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: LOCALLY DEVELOPED MODELS IMPROVE THE ACCURACY OF REMOTELY ASSESSED METRICS AS A RAPID TOOL TO CLASSIFY SANDY BEACH MORPHODYNAMICS
Review round: 1
Reviewer: 2

Output:
Basic reporting: the submitted manuscript is based on a replication of a reasonably well accepted methodology (proposed by Haris et al 2011) for beach classification in the southeast region of Brazil
The paper is well written and has an adequate structure with a good presentation of the scientific question, presentation of data and a proper methodological approach.
Experimental design: The experimental design of the work was well performed, using methods of data collection and analysis compatible with the problem raised (see comments below)
Validity of the findings: The results bring important contributions on rapid beach classification methods from orbital image  platforms (i.e. google earth), which can become a useful tool for management and coastal conservation
Additional comments: Some important points can be raised so that the paper can be accepted for publication
A central point, in my opinion, is the title: although technically using the term 'remote sensing' to describe the process of measuring morphological and topological parameters of beaches is not incorrect, among the scientific community this term is applied when some level of image processing is employed in which spectral (or textural) information is extracted from the images. Using direct distance measurements from the "Google Earth" platform (in which several satellites are used indiscriminately) does not clearly indicate the use of "remote sensing" methods strictu sensu and may mislead the reader about the type of methodology used.
Another important point is that the paper neglects the dynamic aspect of the nature of beaches (and this is also a recurrent criticism of the work of Haris et al 2011 and others who use satellite images in beach classification). Measurements such as slope, wave frequency and surf-zone type are extremely dependent on dynamic conditions that may reflect very different short and long term climatic/oceanographic conditions (which are reflected in the characteristics of the beach profile), and by taking static measurements of these parameters into account, the classification models can yield significant uncertainty. Furthermore, there are other issues that must be raised as problems in the use of satellite images in beach characterization, for example the fact that image collection tends to be biased towards the synoptic characteristics of the beach profile (after all, satellite images are obtained under cloudless conditions, which are associated with fair weather).
In my opinion, the authors in addition to reproducing the methodology of Haris et al (op cit) and comparing the results (convergences and divergences) might consider addressing these issues and constructing a critical review, suggesting improvements and recommendations for improved accuracy and precision for future models that could take into account the morphodynamic aspects of the classification systems.


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 IDENTIFICATION OF XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE GENE FAMILY MEMBERS IN PEANUT AND THEIR EXPRESSION PROFILES DURING SEED GERMINATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this paper, Zhu and colleagues report a genome-wide survey of the Xyloglucan Endotransglucosylase/Hydrolase (XTH) gene family in peanut. The authors performed phylogenetic analysis, compared exon-intron structures, presented genomic distribution, conserved motifs, and analyzed gene expression profiles using publicly available transcriptome data of XTH family genes in peanut. Based on these analyses, the authors found that segmental and tandem duplications contributed significantly to the evolution of XTH proteins in peanut. Moreover, they identified a subset of XTH gene that might function in the seed germination process.
Although the subject of the manuscript fits well with the scope of PeerJ, the manuscript suffers from substantial weakness in several aspects in data analysis. Therefore, it must be subjected to major compulsory revisions prior to considering for possible publication.
Experimental design: The subject of the manuscript fits with the aim and scope of the PeerJ.
Validity of the findings: The analysis is generally sound and acceptable. Conclusions were drawn from the analysis.
Additional comments: Major revisions:
1. Only two species i.e. Arabidopsis and soybean were included in the phylogenetic analysis. Given that numerous plant genomes have already been sequenced to date, the authors are recommend to include several more representative species to clearly elucidate the evolutionary relationships among XTH genes in plants.
2. The authors only described how to define segmental duplication in the Materials and Methods section. However, they did not describe how to define the tandem duplication? It should be clarified what criteria were adopted to justify a tandem duplication.
3. The authors showed that one XTH gene usually had more than one paralogous genes originated from the segmental duplication. For example, AhXTH8 has three different paralogous pairs namely AhXTH20, AhXTH37, and AhXTH50 derived from segmental duplication. However, in the phylogenetic tree (Figure 3), it showed that AhXTH8 is most closely associated with AhXTH37. How to interpret these results? Is it consistent with the chromosomal duplication event during the evolution?
4. The authors detected several clustered XTH gene on the chromosome. They defined them into several paralogous pairs derived from tandem duplication. For example, they defined 5 paralogous pairs i.e. AhXTH3 vs AhXTH4, AhXTH3 vs AhXTH6, AhXTH3 vs AhXTH5, AhXTH4 vs AhXTH6, AhXTH5 vs AhXTH6, for one cluster of XTHs. The same situation also applied to AhXTH29-AhXTH34. Since no criteria were described in defining the tandem duplication as I have mentioned above, these analysis seems questionable.
5. The authors predicted the regulatory elements of hormone signaling in the promoter region of AhXTH genes (Supplementary Figure 1). These results should not be presented in the Discussion section, it should be presented in the Results section wherever is appropriate.
6. To verify their conclusions drawn from the expression analysis and clarify its functional roles, the authors should selected at least one gene to study its functional roles by transforming into Arabidopsis null mutant and/or wild type.
7. The language of the manuscript needs substantial improvement as there are numerous improper descriptions throughout the manuscript. In addition, the manuscript should be critically revised by a native English speaker to eliminate the grammar errs and improper wording.

Minor revisions:
1. No scale bar was provided for chromosome length in Figure 1
2. Segmental duplication was most frequently used throughout the manuscript. However, fragment duplication was occasionally used, it should be unified in description
3. Subfamily I/II was not marked in Figure 3. Bootstraps lower than 50 was not recommend to display at the branch.
4. The gene names in Figure 5 should be italic. Genes with no expression values at FS, DS and GS stages should be excluded in the analysis.


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 IDENTIFICATION OF XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE GENE FAMILY MEMBERS IN PEANUT AND THEIR EXPRESSION PROFILES DURING SEED GERMINATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript meets most of the basic reporting.
Experimental design: Experimental design well planned and executed.
Validity of the findings: Findings are valid. However, some comments are to be addressed.
Additional comments: •	Can qRT-PCR for a few specific genes be considered as transcriptome analysis?
•	Clearly mention how many genes were considered for expression analysis.
•	Was there any effort made to check for primer efficiency and melting curve analysis?
•	Structural analysis of the homologous AhXTH genes has been partly presented. More importantly, the sequence similarity among the homologs can be indicated along with the relevance.
•	More analysis on the function of AhXTH genes would be useful. The DNA tagged mutants of Arabidopsis can be considered to gain more knowledge on the function.
•	Care should be taken to italicize the scientific names and maintain consistency in the main body.


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 IDENTIFICATION OF XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE GENE FAMILY MEMBERS IN PEANUT AND THEIR EXPRESSION PROFILES DURING SEED GERMINATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have responded to all of my concerns raised in last review. Now, the manuscript can be accepted pending minor revisions as follows:
1. There are still some typos and format errors in the manuscript. For instance, Circos instead of Circus, bar instead of ber etc; gene names in Figure 5 should be italic; the naming of promoter:GUS transgenic lines in Figure 7 should be the same as in the text. Pod should be silique for Arabidopsis.
2. The descriptions of figure legend for Figure 7 were not provided in detail. What does the positive control refer to ?
3. The hypocotyl length of Col-0 and AhXTH4 complemented lines in Figure 8 should better be quantitatively measured and present in a Bar graph.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: GENOME-WIDE IDENTIFICATION OF XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE GENE FAMILY MEMBERS IN PEANUT AND THEIR EXPRESSION PROFILES DURING SEED GERMINATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: This study reports genome-wide identification of xyloglucan endotransglucosylase/hydrolase gene family members, their structural and functional characterization and expression profiles during seed germination in peanut. In total, 58 AhXTH genes were identified.
Line # 146: "If two sequences shared over 70% identity and covered over 70% of their sequences, then they were considered to be homologous genes and to have collinearity.". Please provide a reference.
Naming of the members of XTH genes can be revised to make them uniform and clear.
It is interesting to know their distribution on A and B genomes and the extent of homeologous nature of these genes. Of them, 26 AhXTH genes high-level expression during seed germination. Probable function of the remaining 32 AhXTH genes may be provided in the Results.
Promoter analysis and ectopic expression analysis indicated the functional roles of the selected AhXTH genes.
Line # 197: Promoter of 2000 bp was isolated by PCR. Kindly give the details on the PCR. Also tell about delimitting the promoter region.
The details on the RT-PCR like PCR efficiency, melting curve analysis, fold changes etc may be useful for the readers.
Kindly provide the collinearity between the results of RNA-Seq and RT-PCR.
The English language should be improved to ensure that an international audience can clearly understand your text. Some examples where the language could be improved include Line # 40, 113, 115-116, 127, 226 etc
Experimental design: See the above comment
Validity of the findings: See the above comment
Additional comments: See the above comment


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

Input:
Title: A NEW PERLEIDID NEOPTERYGIAN FISH FROM THE EARLY TRIASSIC (DIENERIAN, INDUAN) OF SOUTH CHINA, WITH A REASSESSMENT OF THE RELATIONSHIPS OF PERLEIDIFORMES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript in review is a sound and concise description of a new perleidid species. It is based on well preserved material. I have made some minor corrections in the manuscript.

The presence of a postspiracle (267ff) seems to be somewhat erratic. If it is the first appearance in the perleididae, it should be shown in the reconstruction (fig. 7).

389-390: Peltopleurus nitidus formed a sister group with Peltopleurus nitidus …should be Peltopleurus tyrannos

396ff: the monophyly of the Perleididae is based on two synapomorphies of difficult value: in my opinion the mentioned character states are somewhat shaky due to morphological plasticity (see presence/absence of postspiracle).
Experimental design: The phylogenetic analysis seems to be consistent, but see my comment on above mentioned synapomorphies.
Validity of the findings: The drawings and illustrations are well done and support the descriptive part, as well as the conclusions.
Additional comments: The description of this new perleidid species provides new and interesting data on this important fossil fish family and is a valuable contribution to our understanding of it.


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 PERLEIDID NEOPTERYGIAN FISH FROM THE EARLY TRIASSIC (DIENERIAN, INDUAN) OF SOUTH CHINA, WITH A REASSESSMENT OF THE RELATIONSHIPS OF PERLEIDIFORMES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is well written, clear, unambiguous, technically correct. Literature and background context are correctly provided. Article structure, figures and tables are correctly provided and shared. The manuscript is an important study about a new taxon from the Early Triassic of South China that might have the potential to improve our understanding on the evolution of neopterygian fishes after the Permo-Triassic extinction. However, the manuscript is affected by several issues that must be necessarily considered before re-submitting the manuscript. Based on comments below and in the attached pdf, I suggest MAJOR REVISIONS.
Experimental design: This is an original research, questions are well defined. However, the research lacks of rigorous investigation and several statements are unsupported. See below.
Validity of the findings: The manuscript is an important study about a new taxon from the Early Triassic of South China that might have the potential to improve our understanding on the evolution of neopterygian fishes after the Permo-Triassic extinction. However, the manuscript is affected by several issues that must be necessarily considered before re-submitting the manuscript. Based on comments below and in the attached pdf, I suggest MAJOR REVISIONS.

1)	The authors report the following combination of characters to diagnose the new genus (and species): A new species of Perleididae distinguished from other members of this family by the following features (autapomorphies identified with an asterisk): presence of postspiracle (*); presence of three supraorbitals; presence of two infraorbitals; six pairs of branchiostegals rays; relative deep anterodorsal process of subopercle; the lacrimal separated from maxilla; the nasals don’t contact with each other; the width of posttemporal is half of the width of extrascapular; presence of epaxial procurrent rays; pterygial formula of D26/P14, A22, C36/T39-41 (*).
Although the new taxon described likely represent a new species, the combination of characters used to diagnose Guiyangichthys elegans coincides exactly (or is within the morphological and meristic ranges) with that of the genus Teffichthys Marramà et al., 2017, created on articulated material from Early Triassic of Madagascar. In particular:
•	   Spiracular ossicles are diagnostic of Teffichthys (Marramà et al. 2017), so it cannot be considered as an autapomorphy of this new taxon. These bones are present in all the other early Triassic Teffichthys species, and also in some "paleoniscoid" fishes (although their homology must be still detected). The authors repeatedly ignore in the text that this bone (spiracle, postspiracle, spiracularis, or spiracular) has been used to diagnose Teffichthys, so it is not the first time it appeared in Perleididae (if also Teffichthys must be considered a Perleididae). This bone is indicated in literature with several (similar) names, but since the position of this bone is the same in Peltopleuriformes, Teffichthys, and the taxon described herein, it is likely these bones are homologous in all these taxa. Conversely, it is unclear if the spiracle of paleoniscoids is homologous. The presence of this bone in Teffichthys must be therefore coded in the phylogenetic analysis as present.
•	    Also the presence of three supraorbitals; two infraorbitals; six pairs of branchiostegals rays (used to diagnose Guiyangichthys, are within the range of the genus Teffichthys !!!  although these numbers vary among the other Early Triassic species (T. lehmani, T. lutoensis, T. stoschiensis, T. woodwardi). Variation among the different species occurs also in the squamation formulae.
•     	The same can be said for many other features used to diagnose Teffichthys and characterizing “Guiyangichthys” elegans, including: a body elongate and tapered; dermal cranial bones ornamented with tubercles or ridges; parietal pit-lines (anterior, median and posterior); posttemporals separated; suborbital and spiracular ossicles present; two to five supraorbitals; nasals separated by the rostral; maxilla fixed to an almost vertical preopercle; nearly straight oral margin of maxilla, which is dorso-posteriorly expanded; jaws with styliform teeth; broad vertical or slightly forward inclined preopercle; opercle smaller than subopercle; five to eight branchiostegal rays; dorsal and anal fins inserted in the posterior half of the body; median-fin rays only distally segmented and supported by an equal number of pterygiophores at least in the middle part; fringing fulcra present on all fins; abbreviated heterocercal caudal fin; anteriormost lateral trunk scales higher than wide, with serrated posterior margin.
•	     For these reasons, the creation of a new genus is unsupported, being all these characters within morphological and meristic ranges of Teffichthys. However, since the combination of meristic and morphological character is different from those of the other Teffichthys species recognized so far, the new taxon can be considered a new species of Teffichthys (T. elegans).

2)	Another main problem is the question about the epaxial rays. This terminology has been clarified several times in the literature, but the authors have ignored it. “Epaxial rays" are PRINCIPAL caudal-fin rays (not procurrent rays!! ) positioned dorsal to the notocord (or to the upper caudal fin). This is the original definition sensu Hutchinson 1973; Gardiner & Schaffer 1989; Gardiner 1988; Tintori 1990 (see also Lombardo 2001 for references), that several authors continue to misinterpret or ignore since Stansio (1929). Lombardo (2001) and subsequent authors have clarified this concept, but several authors still misinterpret EPAXIAL PRINCIPAL CAUDAL-FIN RAYS with epaxial procurrent rays.
In this perspective, based on the original definition of “epaxial caudal fin rays”, the new taxon described herein HAS NO epaxial PRINCIPAL caudal fin rays (but just some procurrent rays) dorsal to the upper caudal fin lobe. Therefore, the statement of Ma et al (2021) reported by the authors at lines 99-100 must be considered wrong because Teffichthys HAS NO epaxial principal caudal- fin rays. This would even better support the relationship between T. madagascariensis and the new species described herein.
For these reasons, statements and coding in the matrix for characters 112 and 113 must be changed for the new taxon, Teffichthtys madagascariensis, Plesioperleidus  yangtzensis and for all the other taxa in which the authors considered these procurrent rays as “epaxial rays”.

3)	The authors cannot remove Hydropessidae and Gabanellidae from the order Perleidiformes without testing their phylogenetic relationships. The phylogenetic analysis the authors performed does not include Hydropessum nor Gabanellia. For this reason, their statements at lines 30-33, 411-413, and 507-508, are not supported by data. Remove the statements or include these two taxa in a new phylogenetic analysis to see the validity of the statements.

Moreover, the authors stated that these two taxa cannot be included in their phylogeney because of the poorly preserved material. However, Gabanellia has been erected by Tintori & Lombardo (1996) based on well preserved articulated and nearly complete material. A complete description of Hydropessum with high quality images was provided by Hutchinson (1973). Therefore their statement about the poorly preserved material is not supported. Again, please include Gabanellia and Hydropessum, and test their relationships, or remove these statements.
See:
Hutchinson 1973. A revision of the redfieldiiform and perleidiform fishes from the Triassic of bekkers kraal south africa and brookvale new-south-wales.
Tintori & Lombardo 1996) Gabanellia agilis gen. n. sp. n., (Actinopterygii, Perleidiformes) from the Calcare Di Zorzino of Lombardy (North Italy). Riv It Paleontol Stratigr 742: 227-236.

4)	I would suggest at this point to provide an emended diagnosis of the family Perleididae, because the two characters (the preopercle process length of dermohyal nearly being half the length of the anterodorsal process of the preopercle, and the anteroventral corner of the preopercle being nearly the same horizon as the ventral end of opercle) are just those supporting the monophyly of the family in the phylogenetic analysis. An emendation of the diagnosis of the family is therefore needed.

5)	PHYLOGENETIC ANALYSIS. Using the same parameters stated in Material & Methods with TNT I got a less resolved Strict consensus tree than that depicted in Figure 10. A similar tree to that in Figure 10 can be obtained only as 50% Majority Rule tree, or, alternatively, without saving multiple trees (multiple trees saved OFF). In any case, I got the same tree topology using different states for Teffichthys (epaxial rays absent, and postspiracular present). Teffichthys is still sister to "Guiyangichthys" elegans therefore suggesting that the absence of epaxial rays in Teffichthys does not affect the tree topology.

I would also suggest to include a new character that might give you further grouping information: the caudal fin type: [0] true heterocercal (e.g. paleonisciforms’); [1] abbreviated heterocercal (e.g. Teffichthys); [2] symmetrical heterocercal (e.g. Perleidus); [3] homocercal (Teleostei). ( you might try also to group states 1 and 2 in a single state)

6)	The reconstruction of the skull at Figure 7 does not show the spiracular bones. Please indicate these bones.
Additional comments: I hope that the authors will consider these suggestions. I look forward to see a revised version of the paper.


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 PERLEIDID NEOPTERYGIAN FISH FROM THE EARLY TRIASSIC (DIENERIAN, INDUAN) OF SOUTH CHINA, WITH A REASSESSMENT OF THE RELATIONSHIPS OF PERLEIDIFORMES
Review round: 1
Reviewer: 3

Output:
Basic reporting: Although the ms is mostly well written and understandable, there are several language errors (choice of word, sentence structure, missing or superfluous words, past/present tense, punctuation). I highlighted them in the annotated pdf. Authors must do a language check by a native speaker before resubmission.

In addition, some sentences in the description are not fully clear. Authors must ensure that their major findings are clear and understandable. Several sentences are very long and is is difficult to follow. Authors should try to shorten sentences and make sure their main points are easily understood by readers.

Some citations in the text lack references. Some references are not cited in the text. Authors must check their references carefully before resubmission.

The order of subchapters could be improved. I think after the description a thorough discussion of the morphology of Guiyangichthys is most logical, including a comparison with other perleidiforms and early neopterygians. After that, the phylogenetic analysis should follow. This would be more logical as the authors must first clearly establish the validity of their new taxon before analysing its phylogenetic position. Morphological comparisons between Guiyangichthys, Paraperleidus, etc. can be better supported by adding a figure with their reconstructed skulls (or whole skeleton), and highlighting differences and similarities.

The palaeogeographic maps contain some errors, which need to be addressed. Figure captions are very brief. They should be expanded with all necessary information about each specimen. Figures with labelled skeletal parts should ideally contain the legend in the caption, which makes it easier to read them.

Methods section should include comparative material. For comparisons, authors could also consider publishing figures of comparative specimens to support their arguments (i.e. epaxial rays of Teffichthys).

Since the holotype is preserved in 3D, did the authors consider to ct scan the specimen? The new taxon is mainly described based on external features. With ct data, the endocranial morphology could be described, and the importance of the paper could be further increased. If ct scans of the specimen proved not useful, authors should mention this in their ms.

Regarding other comments, please check the annotated pdf.
Experimental design: No further comment here. The description should partly be expanded to better characterize this new taxon.
Validity of the findings: This is a new taxon of perleidid fish, a group of high interest for the study of early neopterygian phylogeny. The material is well-preserved and adds to our knowledge of ealry perleidids. The analyses are sound.
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: A NEW PERLEIDID NEOPTERYGIAN FISH FROM THE EARLY TRIASSIC (DIENERIAN, INDUAN) OF SOUTH CHINA, WITH A REASSESSMENT OF THE RELATIONSHIPS OF PERLEIDIFORMES
Review round: 2
Reviewer: 1

Output:
Basic reporting: Due to the substantial and thorough remarks of the two other reviewers the paper of Yuan et al. improved substantially. I have read their responses to the reviewers comments and it’s in my opinion, that the paper can be published now.
Experimental design: no comment
Validity of the findings: see 1.
Additional comments: On the second version of the manuscript I have only one comment: On figure 10 the drawings of the four different head reconstructions should be labeled according to the text of the figure: A, B, C, D.


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 PERLEIDID NEOPTERYGIAN FISH FROM THE EARLY TRIASSIC (DIENERIAN, INDUAN) OF SOUTH CHINA, WITH A REASSESSMENT OF THE RELATIONSHIPS OF PERLEIDIFORMES
Review round: 2
Reviewer: 2

Output:
Basic reporting: I really appreciated that my suggestions from the first review were taken into account. The manuscript is now almost ready to be accepted. Only minor revisions are still needed:
1)  Use the correct terminology for phylogenetic analyses. There is no  "at the top" or "at the bottom" in a phylogenetic tree ! You may say Perleidus is recovered sister to... or as the basalmost taxon within the Perleididae but there is no top, bottom, further up, further down...Please use correct terminology.
2) In character comparisons and throughout the ms the caudal fin pattern of Perleidus and Teffichthys needs to be discussed in more detail, as it is very different in the two genera. Please compare the caudal fins described in Lombardo (2001) and Marramà et al. (2017).
3) A further proofcheck is needed, as the technical terminology must be enanched, and grammar or synthax can be improved. Some suggestions and corrections are included within the pdf attached but please check again introduction and description.

Dr. Giuseppe Marramà, PhD
Experimental design: No other comments needed.
Validity of the findings: Findings and the whole research are now valid.
Additional comments: No other comments needed.


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

Input:
Title: A NEW PERLEIDID NEOPTERYGIAN FISH FROM THE EARLY TRIASSIC (DIENERIAN, INDUAN) OF SOUTH CHINA, WITH A REASSESSMENT OF THE RELATIONSHIPS OF PERLEIDIFORMES
Review round: 2
Reviewer: 3

Output:
Basic reporting: The manuscript has improved after the first round of review.

There are a few language errors (highlighted in the annotated pdf).

Some paragraphs are poorly referrenced. Authors must cite sources when discussing similarities or differences between T. elegans and other taxa, or refer to the Supplementary File if applicable. See annotated PDF. In addition to the differences of T. elegans with other closely related taxa, authors should also briefly discuss similarities with T. elegans, as well as Teffichthys/Perleidus stoschiensis and Teffichthys/Perleidus woodwardi. This is important to better support the validity of the Chinese species. Figure 10 looks nice!
Experimental design: No further comments necessary
Validity of the findings: No new comments necessary
Additional comments: No further 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: A NEW PERLEIDID NEOPTERYGIAN FISH FROM THE EARLY TRIASSIC (DIENERIAN, INDUAN) OF SOUTH CHINA, WITH A REASSESSMENT OF THE RELATIONSHIPS OF PERLEIDIFORMES
Review round: 3
Reviewer: 1

Output:
Basic reporting: The terminology of some bones, particularly the suborbitals, spiracular and postspiraculars, needs to be better addressed. The authors indicate two suborbitals in Teffichthys, but Marramà et al. indicate one suborbital and one spiracular (this latter seems identify as suborbital by the Yuan et al.  Please clarify this and check all descriptions of these bones and reconstruction figures.
Moreover, you have to modify the caption for Figure 10, because A is Teffichthys madagascariensis, not Meidiichthys brown (which is C). Moreover, the spiracular of Teffichthys madagascariensis is indicated as suborbital. Please check carefully all bone abbreviations.
Once the authors solved these minor revisions the paper can be published as it is.
Experimental design: OK
Validity of the findings: OK
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: A NEW PERLEIDID NEOPTERYGIAN FISH FROM THE EARLY TRIASSIC (DIENERIAN, INDUAN) OF SOUTH CHINA, WITH A REASSESSMENT OF THE RELATIONSHIPS OF PERLEIDIFORMES
Review round: 3
Reviewer: 2

Output:
Basic reporting: No further comments.
Experimental design: No further comments.
Validity of the findings: No further comments.
Additional comments: I am satisfied with the additions and corrections.


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 POTENTIAL, ANALYSIS AND PROSPECT OF CTDNA SEQUENCING IN HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Please see my additional comments.
Experimental design: Please see my additional comments.
Validity of the findings: Please see my additional comments.
Additional comments: The manuscript entitled “The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinoma” by Yubo Ding et al. investigated that gene mutations using circulating tumor DNA (ctDNA) of 10 patients with hepatocellular carcinoma. They sequenced 560 cancer-related genes and compared their results with the cosmic database. This study is of potential clinical significance with some issues.
1.	The two metastatic samples did not originate from hepatocellular carcinoma. They are metastatic tumors from gallbladder cancer and rectal cancer. Therefore, the statement of “2 cases of metastatic hepatocellular carcinoma” needs revising to avoid confusion.
2.	The manuscript can be improved by moderate English and formatting editing. For example, “According to the global cancer statistics report in 2018, there are 841000 new liver cancer patients and 781000 deaths, accounting for 4.7% and 8.2% of the total cancer Morbidity and Mortality: in the world respectively”, “we found that 6 gene loci (PREX2, ZFHX3, FHIT, CAMTAL, GPHN and SND1) in the high frequency gene did not find mutation sites”, “FOXP1 did not find mutation site, only gene mutation occurred in primary liver cancer, and the specificity was relatively high in the diagnosis of liver cancer”, and “The pathway enrich of is applied to making pathway annotations”.
3.	The resolution of Figure 1 needs improving.
4.	The paragraph describing pathway analysis in text line 236 was misplaced. It should be under the subtitle “Go notes on the filtered pathogenic genes and possible pathogenic genes”.
5.	What is the interpretation of GO annotations of pathogenic genes? How are they related to pathogenesis of hepatocellular carcinoma?
6.	The description of Figure 3 were extremely succinct. What is the interpretation? What is the indication of “44 nodes and 143 edges”? Authors should elaborate and discuss.
7.	The conclusion and significance of this study are overstated.
1)	The study only sequenced 10 patients with hepatocellular carcinoma in one city of China, so it cannot provide “the gene mutation map of Chinese patients with liver cancer”.
2)	Are the pathogenic mutations detected by ctDNA sequencing associated with patients’ treatment response, clinical stage, or prognosis? Are the mutations enriched in cancer samples compared to normal tissues? Without these data, authors cannot “confirms that ctDNA can be used for sequencing, and enriches the understanding of the pathogenesis of HCC” or “identified some new mutation gene sites and screened some genes which are of significance for the diagnosis and prognosis of liver cancer”.
3)	With only one sample for each cancer, it cannot be concluded that “KMT2C/TP53 may be related to the development of gallbladder cancer / rectal cancer. KMT2C may be used as a reference gene for the diagnosis of gallbladder cancer, and TP53 is a reference gene for the diagnosis of colorectal cancer”.


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 POTENTIAL, ANALYSIS AND PROSPECT OF CTDNA SEQUENCING IN HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The title and abstract appropriately reflect the main aspect of the work. The methods are clear and replicable. However, the  samples size may be too small.
Experimental design: Experimental design meet the standards。
Validity of the findings: The final data is plausible but the results are not novel and unlikely to be of interest to readers.
Additional comments: There is need for checking grammar.


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 POTENTIAL, ANALYSIS AND PROSPECT OF CTDNA SEQUENCING IN HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The English language should be improved by a fluent speaker to ensure that an international audience can clearly understand your text. Some examples where the language could be improved include results (lines 196 to 206), conclusion part (lines 319 to 329) et al– the current phrasing makes comprehension difficult.
Figures are not well labelled and illustrated with poor resolution quality.
Experimental design: (1)	A diagram was better than text to show the study design.
(2)	Since HBV infection is closely related to the pathogenesis of primary hepatocellular carcinoma, is there any association on gene mutation spectrum with/without HBV infection?
(3)	To confirm ctDNA could be used for sequencing, it is important to find proper controls such as tumor tissue samples. Or it would be clinical significance if there is correlation between gene spectrum with clinical-pathological parameters. Otherwise, it is not meaningful to just list out all the mutations by sequencing.
(4)	The results part is long and not comprehensively. Since there are 8 patients with primary hepatocellular carcinoma and 2 patients with metastases liver cancer, it would be better to compare spectrum of Mutations of high-frequency mutations between those two groups.
Validity of the findings: Improvement in next-generation sequencing technology and better understanding of genetic or epigenetic alteration of primary hepatocellular carcinoma have allowed comprehensive analysis of mutational landscape of ctDNA. Hotspot mutation panels have both shown promising performance which have been validated in current study as well. But none of these tests including current study have yet been validated. More large-scale tests in longitudinal cohorts are needed for preclinical detection of liver cancers.
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 POTENTIAL, ANALYSIS AND PROSPECT OF CTDNA SEQUENCING IN HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Authors have successfully responded to my comments.
Experimental design: None.
Validity of the findings: None.
Additional comments: None.


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 POTENTIAL, ANALYSIS AND PROSPECT OF CTDNA SEQUENCING IN HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The English language should be improved by a fluent speaker to ensure that an international audience can clearly understand your text. Some examples where the language could be improved include abstract (lines 36 to 37, 60 to 61), introduction part (lines 79 to 80), result part (lines 278 to 281) et al– the current phrasing makes comprehension difficult.
Table text should be labelled & described clearly. For example, the patient groups should be labelled as primary, metastasis et al in Table 1.
Experimental design: Ding et al investigated the gene mutation spectrum of ten patients with liver cancer in blood using 560 cancer-related gene panel by next generation of targeted sequencing technology. They compared gene mutation spectrum in patients with primary or secondary liver cancer, filtered pathogenic mutations, drew gene pathway network, and analyzed impacts of relevant genes on survival using data from public database. Their work is of clinical value and provides insights and novel contributions to the potential utility of ctDNA in diagnosis and management of liver cancer. Yet current study needs to be revised to be more concisely and straightforward throughout the result and discussion.
Validity of the findings: Improvement in next-generation sequencing technology and better understanding of genetic or epigenetic alteration of primary hepatocellular carcinoma have allowed comprehensive analysis of mutational landscape of ctDNA. Hotspot mutation panels have both shown promising performance which have been validated in current study as well. The survival analysis from GEPIA and HPA database have improved the significance of current study.
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 POTENTIAL, ANALYSIS AND PROSPECT OF CTDNA SEQUENCING IN HEPATOCELLULAR CARCINOMA
Review round: 3
Reviewer: 1

Output:
Basic reporting: The authors have addressed my questions nicely and provided sufficient data to support conclusions.
Experimental design: The primary research falls within the journal and research question is well defined. Yet there has been no effective treatment to HCC so far and current study could provide limited insights into clinical practice.
Validity of the findings: The authors provided sufficient data and the conclusion is well stated in the revised version.
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: FIRST RECORDS OF EXTINCT KENTRIODONTID AND SQUALODELPHINID DOLPHINS FROM THE UPPER MARINE MOLASSE (BURDIGALIAN AGE) OF SWITZERLAND AND A REAPPRAISAL OF THE SWISS CETACEAN FAUNA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript "First records of extinct kentriodontid and squalodelphinid dolphins from the Upper Marine Molasse (Burdigalian age) of Switzerland and a reappraisal of the Swiss cetacean fauna" by Aguirre-Fernandez et al. represents an interesting addition to our knowledge of the fossil record of toothed whale in the circum-Mediterranean region. The authors described seven periotics from the Swiss Upper Marine Molasse and revised the previous taxonomic assignment of the specimens. The description is based not only on the external characters but also on the internal characters by using micro CT scan. I suspect that this paper will be widely received by people interested in the evolution of cetaceans.
Experimental design: No comments
Validity of the findings: No comments
Additional comments: I have some comments that I think would improve the paper, but none of them are critical. I annotated the pdf file of the manuscript for the revision. Please see attached file of the annotated manuscript.

My main concern is on the following two points:
1) Lines 115-134: Taxonomical assignment to the Squalodelphinidae
The authors mentioned that "The prominent anterior bullar facet with well-defined medial and lateral boundaries is a diagnostic character also present in other squalodelphinids" (lines 121-122). But, this morphological character is also found in other group of odontocetes (e.g., eurhinodelphinids). The authors also mentioned that "The tuberosity in the posteromedial part of the anterior process is also present in Huaridelphis raimondii....and other squalodelphinids" (lines 123-126). But, as mentioned by the authors, the character is also found in another group of odontocetes. The authors also mentioned that "Some putative family-diagnostic characters...are absent in NMBE5023942" (lines 127-129). So, the reason why the authors diagnose the specimens as Squalodelphinidae remains unclear.

Please state on the characters suggesting that the specimens belong to the Squalodelphinidae. Perhaps, previous papers (e.g., Muizon, 1987; Kimura, 2018) discussing on the combination of the morphological characters in the periotic of the Squalodelphinidae might be help.

Muizon, C. de. 1987. The affinities of Notocetus vanbenedeni, an Early Miocene Platanistoid (Cetacea, Mammalia) from Patagonia, Southern Argentina. Novitates 2904:1-27.
Kimura, T. (2018). First squalodelphinid from the early Miocene of the Pacific realm in the Northern Hemisphere. Journal of Vertebrate Paleontology, 38(4). DOI: 10.1080/02724634.2018.1493595.

2) Lines 90-94 and 202-205: Intraspecific variation of the periotic in Kentriodon
Barnes and Mitchel (1984) discussed on the intraspecific variation of the periotic in Kentriodon based on a large number of the periotic from the Sharktooth Hill Bonebed. The paper might provide an insight on the interpretation of the morphological variations found in the studied specimens.

Barnes, L. G., and E. Mitchell. 1984. Kentriodon obscurus (Kellogg, 1931), A fossil dolphin (Mammalia: Kentriodontidae) from the Miocene Sharktooth Hill Bonebed in California. Natural History Museum of Los Angeles County, Contribution in Science, 353:1-23.


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: FIRST RECORDS OF EXTINCT KENTRIODONTID AND SQUALODELPHINID DOLPHINS FROM THE UPPER MARINE MOLASSE (BURDIGALIAN AGE) OF SWITZERLAND AND A REAPPRAISAL OF THE SWISS CETACEAN FAUNA
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: This interesting paper describes and places into geologic context the cetacean material available from several Swiss collections. It has the added bonus of measurements and descriptions based on CT scans and extracted cochleae of the periotic material, which contributes additional important natural history data for the specimens. Overall this paper is great as is, and I only have minor comments and edits that can be seen in the attached annotated PDF. I do think an introductory figure with a basic composite phylogeny containing the cetacean groups that are covered would place the work into even better evolutionary context for readers unfamiliar with extinct cetacean phylogenetic relationships, but it's not necessary.

With best regards,
Dr. Rachel Racicot


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: FIRST RECORDS OF EXTINCT KENTRIODONTID AND SQUALODELPHINID DOLPHINS FROM THE UPPER MARINE MOLASSE (BURDIGALIAN AGE) OF SWITZERLAND AND A REAPPRAISAL OF THE SWISS CETACEAN FAUNA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The paper is very well written.
Experimental design: See below.
Validity of the findings: Acceptable; though I do have some questions about some of the identifications. See below.
Additional comments: This new study by Aguirre-Fernandez et al. re-describes a modest assemblage of cetacean earbones from the late early Miocene Upper Marine Molasse of Switzerland. This assemblage was previously reported by Pilleri (1986A/B). Pilleri was an enthusiastic and prolific cetologist but contemporary paleocetology has developed more refined standards for descriptions and figures, leaving many of his studies wanting. Therefore, contemporary redescription of this assemblage with updated figures is most welcome. In addition to reporting the external morphology of these earbones, the authors also CT-scanned the bony labyrinths of these specimens. This is remarkable, as this is the first time CT analysis of periotics has been reported for an entire odontocete assemblage; typically analyses focus on the adaptations and ecology of an individual species or are included in a wider morphofunctional analysis of hearing/balance adaptations across cetaceans. This assemblage based approach is novel and provides further ecological insight into Burdigalian-age cetaceans from the molasse of Switzerland. Altogether the paper is a competent advance in the study of Miocene cetaceans and I recommend minor revision. I have made some critical suggestions below. Sincerely, Robert W. Boessenecker, Ph.D., College of Charleston, South Carolina, USA
I am surprised by the apparent absence of eurhinodelphinids – however, I can’t help but notice that NMBE 5023943 looks a bit like one and doesn’t particularly look similar to any named squalodelphinids. In early Miocene assemblages of periotics from South Carolina, there is admittedly a smooth gradient of periotic morphotypes between eurhinodelphinids and waipatiids; indeed, Bianucci et al. (2011) reported some supposed waipatiid periotics that, to me, have some similarities with eurhinodelphinids. Likewise, I would compare both of these figured specimens with the waipatiid periotics from Malta figured by Bianucci et al.
In the conclusion, various morphotypes are mentioned; I could not easily find reference to these in the descriptions, though the description hints at some disparity within the kentriodontid sample. If there are several morphotypes, some more descriptions, comparisons, and commentary is certainly warranted. The different morphotypes ought to be clearly indicated/labeled in the figures.
OMM: Since the current paper is written in English, perhaps SUMM or UMM is a better acronym for the Swiss Upper Marine Molasse.
Lastly, while I appreciate that some paleocetologists prefer not to identify periotics past the family level (e.g. Hiroto Ichishima), I think that perhaps more can be done. Are any of these periotics referable to existing genera, either as “Genus sp.” or “cf. Genus”? For example, it seems as though the authors consider some of the kentriodontid specimens to be referable to Kentriodon proper.
Line 43: perhaps indicate what marine basins (e.g. Mediterranean, Paratethys; others?) are included within the circum-Mediterranean region.
Line 70: Some teeth can be identified to the family level, and occasionally genus level, especially for heterodont dolphins (e.g. Squalodon), and even squalodelphinids and some kentriodontid taxa have distinctive teeth. I suggest some additional attention be given towards teeth, even if not as informative as periotics.
Lines 103-104: what features in particular compare well with Kentriodon spp.?
Line 108: “remains undescribed” (since Kentriodon pernix is singular)
Figures: A figure showing the stratigraphy would be greatly informative, and noting the stratigraphic position of specimens reported within.
Tables: perhaps a table with a faunal list (including additions/revisions made to original faunal list by Pilleri) would be informative.


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: FIRST RECORDS OF EXTINCT KENTRIODONTID AND SQUALODELPHINID DOLPHINS FROM THE UPPER MARINE MOLASSE (BURDIGALIAN AGE) OF SWITZERLAND AND A REAPPRAISAL OF THE SWISS CETACEAN FAUNA
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 made all of my suggested changes and the manuscript is looking great! I only have some minor suggestions for improvement.

Lines 40-41: wording is a little unclear ‘has become isolated in many odontocetes’ – suggest rephrasing to ‘isolated from the skull’

Line 50: portrays = takes (?)

Line 50: Fig 2 sentence start – suggest rephrase to reference the figure in the context of an explanation, e.g., ‘Families present are xyz (Fig 2)

Fig 2: The figure is great; I love the use of silhouettes. It could take up about half the space, however, i.e., the tree branches could be about half the length that they are since the goal is to show the relationships.

Line 78: ‘annd’ = and

Line 127: a period is missing

Lines 150–152: It would be good to specify which ones have larger lengths

Fig. 7: The tree here could also take up slightly less space if branch lengths are not being shown.

Line 202: ‘th’ = the

Line 260: ‘by the eastern coast’ = ‘on the eastern coast’


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: FIRST RECORDS OF EXTINCT KENTRIODONTID AND SQUALODELPHINID DOLPHINS FROM THE UPPER MARINE MOLASSE (BURDIGALIAN AGE) OF SWITZERLAND AND A REAPPRAISAL OF THE SWISS CETACEAN FAUNA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The article is still very well-written.
Experimental design: I am still impressed with the approach; I cannot recall if the authors coded their periotic specimens into a matrix in the original manuscript, but this is an excellent - if laborious - method to confirm family level identifications for odontocete periotics - it's one I've considered for my own study of a large assemblage of isolated periotics from the southeastern USA, so I'm pleased to see it being put into place here.
Validity of the findings: I'm still a little skeptical of the assignment of the two periotics to Squalodelphinidae. The authors have pointed out a couple of features - but also note some squalodelphinid features lacking. A long anterior process is present in some squalodelphinids like Notocetus, but also characterizes most eurhinodelphinids; a dorsally opening, and large aperture for the cochlear aqueduct is also present in eurhinodelphinids like Schizodelphis (e.g. Benoit et al., 2011: fig. 5; Geobios 44:323-334). The ventrally deflected anterior process in 5023942 closely resembles eurhinodelphinid periotics from the Lee Creek Mine as well as Xiphiacetus cristatus. Many of the features found in your specimens can be seen in "waipatiid" periotics from Malta as I previously pointed out. Also: what about the trace of the anteroexternal/parabullary sulcus? If memory serves, that's been pointed out as a useful feature to distinguish between eurhinodelphinids, squalodelphinids, and waipatiids by Lambert, Muizon, and Tanaka in the past.

I'm not trying to be nitpicky here; there are loads of strange, difficult-to-identify but at present unpublished specimens that blur the lines between some of these groups - and it would of course be unfair to cite these. I just think the text needs a little more justification in the following specific areas:

1) Note that some of these features show up in other clades (e.g. deep anterior bullar facet, dorsally opening cochlear aqueduct); 2) these periotics are missing some squalodelphinid features (rectangular pars cochlearis; 3) make some brief comparisons with the similar-looking supposed waipatiid periotics reported by Bianucci et al. 2011 from coeval rocks in Malta; and 4) please label the articular rim in figure 5. In 5023942 it looks to be present but small and in 5023943 it is not apparent at all (perhaps damaged like the posterior process, and admittedly not mentioned in the text, perhaps accordingly).

Also, Fordyce 1994 could be cited on line 142 - he also discussed this tubercle in squalodontids.

On the topic of squalodelphinids, the tympanic bulla is in articulation in the S. fabianii holotype and presumably the periotic is still in situ, so perhaps it's more accurate to state that the periotic is unprepared on line 237-238.
Additional comments: I'm very happy with the manuscript overall, and provided that the authors address my specific points about the section on squalodelphinids, I don't think I'll need to see this again as I trust the authors will make these additions.

I apologize if I was not specific enough with my earlier comments/questions!


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: RESIDENCY, MOVEMENT PATTERNS, BEHAVIOR AND DEMOGRAPHICS OF REEF MANTA RAYS IN KOMODO NATIONAL PARK
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall the article is well-written and easy to follow. I have inserted a number of comments as “sticky notes” directly into the attached PDF with suggestions for small improvements/corrections to the writing, but overall very well-written.

In terms of the literature references and the field background provided, the authors have done a good job with the manta literature and in explaining their approach and methodology. However, the references are woefully incomplete with respect to the conservation background of Komodo National Park. I provide more detailed points on this in the general comments below.

The figures created are clear and well-done, and the raw data is supplied – with the manta sightings data publicly available on the Manta Matcher website.

I do note that the Animal Ethics Approval letter provided here does not seem to be relevant to the present study; it was granted for the purposes of biopsy sampling of manta rays and other filter feeders for a microplastics study. It is not clear to me that the present study would actually require an Animal Ethics Approval letter as it was purely observational and non-invasive, but I simply wonder why a microplastics biopsy sampling Animal Ethics letter is included for this study?
Experimental design: The research presented is within the scope of the journal, and the goals of the study were well-defined, relevant and meaningful. However, the fourth stated goal of the research (an assessment of risks to reef manta rays in Komodo NP to identify management needs) was incomplete in my opinion (see more detailed comments below).

The methods were generally appropriate and well-described, and the “core research” (describing residency, movement patterns and population structure of KNP mantas) was indeed rigorous. I did not feel this was the case with the assessment of the effectiveness of KNP in safeguarding manta rays – as described in significant more detail in my general comments.
Validity of the findings: All underlying data do indeed appear to have been provided, and they seem robust and statistically sound.

As for the conclusions, those related to the core focus of the paper (examining residency, movement patterns and population structure of KNP mantas) are well-stated and interesting. However, I feel strongly that the authors have significantly overstated the conclusions they present with respect to the effectiveness of KNP in safeguarding mantas; the results of their analyses simply do not support this (indeed those results are largely unlinked to conservation success). I provide significant additional commentary in this regard below.
Additional comments: Some of the below comments are also included as “sticky notes” in the PDF, but I’ve pulled out those which I think are most important to my overall assessment and put them below:

-the title of the paper seems inappropriate to me and not a main conclusion justified by the analyses in the paper – which are largely focused on analyzing movement patterns and habitat use and residency/site affinity in Komodo National Park. The title should be reworded to be an “honest advertisement” of the analyses and conclusions justified from these analyses within the paper – something more along the lines of “Residency, movement patterns and population structure of reef manta rays studied at four sites in Komodo National Park”.  Also, I would note that Komodo would not qualify as a “large MPA” under most definitions. Internationally, “large scale MPAs” (LSMPAs) are defined as those MPAs larger than 150,000 km2. The authors note the Komodo National Park is only 1817 km2 including land and sea (I would add that it actually has extensions proposed in 1999 which have not yet been enacted that would bring it to 2,321 km2) – but this is still two orders of magnitude smaller than a LSMPA. Komodo NP is moreover an order of magnitude smaller than the “relatively large” MPAs of Indonesia such as Wakatobi or Cendrawasih Bay or Savu Sea marine national parks.

-Lines 46-47: The authors state that characterization of existing threats to manta rays within the park is limited. While this may be true, the authors have not established this sufficiently to make this claim. They do not even cite the 25 year management plan for KNP, nor any of the MANY MPA management reports and surveys produced by The Nature Conservancy (or WWF-Indonesia) in collaboration with PHKA. The primary document for threat assessment in an Indonesian MPA is its 25-year management plan - so without having read and cited this, the authors cannot claim that threats have not been appropriately characterized or addressed.

-Lines 56-57: Mantas from KM and MW, only 5km apart, showed affinity to one or the other site. This is a very interesting finding and I commend the authors on their rigorous data collection to be able to show this – in my mind one of the most interesting specific findings in the paper. However, this further underscores my point about not being able to claim that this is a "population-level" study - well-known manta aggregation sites in Gili Banta, West Komodo, Southwest Rinca and East Rinca and even Padar are anywhere from 20-50km away from the sites studied here - and very likely also are "home" to mantas that show high affinity to those sites. Without having collected data from these other sites, the authors cannot reasonably claim to have conducted a "population level" analysis for KNP mantas.

-Lines 64-67: the authors state that tourism increased over the course of the study – a statement they back up with their own counts of dive boats at their study sites. However, particularly given that the research team was not based on site at all times and only have sporadic data on boat use from each site (and only from a short period of time each day the data was actually collected and might therefore easily have missed boats arriving and diving there earlier or later in the day), and their observations are only of 4 sites, it would seem prudent to examine the actual tourism numbers to the park, which are readily available from the KNP management authority, who collects an entrance fee and records annual visitation numbers. Given that an official from the KNP authority is listed as one of the coauthors on the paper, it is difficult to understand why the authors would not have tapped this important and readily-available source of data for solidifying their finding of increasing tourism numbers. I suggest this should be included in the revised manuscript.

Lines 68-69: Two important notes:  1) the term "zone" has a very specific meaning in the context of Indonesian National Parks - all of which have a zonation plan. In the case of Komodo NP, there are 9 different zone types, none of which are named "marine conservation zone". The authors should refrain from using the term zone with respect to KNP unless it is used in the narrowly-defined legal meaning of the word.  2) I do not find that the authors' results support this claim of KNP safeguarding mantas. Their analysis does not include any estimate of population growth/decline/stability, and particularly given their implied claim that KNP has been protecting manta rays since its inception, they have not included even any qualitative discussion of the conservation of manta rays in KNP for the 30 years' preceding their study.

-Lines 98-99 (also related to the statements on KNP in the Background section of the Abstract): Several important notes: 1) KNP was established in 1980, but the marine extension to the national park was only added in 1984. This needs to be clarified. 2) As noted above, the authors should refrain from using the term "zone" when referring to KNP unless in the legally correct sense of the word. It would be more appropriate to say "..formally established in 1980, primarily for the conservation and management of the endemic Komodo dragon...".  3) Most importantly, the authors claim that KNP is the “first refuge for M. alfredi” and “has functioned as the longest running protected area for manta rays worldwide.”  These statements are patently incorrect, and quite surprising given many of the authors have lived or worked in Australia and would be very much aware that the Great Barrier Reef Marine Park was established in 1975 and most definitely is every bit the manta ray refuge that KNP is. Other important (and mostly well-known) MPAs worldwide that protect manta rays and have been established since before Komodo’s marine extension was gazetted in 1984 include:  the Galapagos National Park was established in 1959 and began operations in 1968; the Watamu Marine National Park in Kenya was established in 1968 and the inventory done by Cowburn et al 2018 (Atoll Research Bulletin) reports M. alfredi as a key attraction;  Bonaire National Marine Park was established in 1979 and is well-known for manta rays; the Poor Knights Marine Reserve in NZ was established in 1981 and has frequent sightings of M. birostris, though perhaps less resident than manta rays in the other MPAs mentioned here; and finally, Kepulauan Seribu is actually Indonesia’s first marine national park (established in 1982) – mantas are now rare and possibly extirpated there, but it would have served as Indonesia’s “first refuge” for manta rays, if simply being gazetted an MPA equates to serving as a refuge (as seems to be implied here).

-Line 124: I do not feel it is appropriate for the authors to characterize this as a "population-level" study when they only investigate four aggregation sites within KNP (and only really significantly analyze data from 3), and do not even include all of the known aggregation sites studied by Dewar et al 2008, nor the many other known manta sites in and immediately adjacent to KNP. The authors do acknowledge this limitation of their study in the final subsection of the Discussion, but they need to tone down the claims of this being a population-level study in the abstract and introduction. This is a very focused study on 4 aggregation sites, not a population-level study.

-Line 125:  As mentioned above, it is intriguing to me that the authors purport to assess potential threats to mantas to identify management needs within the KNP, but they do not cite the 25 year management plan for the KNP nor any of the extensive reports and recommendations for improving the management of the marine resources of KNP made by The Nature Conservancy, WWF-Indonesia and other institutions who have worked with PHKA/KSDAE on management of the park since 1995. It may very well be that there is still a need to assess threats to manta rays and identify management needs, but this clearly would need to start with a thorough read (and citation) of the management plan and the many reports that have been produced for the park. In fact, there used to be a rather comprehensive list of threats (as well as an extensive library of the reports on the MPA) on the official park website www.komodonationalpark.org , but that website is no longer functional – another indication of the declining management effectiveness of the park which has been discussed extensively in the press (and which is at odds with the authors’ claims of the effectiveness of the MPA). A close read of the “threat assessment” conducted by the authors in this paper (their study goal #4) shows they looked closely at threats from tourism (at least in the 4 sites they intensively monitored) and conducted their standardized manta photo ID protocols, which includes noting injuries, fishing gear entanglement and attempted predations (bite marks) for each manta photographed. This is of course invaluable data and very much worthy of reporting, but this does not constitute a comprehensive threat assessment for mantas in KNP – which would most definitely need to explicitly address data from park patrols and dive operator reports on incidences of blast fishing, drift gillnets, possible targeted harpoon fisheries, water quality issues including increasing pollution and run-off from the rampant coastal development around Labuan Bajo and the large number of boats likely dumping sewage and ballast water in the park, microplastics (which the lead author is an expert on), etc. Moreover, the authors suggest they are assessing these threats to help identify specific management needs in KNP – but the discussion does not include a concise and clear list of manta management/conservation recommendations to the park authority. The section of the discussion on threats from tourism does contain a number of important observations and recommendations, but many of them stop short of providing easily actionable recommendations to the park authority – eg, “Consideration should be given as to how these codes of best practice could be implemented effectively in KNP.” The authors are experts in manta rays, and if their aim with this paper is to provide manta conservation recommendations to the park authority, they should make a clear subsection in the Discussion section with tight, actionable recommendations to the park authority. If “consideration should be given” as to how codes of practice can be implemented in KNP, the authors should indeed give this consideration and make recommendations based upon their expertise.

-Lines 494-502: The authors note that more immature male rays and fewer mature female rays were observed at CL, and that this site might possibly serve as a nursery for reef mantas. They then list the 3 criteria of Heupel et al 2007/2019 that define an elasmobranch nursery, but do not systematically examine how CL conforms to these criteria. It would seem to me that the authors have a significant enough data set to be able to systematically “test” each of these criteria for the CL site, in much the same way that Setyawan et al 2020 did for each of the sites they proposed as nursery areas for reef mantas in Raja Ampat (and as Germanov et al 2019 did when proposing “Manta Bay” in Nusa Penida as a reef manta nursery).  Given the high conservation importance of identifying manta nurseries and providing them extra protections (including from tourism disturbance), I would recommend that the authors make the effort to apply their data to the Heupel et al definition – as identifying Komodo’s manta nurseries and providing recommendations to the park management authority on extending special protections to these areas would be one of the most valuable things a study like this could do from a conservation perspective. I would moreover note that based upon what we do know of reef manta nurseries, and their tendency to be in relatively shallow, protected bays and lagoons, the CL site generally conforms to these physical characteristics, but in fact the large islands of Komodo, Rinca and Gili Banta have NUMEROUS shallow, well-protected bays that might possibly function as manta ray nurseries – something the authors might consider for follow-up study. Of course, that would require  chartering a vessel to actively explore the lesser known bays of KNP, but that’s how good conservation science proceeds…

-Lines 506-509: For the discussion of demographic parameters, it would seem appropriate that the authors generally compare their demographic findings not only to Mozambique, Japan and the Maldives, but also to the nearest large population for which such parameters have been calculated - Raja Ampat. Setyawan et al 2020 provide a wide range of observations from an even larger study - and comparing the KNP findings to other populations within Indonesia is clearly appropriate.

-Lines 518-522: I don't follow the logic of this sentence - it is not clear why observations at other manta ray feeding grounds would suggest that immature individuals would disproportionately use German Flag?? The authors seem to be suggesting that immature individuals are more likely to be seen at feeding grounds than at cleaning stations, but they need to reword this particular sentence to be more clear. Moreover, while its good that they recognize the limitation of their study in not actually focusing on the site (German Flag) that had the most recorded manta visitations of any site in the Dewar et al 2008 study, they then seem to imply that German Flag is only a feeding site. German Flag most definitely has several associated cleaning stations! Moreover, our extensive observations of immature reef mantas in nursery areas in Raja Ampat definitely do not support the supposition that immature mantas do not need to clean; each of the nurseries we've examined has numerous associated cleaning stations (which as the authors rightly note, are also important for social interactions, including for juveniles). I might suggest that the reason the authors have not found as many immature individuals in KNP as they have in Nusa Penida is simply because they have not sufficiently explored the many shallow protected bays around Komodo, Rinca, and Gili Banta that are likely preferred nursery habitats.

-Lines 675-678: the authors claim, with no supporting evidence or references, that KNP has likely acted as a refuge for reef mantas 30 years before nationwide manta ray protection. This is most definitely a bold overstatement for which the authors provide no evidence. If they had carefully read the extensive grey literature which exists on KNP marine resource management, they would know that there was very little enforcement of the MPA prior to 1996 when The Nature Conservancy began working closely with PHKA to support management of the MPA (and purchased several patrol boats). Prior to that time, the region was considered a “Wild West” with extensive blast fishing, cyanide fishing, shark finning and large net fishing – all of which would have threatened manta rays. It took a number of years to reign in the illegal fishing, and sadly, once The Nature Conservancy was forced to leave the park in 2010, illegal fishing once again became rampant. This is even reported in the official “Wikipedia” page on Komodo National Park, which states clearly:   “After that, more illegal fishermen arrived as enforcement declined greatly following the exit of TNC which had helped fight destructive fishing practices. In early 2012, dive operators and conservationists found many desolate coral sites, reminiscent of grey moonscapes. Illegal fishermen continue to blast sites with 'bombs' in a process known as blast fishing. The fisherman use a mixture of fertilizer and kerosene in beer bottles as explosives, or use squeeze bottles to squirt cyanide into the coral in order to stun and capture fish. In the past two years more than 60 illegal fishermen have been arrested. One of the suspects was shot and killed after he tried to evade capture by throwing fish bombs at the rangers.[14]”
This statement is simply not supported by evidence and should not be made in this paper; it moreover is not related to the methods and analyses of this paper.

-Line 785-787: This statement is rather mind-boggling in its implications; if the authors believe that it is logistically prohibitive to enforce the no-take zones and regulations of KNP, how can they possibly claim that the park has acted as a refuge for 30 years? Paper parks are not refuges. More to the point, however, KNP is a relatively small and readily accessible MPA which at one point in its history  (from about 1998-2010) was extremely well-enforced. In comparison to most other MPAs in eastern Indonesia, KNP could hardly be considered to be logistically prohibitive to enforce! The sites discussed in this paper are only 30-50km from the nearby large town of Labuan Bajo, and generally within 5-10km max of ranger stations within KNP. By comparison, 5 of the 9 MPAs in Raja Ampat are 170-210 km from the nearest large town of Sorong. Those MPAs ARE logistically challenging, yet they have regular patrols that have largely eliminated illegal and destructive fishing. This statement should be removed - it is not in line with conservation reality in Indonesia and is moreover at extreme odds with the claims of the paper about the conservation success of KNP.

-Line 817: This statement suggests that the authors primarily engage with only one component of the tourism sector in KNP - the land-based operators located in Labuan Bajo. I have made perhaps 30 liveaboard dive vessel trips to Komodo since 1996, and I have visited German Flag and Padar Kecil on most of those trips. The longer-term liveaboard operators, many of whom have extensively explored KNP over the past 25 years, and who are catering to a much more experienced diver clientele than the operators based out of Labuan Bajo, actually largely avoid the sites the authors have mentioned and studied in the north of the park due to the overcrowding of day boats there. If the authors are serious about truly surveying KNPs mantas at the "population level", engagement with these liveboard operators that travel much further afield in KNP (including to Gili Banta and Gili Motang and West Komodo) would be a clear next step for their efforts.

-Line 840:  While I would agree that it is almost certain that KNP has provided SOME protection to reef manta rays (interestingly, this protection is likely most directly attributable to the de facto enforcement role which the tourism boats play at the main manta aggregation sites), without any baseline data to compare to, nor data on population growth, nor any historical data or observations reported in this study, it is only appropriate to suggest this as a hypothesis/possibility and certainly not a main conclusion of the paper (and consequently should not be part of the title of the paper).

-Line 845: Normally, in a conservation-focused paper, the authors might conclude with a set of recommendations explicitly targeted to the management authorities in charge of managing an MPA or other jurisdictional waters. The recommendation to expand the survey area, which the authors recognize will require a dedicated research program, is intriguing in this regard. To whom is this recommendation made? At the present time, it seems the only ones conducting these manta surveys in KNP are the authors themselves, in which case are they making a recommendation to themselves? If this is the case, it would seem the more appropriate way to state this would be “To overall increase the current understanding of site use , movements…., we hope to be able to expand our surveys to other locations….”. Or “we intend to”. If it is a recommendation, the authors need to clarify to whom they are recommending this.

In summary, the authors have done an excellent job of analyzing an important data set and providing some very interesting insights on residency, movement patterns and population structure of reef manta rays in Komodo NP. Certainly this dataset and the analyses included are worthy of publication and a useful contribution to the reef manta literature, and I recommend that the article be accepted after some important revisions. I have provided a number of small recommendations to improve the clarity of the narrative, but more importantly I have listed above a number of concerns about statements the authors have made which I believe are either inaccurate (eg, that KNP is the world’s first manta reserve) or significantly overstate what can be concluded from the data and analyses presented here. At its core, this is a solid scientific study with some important findings. However, my two main concerns relate to the limited geographic focus of the study (4, and often only 3, manta ray aggregation sites for which the authors analyze data, despite there being at least three times that number of known aggregation sites within and immediately adjacent to the park) and the unsupported claims about the conservation effectiveness of KNP in safeguarding mantas. My suggestion would be that the authors simply revise the title of their paper to be more in line with their actual analyses, and tone down their claims about the comprehensiveness of this study and the conservation effectiveness of KNP. They should also consider including a tight, concise recommendations section for the park management authority based on their analyses and expert opinion on what needs to be improved in the KNP to better protect manta rays.

If, on the other hand, the authors want to properly examine the conservation effectiveness of KNP for manta rays, it will require a MUCH more detailed study and description of the long and tortuous history of KNP MPA management, including a more thorough description of the conservation setting of the park (including that it is a Man and Biosphere Reserve and a UNESCO World Heritage Site). The authors will need to not only thoroughly familiarize themselves with the KNP 25-year management plan, but also need to dive deep into the grey literature (as there is an ENORMOUS amount of project reports, surveys and management recommendation papers that were produced in the period 1995-2010 for KNP) and interview the conservation professionals who designed KNP’s management plan, as well as those that were involved in the management after 2010 when The Nature Conservancy left KNP. They also would need to interview many of the long-term tourism operators that were exploring KNP in the 1990s and early 2000s, and provide historical context and observations on KNP’s manta population – this data absolutely DOES exist, but it is not published in the peer-reviewed literature and requires a much more intensive approach to data collection. Unfortunately, this is typical of the conservation histories of almost all MPAs in Indonesia and much of the developing tropics – publication in peer-reviewed literature is not a priority for conservation organizations and government agencies working hard to implement and manage MPAs. Finally, the authors would also need to provide some indication of the stability or growth of the KNP manta ray population to be able to claim that KNP is effectively safeguarding its manta rays. They did show that their best-fit resighting model suggested low mortality, but that does not seem sufficiently robust to claim conservation success, particularly in light of the abundant public criticism of the current lack of management effectiveness of the park. At any rate, such an analysis would most definitely be an extremely worthwhile endeavor and a most useful paper – but unfortunately, in my strong opinion the data and analyses presented in the current study are not sufficient to address the question of the relative effectiveness of KNP in safeguarding reef manta rays. This would require a rather major revision to the manuscript.

-My final comment – I noted in one of my comments that I recorded more sites with manta rays during my first two-week survey of Komodo in 1995 than the authors have recorded for the whole of their 14 year survey. This is not meant as a major criticism, but rather a “reality check” on the large swaths of KNP that are not addressed in this paper. I of course should not criticize what I would classify as “unadventurous science”, but likewise the authors should not overclaim the utility and representativeness of their study, when it was in fact confined to a small area of a relatively small park. The authors conclude that further research is needed to identify and protect other critical aggregation areas within the region – indeed, but I cannot stress enough that Komodo is not a very large park and there has been an ENORMOUS amount of marine survey effort put into this region, dating all the way back to Salm and Halim 1984 and including numerous surveys in the nearly 4 decades since by NGOs, the Indonesian Institute of Sciences and various local universities. The authors do not cite any of these papers or reports, and while they most definitely will not include the type of detailed data the authors have been collecting, there is likely a wealth of anecdotal observations on manta rays that would prove useful to any truly comprehensive study on KNP mantas with a focus on putting forth recommendations to improve their conservation and management. As a single concrete example, surveys of the park in the late 1990s revealed significant aggregations of manta rays (as well as some beautiful reefs and large aggregations of reef fish) at Gili Banta, a large island to the NW of Komodo Island. As the 25-year management plan for the park was being prepared, a proposal was also put forth in 1999 to expand the park to include Gili Banta – both to include the important marine resources around the island as well as to prevent Banta from becoming a base for illegal fishers and deer poachers to make excursions into the park. Sadly that does not appear to have been acted upon, but it nonetheless still exists as a formal proposal to the government that could be revived. If the authors are keen to truly improve the conservation of manta rays in Komodo NP, I believe an exploration of the current status of the manta aggregation sites in Banta would be a top priority, and assuming they are still intact (anecdotal evidence from liveaboards pre-Covid pandemic suggests they were), expanding the park’s boundary to include Banta would certainly be a top conservation recommendation.


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: RESIDENCY, MOVEMENT PATTERNS, BEHAVIOR AND DEMOGRAPHICS OF REEF MANTA RAYS IN KOMODO NATIONAL PARK
Review round: 1
Reviewer: 2

Output:
Basic reporting: - The language use is this paper is overall clear and unambiguous.
- Literature referenced by the authors were not incomplete to provide a strong background written in Introduction. This also lead to misleading and incorrect overstated claim on the longest running protected area for manta rays worldwide. Another example of insufficient literature referenced is that the authors didn't cite the management plan of Komodo National Park when they intended to discuss the effectiveness of this park to protect manta rays. In the context of manta ray conservation in Komodo and Indonesia in general, the authors insufficiently referenced several important milestones preceeding the full protection of manta rays in Indonesia in 2014, including regional level protection for manta rays in Raja Ampat in 2012 and importantly in Manggarai Barat (Komodo) in 2013.

I recommend the authors to make correction on the incorrect overstated statements and fully acknowledge manta ray conservation efforts in place in the region and Indonesia fairly.
Experimental design: The research questions are well defined and are useful to fill knowledge gap on the absence of population level studies investigating manta ray demographics and habitat use within Komodo National Park. I also commend the authors for strong analyses performed in this study.
Despite this, it is unclear to me whether the sighting data submitted by public/citizen science were also included in the analyses combined with contributed data.
Validity of the findings: In this paper, the authors made an effort to link between the main findings (site affinity and population structure) and conservation and management effectiveness to protect manta ray in the park. However, this was done without referring to management plan of the Komodo National Park. Moreover, instead of using 14 years of data, the authors in fact used limited data from 2013 to early 2018 contributed by citizen science covering four manta aggregation sites in the park. The authors also emphasized the crucial role of the park for regional population recovery. However, the arguments for this statement were invalid as noted in my comments in the manuscript. Apart from this, I note that most part of the discussion on environmental influences on seasonal movements were unnecessary as this paper didn’t include any environmental data in the analyses.

Please see my suggestions in the reviewed manuscript.
Additional comments: Overall, this study provide important findings on the site affinity, population structure, and behaviours of reef manta rays in Komodo National Park. However, there several major points must be addressed in order to make this study more suitable for publication. I strongly suggest that the authors consider focusing only on the main findings, which were supported strong statistical analyses, and then briefly discuss about the management implications of these main findings. I also suggest that the authors should address some more detail corrections in the annotated manuscript.

I also note that the permits (including permit extensions) issued by the Indonesian Ministry of Research and Technology allowing the first author was granted only from 2015-2017. It is unclear to me whether these permits also covered the research in Komodo National Park or in addition to Nusa Penida. It is also important to note that the permit from the Komodo National Park management authority was issued only for 2016, while the sighting data collected from 2013-2018. I am afraid that the data can be used in the analyses only include those collected in 2015-2017 or even only in 2016. Please provide more clarification on 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: RESIDENCY, MOVEMENT PATTERNS, BEHAVIOR AND DEMOGRAPHICS OF REEF MANTA RAYS IN KOMODO NATIONAL PARK
Review round: 2
Reviewer: 1

Output:
Basic reporting: Overall the article is well-written and easy to follow. I have again inserted a number of small comments as “sticky notes” directly into the attached PDF with suggestions for small improvements/corrections to the writing, but overall very well-written.

In terms of the literature references and the field background provided, the authors have done a good job with the manta literature and in explaining their approach and methodology (I did suggest considering adding one brand new reference – Lassauce et al 2022 – on using genetic methodologies to look at population connectivity).

The figures created are clear and well-done, and the raw data is supplied – with the manta sightings data publicly available on the Manta Matcher website.
Experimental design: The research presented is within the scope of the journal, and the goals of the study were well-defined, relevant and meaningful.

The methods were generally appropriate and well-described, and the “core research” (describing residency, movement patterns and population structure of KNP mantas) was indeed rigorous. The authors moreover did an excellent job of taking on board a number of my previous comments and suggestions related to providing meaningful recommendations to improve conservation and management of manta rays in KNP.
Validity of the findings: All underlying data do indeed appear to have been provided, and they seem robust and statistically sound, with the conclusions well-stated and interesting.
Additional comments: Overall the authors have done an admirable job of significantly “tightening” this manuscript, focusing in on detailed analyses of the valuable dataset they’ve collated and providing a number of valuable insights on reef manta ray residency, movement patterns, behavior patterns and demographics in KNP. I was particularly pleased to see their analysis of tourism growth and impacts on manta rays in the park and the effort put into providing clear, actionable recommendations to the KNP Management Authority (and tourism operators) to improve management of manta ray tourism, and in outlining future research priorities in KNP and the immediate surrounds to best inform conservation and management.

Other than addressing the various minor comments and corrections I’ve provided, my only overarching suggestion is for the authors to reconsider their abstract to ensure it conveys all of the points the authors consider most important from this study. There’s a LOT covered in the study, and the abstract is necessarily short and can only cover key points – but I note that for instance none of the discussion of tourism impacts nor the recommendations included in the discussion section are mentioned in the abstract. That of course is the prerogative of the authors to choose what they most want to highlight – I would simply note that I think there are some key findings/recommendations that at least I found very compelling that are not in the abstract.

With minor revision, this paper is ready for publication and will be a valuable contribution to our knowledge of reef manta rays while also providing excellent recommendations to the KNP Mgmt Authority and laying out a clear vision for future manta ray research priorities in KNP.