detection of alternative splicing events in circular RNAs. This reviewer found the topic timely and of great interest, and the article informative. Overall, I recommend this manuscript for publication pending minor edits.
Experimental design: 'no comment'
Validity of the findings: 'no comment'
Additional comments: A few suggestions would help to provide a bit more in-depth detail and answer questions that naturally arise from the article's discussion. Also, moderate English editing would be helpful to clarify the point of several sentences.


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

Input:
Title: THE MECHANISM AND DETECTION OF ALTERNATIVE SPLICING EVENTS IN CIRCULAR RNAS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The present manuscript submitted by the authors on circRNA is considered suitable for publication pending major edits. Despite presenting a fairly complete content regarding the topic it develops, it is recommended to detail a little more information, as well as a review of the English language. However, I consider it is important to emphasize that they bring very interesting information to the field, giving enough literature references and an adequate article structure.
Experimental design: The article presented complies with PeerJ's aim & scopus and the information they provide is considered sufficient and appropriate. However, some claims are requested to be discussed and more detailed.
Validity of the findings: Despite not being a research article, they review interesting information for the circRNA field, providing concise information on the subject.
Additional comments: The present manuscript submitted by the authors on circRNA is considered suitable for publication pending major edits. Despite presenting a fairly complete content regarding the topic it develops, it is recommended to detail a little more information listed below, as well as a review of the English language. However, I consider it is important to emphasize that they bring very interesting information to the field.


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

Input:
Title: THE MECHANISM AND DETECTION OF ALTERNATIVE SPLICING EVENTS IN CIRCULAR RNAS
Review round: 2
Reviewer: 1

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


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

Input:
Title: THE MECHANISM AND DETECTION OF ALTERNATIVE SPLICING EVENTS IN CIRCULAR RNAS
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The authors have adequately answered all the queries proposed in the previous review. I believe that figures, with the modifications that they made and the greater explanation of them in the figure caption, are much better understood. Congratulations for your job.


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

Input:
Title: GLOBAL GENE EXPRESSION ANALYSES OF THE ALKAMIDE-PRODUCING PLANT HELIOPSIS LONGIPES SUPPORTS A POLYKETIDE SYNTHASE-MEDIATED BIOSYNTHESIS PATHWAY
Review round: 1
Reviewer: 1

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

Manuscript # peerj-45349

The manuscript describes the identification of candidate genes for alkamide biosynthetic pathway. The authors performed RNA-seq on plant materials with tissues from alkamide-producing plant Heliopsis longipes and its related species H. annua, a non-alkamide-producing plant. The sequencing data were then assembled, annotated and compared. Based on the differential expression data, ketosynthase domain search, phylogenetic analyses and RT-qPCR data, the authors proposed a model for alkamide acyl chain biosynthesis, a PKS type I-like complex (PKS alk) with four modules which had not been reported previously for plant kingdom.

Overall, the experiment design was permissible and apparently well-executed, and the manuscript is well written. I have relatively minor points for the authors to address.

If the journal allows, consider adding a small section for abbreviations. It seems difficult to read it through without it.

The figure titles and legends are missing.

Consider using “RT-qPCR” in your manuscript by following the MIQE guidelines (Bustin et.al. 2009, Clinical Chem 55:4). Of course, it is up to the editor and the journal standard.

Fig 5 – how consistent are your RT-qPCR results with the RNA-seq data? Is it possible to include the comparison of the “target genes” with the sequencing data in the figure?


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

Input:
Title: GLOBAL GENE EXPRESSION ANALYSES OF THE ALKAMIDE-PRODUCING PLANT HELIOPSIS LONGIPES SUPPORTS A POLYKETIDE SYNTHASE-MEDIATED BIOSYNTHESIS PATHWAY
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript aims to address an interesting and important challenge - the biosynthetic route to alkamides in plants.  The overall strategy is clear - comparative transcriptomics of two related Heliopsis species, one that is reported to produce alkamides and one that does not. The producing species, H. longipes, is reported to produce these compounds in the roots but not the leaves, so enabling comparisons to be made both at the levels of species and tissues.  The writing needs some improvement and is ambiguous in places. While the generation of transcriptome resources is valuable, there is far too much unsupported speculation about the types of enzymes that may be involved.  Functional analysis is needed in order to back this up.
Experimental design: The two species used in these experiments were harvested at different times of the year, and so seasonal differences may influence the results.  A more rigorous approach would be to use material grown under controlled conditions (in a controlled environment glass house or growth chamber).  It would also have been reassuring to analyse the alkamide content of the material used for transcriptomics to confirm the expected differences between species and organ types.
Validity of the findings: The apparent finding of type I PKS enzymes in plants is surprising and warrants a good degree of caution.  A more detailed analysis is needed, both in terms of phylogenetic comparisons and text of function.  It would be very interesting if such enzymes are involved in alkamide biosynthesis in the roots of H. longipes.  The possibility remains that such sequences could originate from microbial symbionts or endophytes that grown in/on the roots.  Without further investigation this work is very preliminary in nature.
Additional comments: This is a really interesting system. I encourage the authors to carry out further investigation to test/substantiate their hypotheses.


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

Input:
Title: GLOBAL GENE EXPRESSION ANALYSES OF THE ALKAMIDE-PRODUCING PLANT HELIOPSIS LONGIPES SUPPORTS A POLYKETIDE SYNTHASE-MEDIATED BIOSYNTHESIS PATHWAY
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment (some minor language errors, for example "in any the other" in line 47)
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I think this work deserves publishing: it gives at least an alternative explanation for the biosynthesis of Nalkylamides in plants. As such, and while it is not a complete proof awaiting additional experiments, it can be further challenged by other investigations.


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

Input:
Title: DISTRIBUTION, HABITAT SUITABILITY, CONSERVATION STATE AND NATURAL HISTORY OF ENDANGERED SALAMANDER BOLITOGLOSSA PANDI
Review round: 1
Reviewer: 1

Output:
Basic reporting: In general, this manuscript is well written but I have noted numerous grammatical and wording changes that need to be made. While I do not know if any of the authors are native English speakers, and while the quality of the English is very high throughout the manuscript, it would benefit from having a native speaker revise it briefly (if none of the authors are native speakers) to pick up on odd phrasings that I have not noted. I tried to note them all but became less diligent about it toward the end of the manuscript. Finally, the literature cited has numerous formatting errors, which I did not note specifically because it appears that this section has not yet been formatted carefully for the journal.

In Figure 1, what is the orange color in the inset map? Does it correspond to the department of Cundinamarca? If so, this should be stated. It would be good to put a box around the area in the inset that corresponds with the bigger map. In Figure 2, it is almost impossible to determine what the relation of perch height is with the other two variables because there are simply too many points on the plot. Because mass and SVL are correlated for obvious reasons, I recommend plotting perch height against only one of these variables if there is a relationship between perch height and either mass or SVL. Figure 4 is also of somewhat low quality and doesn’t add much to the description in the text; I recommend deleting this figure. I don’t think that both Figures 8 and 9 are necessary, as they both show variation in color pattern. I recommend either combining them or deleting one.
Experimental design: This paper has a well-structured sampling design and seeks to provide data on several important aspects of population biology and ecology of a little-known species of salamander. It clearly fills a gap in our knowledge of this species and contributes to our understanding of South American Bolitoglossa, for which relatively little ecological or population information is available.
Validity of the findings: There are some statements of novelty and impact (which I tried to note in my specific comments) that are inappropriate for the format of this journal. Some aspects of the discussion and conclusions are not firmly based on the findings (see below). My main concern with the paper is in the discussion, which often strays from conclusions that can be drawn directly from the data. We lack these kinds of data for almost all species of Neotropical salamanders, and I think that the discussion and conclusions would be strengthened by really focusing on what can be concluded from the data available about the species and its natural history. The results section is a little odd as well, because it mixes primary data with what is effectively a re-description of the species. I suggest focusing more on the primary data, but this could be worked into a formal re-description if the authors desire.
Additional comments: This paper presents a lot of very valuable new information on abundance over time and space, as well as morphological and color variability, for a salamander that has been poorly known and little studied since its discovery. I give specific comments below by line number.

Line 36: Change n-dash to comma between Cundimamarca and Colombia

Line 50: Add “population” after “highly dense”

Line 69: Change “Bolitoglossa genus” to “genus Bolitoglossa”

Line 72: Change “Plethodontidae” to “plethodontid”. Additionally, Bolitoglossa is the most diverse and widespread genus of salamander in general, if the authors want to expand this statement beyond the Neotropics.

Line 73: AmphibiaWeb lists 133 species of Bolitoglossa, so this should be updated. It’s better to cite an online database like AmphibiaWeb because any publication on diversity numbers in the Neotropics is almost immediately out of date given the high rate of species descriptions.

Line 77: I don’t think it’s grammatically correct to say “high morphological crypsis”. You could change this to “high level of morphological crypsis” or “highly conserved morphology”.

Line 82: delete “so”

Lines 82–88: I don’t think that this statement is accurate. Almost all modern descriptions of species (including those dating back decades) include information on microhabitat use and habitat where species occurs. Books not cited here like the Amphibians and Reptiles of Costa Rica (Savage) or the Amphibians of Honduras (McCranie and Wilson) include detailed information on habitat and microhabitat use. There are also papers (Wake, 1987) with a lot of information on microhabitat use by Bolitoglossa.

Line 102: Change “nearby” to “near”. Also, if the exact type locality is unknown, how can this specimen be said to be from near the type locality?

Line 147: Change “at the municipalities” to “in the municipalities”

Line 155: I don’t know what is meant by “grove pastures”

Line 160: Insert space between “measured” and “its”

Lines 164–165: Were the live salamanders examined to see if they had a mental gland? This is typically a fairly reliable way to identify sexually mature adult males, although I am unfamiliar with the mental gland of this species.

Line 182: Change “estimatioof” to “estimation
Lines 198, 210: Change “vegetation percentage cover” to “percentage vegetation cover”

Line 201–202: I understand the logic here, but this analysis will not tell you what factor is responsible for the difference between detection and non-detection. The actual factor responsible could be correlated with one you measured but not actually in the dataset.

Line 206: Change “non-detected” to “not detected”

Line 210: This is a minor point, but here and elsewhere I would change “altitude” to “vegetation”. Altitude typically refers to the distance above ground (like the altitude at which planes fly).

Line 231: What exactly is meant by “population structure”? This phrase has different meanings in different disciplines (like ecology and population genetics) and it would be helpful to define it (i.e. as population age structure).

Line 236: change “nine-time intervals” to “nine time intervals” or “nine time-intervals”

Line 238: Change “employed” to “used”

Lines 247–251: Did these publications define these age categories for this species, or in general? I am not very familiar with South American Bolitoglossa, but there are very few species with sexually mature adults at 30 mm SVL. It would also be important to distinguish between males and females because males tend to mature at a smaller size than females.

Line 261: Change “in” to “at”

Line 268: I don’t think it’s grammatically correct to begin a sentence with “Also”. You could say “Additionally” instead.

Lines 272–273: I don't think that “natural history” is the right way to describe these traits. I suggest “morphological traits” or “morphology” instead.

Line 280: Instead of “explain”, why not say “are significantly associated with”? Explain implies that they completely explain the detection of salamanders, unless it is qualified (i.e. “partially explain”).

Line 282: I would only report values to one decimal place to not imply greater precision than there actually is in the analysis.

Line 284: Change “spaces” to “space”

Line 285: I recommend changing “strongly differentiated” to “differentiated”, given that they do overlap.

Line 286: Change “quadrats highly structure” to “highly structured quadrats”

Line 287: Remove “a” before “depth” or change to “with deep leaf litter”

Line 293: Change “environmental mean temperature” to “mean environmental temperature”

Line 296: The methods section states that an autocorrelation between 1 and 3 is moderate and this value is very close to one. If it were only 0.1 less, it would be “strong autocorrelation”. I think this sentence needs to be modified to reflect that there is moderate autocorrelation.

Line 301: Change comma after “nocturnal” to semicolon.

Line 302: Either say “beginning at… and ending at” or from…until…”.

Line 307: If I am interpreting this correctly, it should be rephrased as something like “whereas it was moderately and negatively correlated with relative humidity”

Line 308: “Despite” isn’t the right word here. Maybe “Across sampling occasions”?

Line 328: What is meant by “replacement rate” here?

Line 332: Delete “notorious” to remove value judgement

Line 339–340: There is literally no way that there are 13.4 mm adult males. This would be smaller than the smallest adults of Thorius, which are the very smallest salamanders. Furthermore, the size variation in Figure 7 implies that all adults measured were >30 mm. The proper way to determine if the specimens are adults or not is to assess sexual maturity either via examination of the mental gland, chloacal morphology, or internal reproductive organs. It’s fine to divide individuals into rough size classes to look at population age structure, but these data can’t then be used to make statements about adult size.

Line 339: This section is titled “morphological variability’ but is in fact basically a redescription of B. pandi. I suggest that the authors either reformat this section as a redescription based on additional material or limit themselves to describing the morphological variability without providing a diagnosis for the species.

Line 358: All of the species of Neotropical salamanders of which I am aware undergo an ontological change from white to black testes. The fact that the authors state that B. pandi has white testes makes me suspect further that many of the individuals they examined were not adults, although it is possible that this species retains white testes into sexual maturity. The appropriate way to determine this would be to examine the mental gland of the male specimens collected to determine if they are, in fact, sexually mature adults.

Lines 370–371: Change “less head width” to “shorter head”

Line 374: What does “wide polychromatic variability” mean? I think it would be better to just say “wide variation in color”.

Line 376: Change “diffused” to “diffuse” I can’t tell whether this should be rephrase as “dark blotches scarcely distinguishable from the dorsolateral region” or “scarcely distinguishable dark blotches that extend to the dorsolateral region”.

Line 379: “Exceptionally” implies a value judgment. Sah “very” instead.

Line 388: Change “creams” to “cream”

Line 396: Change “added to Bolitoglossa pandi distribution” to “added to the distribution of Bolitoglossa pandi”

Line 400–404: Bolitoglossa pandi is still a narrow endemic, occurring within only one department of Colombia. I don’t quite understand what is meant by this. Furthermore, what does “lack of comparisons [sic] with the relevant type material” mean in this context? Were salamander specimens available from this area but not assigned to B. pandi? I also don’t understand what is meant be the last part of the sentence about incomplete knowledge of morphological variability of Bolitoglossa. We know an enormous amount about the morphological variability of Bolitoglossa, and this manuscript really don’t have much to do with that. Rather, it improves our knowledge of one species of Bolitoglossa through the addition of detection data and morphology. I think that the real contribution of this paper could be stated much more accurately and concisely without making it something it isn’t.

Line 408: Delete “significantly”, as it implies a value judgment.

Line 409: The color data presented here don’t contrast with the original description because it presented no data on color in life. Rather, the new data add to the original description.

Line 412: “Polychromatism” seems like an unnecessarily complex (and partially inaccurate” word to describe color pattern variation.

Lines 418–423: I don’t quite understand what is meant by this sentence.
“Inconspicuous” just means that they are hard to see or notice. Is the idea that they are more abundant than previously suspected? If so, does this account for species like Bolitoglossa adspersa that are (or at least were) quite abundant at many localities?

Line 426: Change “arise” to “were” and remove quotes around “best”

Lines 427–431: I don't understand what is meant by this section either. Two of the references cited are for different, individual species of Bolitoglossa, whereas this sentence makes it seem like the results were expected based on what we already know about this species or about the genus in general. Bolitoglossa is extremely variable; some species are entirely terrestrial, in contrast to the “arboreal habits” listed here. I recommend deleting this entire sentence or at the very least rephrasing it so that it says something accurate that adds to the discussion.

Line 445: Change “promoting” to  “were associated with”

Line 449: This is patently untrue. There is published information on females of Bolitoglossa dofleini being terrestrial while males are arboreal, and this is true of other species as well. Furthermore, it’s not clear to me which of the results presented here suggest that there is intraspecific habitat partitioning.

Conclusion: The conclusion section seems based on only one aspect of the results (the conservation status of the species). There is a lot of really important information on life history and abundance presented here and I suggest refocusing this section on what is directly able to be concluded from the data presented.

Figure 5: This figure is odd, because it seems like the same peak is repeated on both sides of each panel. It would be better to cut off the figure at 0:00 and 24:00 for clarity of interpretation.


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

Input:
Title: DISTRIBUTION, HABITAT SUITABILITY, CONSERVATION STATE AND NATURAL HISTORY OF ENDANGERED SALAMANDER BOLITOGLOSSA PANDI
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper is clear, only some mistakes regarding the english used. The English language should be improved to ensure that an international audience can clearly understand your text.
Please correct it.
In the Background section, please add the description for the microhabitat use in Bolitoglossa pandi.
Experimental design: Methods are sufficient, but please add Heyer et al.  for the visual encounter surveys (VES):
See Heyer, R., Donnelly, M. A., Foster, M., & Mcdiarmid, R. (Eds.). (2014). Measuring and monitoring biological diversity: standard methods for amphibians. Smithsonian Institution.
And explain clearly Why did you choose this method ?
(not disturb the target sp. etc...)
Validity of the findings: All underlying data have been provided; they are robust, statistically sound, & controlled.
Please add in the discussion part, a comparison with other Bolitoglossa's habitat use;
and describe in details their habitat needs before conservation section.
Additional comments: This paper describes some new natural history observations on one species of threatened Bolitoglossine in Colombia, Bolitoglossa pandi. Although the methods are fairly routine and the sample sizes are small, this species is a part of a group of considerable conservation interest and the data presented do therefore provide an important addition to our understanding of their distribution, natural history and conservation.
However, many interesting findings in your data to underline clearly especially through the discussion part:
Describe in details Habitat + microhabitat use by B. pandi in comparison to other Bolitoglossines.
If you show its ecological specificities it's better in terms of conservation perspectives. This last point is really important to ensure your paper as a reference in ecology for Colombian salamanders.


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

Input:
Title: DISTRIBUTION, HABITAT SUITABILITY, CONSERVATION STATE AND NATURAL HISTORY OF ENDANGERED SALAMANDER BOLITOGLOSSA PANDI
Review round: 2
Reviewer: 1

Output:
Basic reporting: The English of the manuscript has been improved (but see comments for specific changes). In general, the article is relatively well-written with adequate citations, figures, and tables.
Experimental design: This paper provides important ecological and life history data for a species of salamander whose basic biology is essentially unknown. The methods used are appropriate and adequately explained .
Validity of the findings: In general, the data in this manuscript are robust and reasonably analyzed. Some of the conclusions in the new version go beyond what can be stated from the data (see specific comments below) and some of the statistical differences seem like they might be so minor as to be of little biological meaning. While it is impressive how many individual salamanders the authors were able to sample, statistical analysis of such a large data set will nearly always show differences between groups. The question is then whether such differences mean anything. There are a few claims of priority and novelty in the conclusions that are unnecessary and detract from the genuine contribution of the manuscript, which is to provide a large amount of data about a species for which almost noting was previously known.
Additional comments: Specific comments by line number:

Lines 30–31: It is inaccurate to say that this species is one of the most threatened in South America. There are many frogs that have not been seen in decades despite intense search efforts and are likely extinct. This species seems more understudied than highly threatened (even by the authors’ own criteria in the conclusion). Also, change “on the Colombian conservation agenda” to “for the Colombian conservation agenda”.

Lines 33–34: Change “presenting a narrow elevational range only within the Cundinamarca department” to “occurring only in the department of Cundinamarca within a narrow elevational range”

Line 36: change “covered” to “cover”

Line 43: Change “a multivariate analyses” to “Multivariate analyses” (if multiple analyses were conducted) or “A multivariate analysis” (if only one analysis was done).

Line 44 and elsewhere: Change “not detection” to “nondetection”

Line 49: Delete “distribution of this”

Line 54: Spell out genus name when it is the first word in a sentence

Line 78: Change period to comma after “Frost”

Line 89: While this section has been rephrased, it is still incorrect as written. Does the 12% figure refer only to South American species of Bolitoglossa? If so, it could be correct. As written, the sentence seems to refer to 12% of all Bolitoglossa species. The vast majority of Bolitoglossa species descriptions contain information on microhabitat use and habitat preference. If all species with some information on microhabitat use or habitat preference were included, the figure would be far higher than 12%. I agree that we do not know much about many species of Bolitoglossa, but we have at least some information on microhabitat use for most of them.

Line 102: delete “the” before “primary cloud forest”

Lines 98, 105: Snout-vent length should be spelled out and then abbreviated on the first mention, not the second.

Line 108: I recommend reporting SVL to only one decimal place (i.e. 37.6 mm)

Line 115: Change “describe the geographic range extension” to “describe the geographic range”

Line 138 and elsewhere: Change “altitudinal” to “elevational” and “altitude” to “elevation”

Line 162: Change “was recorded” to “were recorded”

Lines 184, 191: “Life forms” usually means something different than this (basically, living things in general). I would change this to “growth forms” or just “categories”.

Lines 198–202: Which of these were dependent variables and which were independent variables?

Line 206: Delete “analysis” (because it’s already included in PCA)

Line 217: Change “Smirnov’s” to “Smirnov”

Line 219: Change “data size” to “sample size”

Line 234: Avoid words like “remarkable” because they imply a value judgment. I would change this to “high”

Line 246: Again, you need to say what you mean by “population structure”. In previous sections of the manuscript, you say “population size-structure”. I think this is still slightly misleading because “population size” usually refers to the number of individuals in a population. I recommend changing this to “population age-structure”, because it seems like the main point is to classify individuals into life stages (adult, juvenile, etc).

Line 262, 263: change “Km” to “km”

Line 267: Change “sighted” to “found”

Line 277: Change “squared coefficients” to “R-squared values” or “squared correlation coefficients”

Line 278: Delete comma after “variables”

Line 282: Delete “analysis” after “PCA” and change “retrieved” to “accounted for”

Line 284: Change “overlapped” to “overlapping”

Line 295: Why is “best” in quotation marks here? This is the right word and it has an understood meaning in this context; there is no need to put it in quotes.

Lines 307, 308: If these are correlation coefficients, they should be “r”, not “R”.

Line 312: Change “being more abundant” to “being higher”

Lines 310–312: I don’t think that much is gained by analyzing the sampling events separately. Conditions vary daily and what happened on any one particular day is not particularly interesting, whereas patterns of activity that are consistent across days are interesting. I recommend combining all sampling occasions and seeing if there are peaks of activity and if they are significantly different. Also, Figure 4 would be easier to read if it were centered on midnight rather than noon (so that the activity period were in the center of the figure).

Line 320: Change “in contrast with” to “in contrast to”

Line 321: Change to “variation in salamander SVL was between peaks was consistent…”

Lines 327–328: High compared to what? Most species of Bolitoglossa have a generation time of two years, and they likely all transition quickly from neonates to juveniles. Given that the sampling locations were spread throughout a large part of the year, this seems about what would be expected.

Line 330: Change “of the individuals” to “of individuals”

Line 332: Change “SVL median value” to “median SVL “

Lines 334: I don’t think that the timing of the recruitment peak can be determined, because no samples are available between October and March.

Line 338: Change “tiny” to “small” or “very small”. There are much smaller salamanders in the Neotropics, so I don’t think that calling it “tiny” is accurate.

Line 337: I must insist: if you are giving diagnoses from other species within the genus, this section cannot be titled “Morphological variability”. This is basically a redescription without reference to the type material. At a minimum, you could say “Morphological variability and comparisons to other species” or something like that, but there is very little data on actual morphological variability presented in the section.

Lines 349–350: No species of South American Bolitoglossa has a complete lack of webbing. I would delete “absent”. Compared to species in Mesoamerica or North America, the least webbed South American Bolitoglossa is highly webbed.

Line 352: Change “for having” to “by” or “by having”

Line 353 and elsewhere: Spell out genus name when it is the first word in a sentence.

Line 353: All of the digits are typically referred to as “toes” or “digits”, not “fingers”. It is also important to specify whether this refers to digits on the hand or foot.

Line 359: What is meant by “digital depressions”? This is not a standard term in salamander morphology.

Line 373: Change “exhibited” to “exhibits”

Line 385 and elsewhere: I do not understand what “pits” refers to in the context of color pattern.

Line 390: This is almost universally referred to as the “mental gland”, not the “submental gland”.

Line 394: Change “added” to “add”

Line 395: Change “have allowed” to “allowed”. I also recommend making this section shorter and just focusing on how examination of this population provided detailed ecological and morphological data that was previously lacking for the species.

Line 398: “Enormous” implies a value judgment and should be deleted. “Efforts” is fine.

Line 434: Italicize “B. pandi”

Line 438: Change “opposite or absent” to “a negative correlation or no correlation”

Line 452: Do not start a sentence with “Also”. You could say “Additionally”

Line 453: Change “that agrees” to “which agrees”

Lines 468, 470, elsewhere: Change “Bolitoglossines” to “bolitoglossines” or “Bolitoglossa”. “Bolitoglossines” is not a recognized taxonomic rank and thus should not be capitalized.

Line 480: I don’t understand what is meant by “suggesting independence of climatic variability”

Line 495: Delete “Meanwhile” or change it to “However”

Line 497: What is meant by use of resources? The only thing measured here was when salamanders were found and where; no resources (aside from perch height, which is essentially an unlimited resource in the forest) was measured. I would focus on timing and not bring resources into it.

Lines 498–501: Avoid statements of priority and novelty; have the authors read every thesis, paper, and report on tropical salamander activity? Let the results speak for themselves. It is clear that we have learned a lot from this study, without saying that it is the first to demonstrate a point.

Lines 501–504: It’s not that the data are insufficient, but rather that these aspects of salamander ecology were simply not part of this study. I recommend deleting this sentence entirely.

Lines 506–507: It’s not clear to me how life history strategy relates to anything presented in this paper. I recommend deleting this sentence.

Lines 510–513: Adaptive radiation has to do with morphological differences between species, not within them. This sentence is inaccurate.

Line 514: Delete “the” before “suitable habitat conditions” and change “predicting” to “predictor”

Line 515: “Across the Andes” makes it sound like this species has a distribution throughout the mountain range. This should be deleted.

Lines 517–520: I don’t understand what is meant by this sentence. Extinction rates refer to species, not populations. If the authors are referring to population extirpation rates, these are not possible to estimate if the species has not been extirpated at known localities. “Predictive scenarios” doesn’t really mean anything; do the authors mean “predictions”, and if so, predictions of what? Honestly, I don’t think that much can be said about the conservation of this species based on the data presented here, except that it is more widely distributed and more abundant than previously known.

Line 537: Change “is” to “are”

Line 539: Change “as” to “such as”. I would delete this entire sentence; ecological studies are much less important than accurate distributional data in nearly all conservation planning. It doesn’t matter when a species is active or what microhabitat it uses if a forest is destroyed, which is the level at which most conservation planning in the Neotropics (and elsewhere) is done.

References: There is a relatively high degree of self-citation in this manuscript. I would avoid this; Zootaxa was just removed from the list of indexed journals for exactly this problem and we don’t want PeerJ to be next.

Figure 2: Are the “R” values correlation coefficients (in which case they should be “r”) or R-squared? If they are correlation coefficients, it is more appropriate to report them as R-squared values. It would also be worth pointing out in the text that although these values may be statistically significant, they are quite small and might not be very biologically significant.

Figure 4: As stated previously, I would combine data across sampling events and to focus on temporal differences.

Figure 5: Looking at these plots, it seems like the results of the nested ANOVA may not be saying much. That test would only say if there were a difference between any two time periods. Overall, there is very broad overlap in abundance and salamander size across all times; I don’t think that much can be concluded from this.


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

Input:
Title: DISTRIBUTION, HABITAT SUITABILITY, CONSERVATION STATE AND NATURAL HISTORY OF ENDANGERED SALAMANDER BOLITOGLOSSA PANDI
Review round: 2
Reviewer: 2

Output:
Basic reporting: The paper is important for the knowledge of a scarce and poorly known species of Andean bolitoglossine. The manuscript is clear and the structure shows standard sections requested. Figures are relevant. I accept it for publication with minor revisions.
Experimental design: This research is relevant; Methods used show sufficient details.
Validity of the findings: Important data are given to define the distribution and conservation status of B. pandi. It's an important paper for its natural history.
Additional comments: Good paper in general. However, please check well your manuscript with an english speaker.
You can also include in the discussion section an overview (some sentences) of the conservation status of the genus Bolitoglossa and other Salamander species, which are the most endangered vertebrate group on Earth. Be that as it may, more than 41% of amphibian species are thought of as ‘endangered’, including 54.7% of the Urodela group. North and Central America and Asia are most severely affected by the continued destruction of habitats and the spread of chytrid (Bd). See my previous book : Hernandez A. 2016. Etude sur les Urodèles en voie de disparition. Edilivre editions, Paris. 120 p.


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

Input:
Title: A NEW SPECIES OF SCAPHOLEBERIS SCHOEDLER, 1858 (ANOMOPODA: DAPHNIIDAE: SCAPHOLEBERINAE) FROM THE COLOMBIAN AMAZON BASIN HIGHLIGHTED BY DNA BARCODES AND MORPHOLOGY
Review round: 1
Reviewer: 1

Output:
Basic reporting: Paper is in general OK and could be published after some corrections. See comments to the authors.
Experimental design: The study did not contain the experiments.
Validity of the findings: The conclusion is properly confirmed.
Additional comments: I can recommend to publish this paper. At least the last author has a necessary qualification for an adequate species description. The paper agrees with the taxonomic rules (but see comments below), the taxon name is deposited to the Zoobank, and sequences are also properly deposited, and their deposition is clearly noted in the manuscript. Field studies made with all necessary permits.

I can not verify that English is perfect (or not). I recommend to show the paper to native speakers.

Critical comments:

I have no doubts that the authors have really a new species. I did not see their material, but I recommend to diminish the discussion of characters of the ventral portion of carapace. This opinion is based on study of few specimens under SEM, as observation of this portion using optical miscroscope is problematic, as this structures not so transparent. I saw a lot of specimens of Scapholeberis and I argee with the opinion of Dumont & Pensaert (1983) that this portion id very variable among specimens. Moreover, preservation of the membranes in this portion is different in different specimens from same sample due to different level of fixation and destruction of the membranes during the animal life. I saw specimens from same populations with well-preserved and very shabby membranes. Therefore I believe that the differences exist, but I stronglu recomment to the authors to be concentrated on obvious characters on the ventral valve portion, and reduce as much as possible the discussion of the differences in fine characters, because this comparison is based on few animals from few populations.

This is a relative short paper, but its reference list is specially short, what is uncharacteristic for taxonomic papers. In reality, some contribution to the studies of Scapholeberis is made recently by Alonso (1996), Hudec (2010). Moreover, Taylor et al. (2020) concluded that in general the conclusions of morphologist for the taxon delimitation in Scapholeberis were quite correct. I think that the solely morphological systematics must be noted (1 paragraph with some references).

See also a list of particular comments:

9, 37, 57. The first mention of a taxon of generic and species rank must be accompanied by the taxon author(s) name(s) - in the title, the Abstract and the Manuscript body. Also first reference on the genus in the title, Abstract and the main body must be accompanied by explanation of its taxonomic position, preferably with family information ? (Cladocera: Anomopoda: Daphniidae).

53. Abstract is solely descriptive. I recommend to add a final conclusion to the end. At the same time, the differential diagnosis in the Abstract could be shortened.

57 and further. Please check everywhere, are taxon names italized?

70. This "Scapholeberis" is extremely dubious. In reality, no evidences that this is a cladoceran were provided by the authors! Moreover, this "Scapholeberis" has segmented postabdomen impossible for cladocerans. See Van Damme K., Kotov A.A., 2016. The fossil record of the Cladocera (Crustacea: Branchiopoda): Evidence and hypotheses. Earth-Science Reviews 163: 162–189.

134, 136. Please fill the numbers XXXX-XXX!

162-167. Please provide the AUTHORS of each taxon.

169 and further. Incorrectly organized. The type locality is a single water body (not several!), from where the holotype is selected.

171 and further. The symbols of degree is necessary for coordinates.

192-193. The measurements like 544 plus-minus 13.3 have no sense, as an instar variability is strong. Only range will be more realistic.

195 and further "so-called rostral pore". This is apparently an outdated term. This is a frontal head pore, with very clear homology, which could be found in many anomopods, including other daphniids except Daphnia.

198 and further. See general comments on the variability of valve ventral portion armature below.

217. Head shiled. Why not head? Really the daphiiids have no headshield in terms of Fryer (1963). They have head capsule.

216. "Endopod" is not proper term here. Endopod is an internal branch of the biramous limb. Your "endopod" is a single "endite 4 only". In reality, endopod consists of "endites 2-4" in your understanding.

218. "A long accessory seta" is a part of exopod also.

309, 313. See on size range above.

326. Why Molecular sequences (it seems that all genetic sequences are molecular ones)? May be "COI geetic barcoding" is better title?

365. Really not Neotropical one, but endemic of the southern most portion of S America

376. Scapholeberis freyi, not armata freyi.

380. Repetition of previous phrase.

Illustrations: For some reason, the illustrations have a huge black margin. All this "empty" black space needs to be cropped.


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

Input:
Title: A NEW SPECIES OF SCAPHOLEBERIS SCHOEDLER, 1858 (ANOMOPODA: DAPHNIIDAE: SCAPHOLEBERINAE) FROM THE COLOMBIAN AMAZON BASIN HIGHLIGHTED BY DNA BARCODES AND MORPHOLOGY
Review round: 1
Reviewer: 2

Output:
Basic reporting: Line 71 The statement “it is not possible to have only eight species known around the world” because of a Cretaceous fossil appears overstated. The existing fossil has not been assigned to the Genus Scapholeberis. Also, why can’t widespread ancient groups that have been exposed to extinctions be species-poor? Replacing “it is not possible” with “unlikely” would be more prudent.

There are several sentences where the grammar, typographic errors, or language style should be improved for readability. I have listed a few examples below:

Line 34 rich freshwater should be species-rich freshwater

Line 38 light traps of recent design: recently designed light traps

Line 47 “a filament-like projection” doesn’t match the “lament-like projection” in the first abstract of the .pdf (lament is a typo?)

Line 58 hiponeuston should be hyponeuston

Line 60 pellicle should be surface

Line 61 “The structure was detailed described” omit “detailed”

Line 80 sentence needs rewording “not any barcoding study”

Line 92 realized should be carried out

Line 103 “Normanski in a” should be Normanski microscopy (BX51…)

Line 105 in should be with

Line 110 glass fiber method should be glass fiber filtration method

Line 132 keep to past tense in the methods

Line 142 the best fit should be best fit substitution model

Line 160 space needed after and in “andCLOCKSS”

171-172 add degrees symbols to coordinates

Line 231 in should be on

Line 264 not-segmented should be unsegmented

Line 311 epphipial should be ephippial
Experimental design: Lines 369-371

I like the addition of light traps to sampling, but in the text, the relationship between light traps, phototaxis, and the sexual stages is unclear. Are you suggesting that the sexual stages are more positively phototactic than clonal females?  Won’t the sexual stages be absent from most light traps because most species are clonal for much of the year? Please clarify.
Validity of the findings: Line 192 “medium-sized daphniids”.  I have never plotted daphniid size distributions.  However, 0.541 mm seems small for daphniids as nearly all species (mostly Daphnia and Simocephalus) have upper sizes greater than 1mm and many are greater than 3 mm. Consider using “small-sized”.

Lines 347-349 The authors state that the clade for S. yahuarcaquensis is “well supported” by Bayesian analysis. Please give more details about the quantification of this support. Is there a posterior probability? I can’t find the figure caption for Supplementary File 2. Also, please add support values (posterior probabilities?) to Figure 8. Can you provide more details on how the BIN analysis indicates support for new species?

Lines 351-354

The authors use the “armata group” for a large clade and suggest that it needs further study (see also the label on Figure 8.). However, the sampling locations more closely match the geographic range of S. rammneri than S. armata (according to Pensaert & Dumont 1983 and Taylor et al. 2020).   Why is “armata” the most appropriate name for this major group? The database names are a mix of no species names, armata group and D. rammneri.
Additional comments: The manuscript provides a detailed species description of a neglected genus of waterfleas, Scapholeberis, from an understudied geographic region for freshwater biology. The morphological description is very detailed with high quality SEM’s, line drawings of limbs and rare information from the sexual stages. The evidence of this new species is bolstered with DNA sequence information from the DNA barcoding region of mitochondrial DNA. I find the evidence of a new species of Scapholeberis to be compelling and in accordance with new species policies and standards. My suggestions above might improve the manuscript and are minor.


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

Input:
Title: A NEW SPECIES OF SCAPHOLEBERIS SCHOEDLER, 1858 (ANOMOPODA: DAPHNIIDAE: SCAPHOLEBERINAE) FROM THE COLOMBIAN AMAZON BASIN HIGHLIGHTED BY DNA BARCODES AND MORPHOLOGY
Review round: 1
Reviewer: 3

Output:
Basic reporting: As mentioned in the previous section, give more context on current lit in the introduction.
Experimental design: 1. For research ethics purposes, cite (in acknowledgment), where applicable, permits acquired to conduct the field sampling.

2. Please add one table about pairwise COI sequence divergence within the Scapholeberis species analysed.

3. Please add key to the species of Scapholeberis.

4. please add bootstrap in Bayesian tree.
Validity of the findings: It is a nice manuscript. I just suggest to overlying the map in figure I think, it will be easy for the readers to understand.
Additional comments: I enjoyed reading your MS but struggled to easily grasp the details largely because of how results were presented and having had to go back and forth from one figure to another. I think your figures are good but contain too much information and need to be explained for e.g. see sections of the discussion highlighted in the PDF. With a little tweaking of how results are conveyed- I think the paper will be widely read and comprehended easily.


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

Input:
Title: A NEW SPECIES OF SCAPHOLEBERIS SCHOEDLER, 1858 (ANOMOPODA: DAPHNIIDAE: SCAPHOLEBERINAE) FROM THE COLOMBIAN AMAZON BASIN HIGHLIGHTED BY DNA BARCODES AND MORPHOLOGY
Review round: 2
Reviewer: 1

Output:
Basic reporting: English is improved. Reference list is adequate. Figure, tableas are OK. The paper is improved
Experimental design: The paper is OK for PeerJ. Ethics is OK.
Validity of the findings: Conclusions are supported.
Additional comments: The paper is improved.


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

Input:
Title: A NEW SPECIES OF SCAPHOLEBERIS SCHOEDLER, 1858 (ANOMOPODA: DAPHNIIDAE: SCAPHOLEBERINAE) FROM THE COLOMBIAN AMAZON BASIN HIGHLIGHTED BY DNA BARCODES AND MORPHOLOGY
Review round: 2
Reviewer: 2

Output:
Basic reporting: OK, Please contineu to next process.
Experimental design: OK, Please contineu to next process.
Validity of the findings: OK
Additional comments: OK, Please contineu to next process.


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

Input:
Title: A MODEL OF TWENTY-THREE METABOLIC-RELATED GENES PREDICTING OVERALL SURVIVAL FOR LUNG ADENOCARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The Zhao et al. contrasted a model of twenty-four metabolic-related genes predicting overall survival for lung adenocarcinoma, but some questions were needed to be optimized:
1. More detailed description (such as the packages and functions) should be given for readers for the three-step method in the Materials and Methods section.
2. The order of subtitles should be corrected, such as 2.6, 2.8 …
3. Authors should provide clearer figures for readers.
4. Authors use LUAD RNA-Seq data and clinical data from The Cancer Genome Atlas (TCGA) were regarded as a training cohort, and microarray data from GEO (GSE30219) was regarded as a testing cohort and utilized for validation. Authors should interpret the advantages and limitations of this experimental design.
5. Authors should perform the Gene Ontology analysis and interpret the biological function.
6. The grammar and English style were needed to be optimized.
7. More references are needed in the Introduction section.


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

Input:
Title: A MODEL OF TWENTY-THREE METABOLIC-RELATED GENES PREDICTING OVERALL SURVIVAL FOR LUNG ADENOCARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors identified 24 metabolic-related genes predicting overall survival for lung adenocarcinoma (LUAD) by existing statistic methods in this paper. The method of this paper is not a new method, and the results are not exciting.
The authors identified the 24 metabolic-related genes by TCGA dataset with 445 samples, and verified the results by a GEO dataset with 83 sample? I think that the authors should add more independent datasets to verified the validation of the 24 metabolic-related genes.
The method section in this paper is not clear, and I suggest that the authors should re-write the method section and make the method thread clearly. A flowchart for calculation process can help reader to understand the method section of this paper.

The authors should explain some items in the paper, for example:
What’s the meaning of “logFC” in line 87?
The authors need explain the meaning of the “Coefficient” in line 92?
What kind of index is “C-index” in line 216?
What’s the meaning of “CoefficientmRNA1” and “CoefficientmRNA2”?


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

Input:
Title: A MODEL OF TWENTY-THREE METABOLIC-RELATED GENES PREDICTING OVERALL SURVIVAL FOR LUNG ADENOCARCINOMA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The language should be improved
Experimental design: Fair
Validity of the findings: Fair
Additional comments: The authors proposed 24 key  genes of LUAD , and then built the model based on these 24 genes. This is an interesting paper. However, there are some problems.
1. the authors applied survival curve to test the proposed genes. This is not enough. As the sample is limitted, the validatoins should be performed from different aspects.
2.Figure 4 is unclear.
3.The authors should compared their model with referencec.


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

Input:
Title: A MODEL OF TWENTY-THREE METABOLIC-RELATED GENES PREDICTING OVERALL SURVIVAL FOR LUNG ADENOCARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have addressed all of the comments/suggestions raised by the reviewers.


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

Input:
Title: A MODEL OF TWENTY-THREE METABOLIC-RELATED GENES PREDICTING OVERALL SURVIVAL FOR LUNG ADENOCARCINOMA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The MS has been well revised, and the authors' responds are satfified
Experimental design: OK
Validity of the findings: OK
Additional comments: The MS has been well revised, and the authors' responds are satfified