DNA Barcoding Is a Useful Tool for the Identification of the Family Scaridae in Hainan
, Yali Yan 1, Nan Zhang 1,3, Huayang Guo 1,3, Baosuo Liu 1,3, Jingwen Yang 1, Kecheng Zhu 1,3 and Dianchang Zhang 1,3,4,5,*
Round 1
Reviewer 1 Report (Previous Reviewer 2)
Review
Paper title: DNA barcoding is a useful tool for the identification of the family Scaridae in Hainan
The authors applied DNA barcoding to reveal the species composition of parrotfish in the family Scaridae collected in Hainan. The authors identified 43 species genera, found that Chlorurus sordidus and C. spilurus represent the same species, and concluded that the method is useful for careful species identification.
All these reasons explain the relevance of the paper by Bo Liu and co-authors submitted to "Journal of Marine Science and Engineering".
General scores.
The data presented by the authors are original and significant. The study is correctly designed and the authors used appropriate sampling methods. In general, statistical analyses are performed with good technical standards. The authors conducted careful work that may attract the attention of a wide range of specialists focused on fish ecology.
Specific remarks.
L 51. Consider replacing “and improves” with “and improve”
L 73. Consider replacing “development appropriate” with “develop appropriate”
L 93. Consider replacing “intra, and interspecific” with “intra- and interspecific”
L 146. Consider replacing “data-set” with “data set”
L 162. Consider replacing “ustahad” with “usta had”
L 180. Consider replacing “There was a close relationships” with “There were close relationships”
L 190. Consider replacing “mainland China to species” with “mainland China species”
L 201. Consider replacing “data-set” with “data set”
L 202. Consider replacing “data-set” with “data set”
L 206. Consider replacing “An average” with “On average”
L 212. Consider replacing “faster is the” with “faster the”
L 256. Consider replacing “gerus, their genetic distiance” with “genus, their genetic distance”
Author Response
Dear reviewer,
Thank you very much for your comments and professional advice. These opinions help to improve academic rigor of our article. Based on your suggestion and request, we have made corrected modifications on the revised manuscript. Meanwhile, the manuscript had be reviewed and edited by language services of editage. We hope that our work can be improved again. Furthermore, we would like to show the details as follows:
Specific remarks.
L 51. Consider replacing “and improves” with “and improve”
Response: Thank you for your valuable suggestion. We have been modified. Change “and improves” to “and improve”
L 73. Consider replacing “development appropriate” with “develop appropriate”
Response: Thank you for your valuable suggestion. We have been modified. Change “development appropriate” to “develop appropriate”
L 93. Consider replacing “intra, and interspecific” with “intra- and interspecific”
Response: Thank you for your valuable suggestion. We have been modified. Change “intra, and interspecific” to “intra- and interspecific”
L 146. Consider replacing “data-set” with “data set”
Response: Thank you for your valuable suggestion. We have been modified. Change “data-set” to “data set”
L 162. Consider replacing “ustahad” with “usta had”
Response: Thank you for your valuable suggestion. We have been modified. Change “ustahad” to “usta had”
L 180. Consider replacing “There was a close relationships” with “There were close relationships”
Response: Thank you for your valuable suggestion. We have been modified. Change “There was a close relationships” to “There were close relationships”
L 190. Consider replacing “mainland China to species” with “mainland China species”
Response: Thank you for your valuable suggestion. We have been modified. Change “mainland China to species” to “mainland China species”
L 201. Consider replacing “data-set” with “data set”
Response: Thank you for your valuable suggestion. We have been modified. Change “data-set” to “data set”
L 202. Consider replacing “data-set” with “data set”
Response: Thank you for your valuable suggestion. We have been modified. Change “data-set” to “data set”
L 206. Consider replacing “An average” with “On average”
Response: Thank you for your valuable suggestion. We have been modified. Change “An average” to “On average”
L 212. Consider replacing “faster is the” with “faster the”
Response: Thank you for your valuable suggestion. We have been modified. Change “faster is the” to “faster the”
L 256. Consider replacing “gerus, their genetic distiance” with “genus, their genetic distance”
Response: Thank you for your valuable suggestion. We have been modified. Change “gerus, their genetic distiance” to “genus, their genetic distance”.
Thank you very much for you attention and time. We are looking forward to hearing from you.
Yours sincerely,
Dian-Chang Zhang
231 Xingang Road West, Haizhu District, GuangzhouCity, Guangdong Province,
510300, PR China.
E-mail address: [email protected]
Phone: +86 02089108316; fax: +86 02089022702
Author Response File: 
Author Response.docx
Reviewer 2 Report (Previous Reviewer 1)
Notes to authors:
Thank you for considering our comments, which were made to improve the quality of the manuscript. Now I think that the manuscript is suitable for publication in the scientific journal.
Author Response
Dear reviewer,
Thank you very much for your comments and professional advice. These opinions help to improve academic rigor of our article. Based on your suggestion and request, we have made corrected modifications on the revised manuscript. Meanwhile, the manuscript had be reviewed and edited by language services of editage. We hope that our work can be improved again.
Thank you very much for you attention and time. We are looking forward to hearing from you.
Yours sincerely,
Dian-Chang Zhang
231 Xingang Road West, Haizhu District, GuangzhouCity, Guangdong Province,
510300, PR China.
E-mail address: [email protected]
Phone: +86 02089108316; fax: +86 02089022702
Author Response File: Author Response.docx
This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.
Round 1
Reviewer 1 Report
Positive notes:
1. The topic of the publication is particularly relevant, since DNA barcoding data generated will be used as an effective molecular tool to achieve better monitoring and conservation effects for the family Scaridae. In this aspect, the manuscript is in the field of molecular biology and biochemical genetics of hydrobionts;
2. The literature review provides up-to-date information on the state of the problem and scientific achievements so far;
3. The material and methods section is well laid out and, with few exceptions, describes in detail the sampling and processing of the biological material;
4. The results are presented relatively well in tabular and graphic form;
5. The discussion uses own and foreign data for qualitative scientific interpretation of the material;
6. A timid attempt has been made to form conclusions as a result of the scientific research conducted;
Negative comments and recommendations:
1. The number of individuals studied was only 51. It would have been good if the authors had provided more samples collected from other locations.
2. The "Results" section on line 137 should be in bold;
3. In Figure 1, the dimensions of the ordinate are not indicated;
4. To increase the scale of figure 2 for better visualization;
5. The "Discussion" section on line 190 should be in bold;
6. I recommend to differentiate clear conclusions after the discussion, which will be concrete and useful for the scientific community engaged in the identification of genetic barcodes for individual species of hydrobionts.
Author Response
Dear reviewer,
Thank you very much for your comments and professional advice. These opinions help to improve academic rigor of our article. Based on your suggestion and request, we have made corrected modifications on the revised manuscript. Meanwhile, the manuscript had be reviewed. We hope that our work can be improved again. Furthermore, we would like to show the details as follows:
Negative comments and recommendations:
- The number of individuals studied was only 51. It would have been good if the authors had provided more samples collected from other locations.
Response: Thank you for your valuable suggestion. At that time, we only collected 51 live fish samples.
- The "Results" section on line 137 should be in bold;
Response: Thank you for your valuable suggestion. We have been modified. Line 141.
- In Figure 1, the dimensions of the ordinate are not indicated;
Response: Thank you for your valuable suggestion. We have been modified. Line 166.
- To increase the scale of figure 2 for better visualization;
Response: Thank you for your valuable suggestion. We have been modified. Line 179.
- The "Discussion" section on line 190 should be in bold;
Response: Thank you for your valuable suggestion. We have been modified. Line 198.
- I recommend to differentiate clear conclusions after the discussion, which will be concrete and useful for the scientific community engaged in the identification of genetic barcodes for individual species of hydrobionts.
Response: Thank you for your valuable suggestion. We have been modified.
Line 262-269: By analyzing the sequences of the CO I gene of 401 parrotfish, we found that the average intraspecific genetic distance was 0.003, and the average interspecific genetic distance was 0.159, approximately 53 times the average intraspecific genetic distance. The NJ tree shows that C. sordidus and C. spilurus of blue-headed green parrotfish gather together, and individuals of other species grouped together, with high support, and different species can be effectively distinguished. The results showed that DNA barcode technology based on the CO I gene could be used to identify species of Scaridae.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Review
Paper title: DNA barcoding is a useful tool for the identification of the family Scaridae
The authors applied DNA barcoding to reveal the species composition of parrotfish in the family Scaridae collected in China. The authors identified 44 species and 10 genera and concluded that the method is useful for careful species identification.
All these reasons explain the relevance of the paper by Bo Liu and co-authors submitted to "Journal of Marine Science and Engineering".
General scores.
The data presented by the authors are original and significant. The study is correctly designed and the authors used appropriate sampling methods. In general, statistical analyses are performed with good technical standards. The authors conducted careful work that may attract the attention of a wide range of specialists focused on fish ecology.
Recommendations.
In the Title and Abstract, the authors should include a mention of the geographical location where the study was undertaken.
L 97. Please, include the period when the fish were captured.
L 178-180 and L 217-218 contain similar information. I suggest deleting L 178-180.
Specific remarks.
L 36. Consider replacing “that lives in tropical and subtropical coral reefs, and is” with “that live in tropical and subtropical coral reefs, and are”
L 47. Consider replacing “body shape and bright color” with “body shapes and bright colors”
L 50. Consider replacing “its biomass” with “their biomass”
L 64. Consider replacing “morphologically identifying the Scaridae” with “morphological identification of the Scaridae”
L 65. Consider replacing “its role” with “their role”
L 66. Consider replacing “its effects in coral reef ecosystems [9, 18]. The fish have the ability to” with “their effects on coral reef ecosystems [9, 18]. The fish have the ability to be”
L 71. Consider replacing “information of” with “information about”
L 73. Consider replacing “small specimens of otoliths” with “small otoliths”
L 79. Consider replacing “techniques is” with “techniques are”
L 85. Consider replacing “is accurate” with “are accurate”
L 120. Consider replacing “parrotfishes” with “parrotfish”
L 128. Consider replacing “Based on Kimura” with “Based on the Kimura”
L 179. Consider replacing “(Wu et al., 2017)” with “[16]”
L 197. Consider replacing “53 times” with “53 times higher than”
L 218. Consider replacing “are the same species” with “are the same species [16]”
L 246. Consider replacing “researchers in China” with “researchers from China”
Author Response
Dear reviewer,
Thank you very much for your comments and professional advice. These opinions help to improve academic rigor of our article. Based on your suggestion and request, we have made corrected modifications on the revised manuscript. Meanwhile, the manuscript had be reviewed. We hope that our work can be improved again. Furthermore, we would like to show the details as follows:
Recommendations.
In the Title and Abstract, the authors should include a mention of the geographical location where the study was undertaken.
Response: Thank you for your valuable suggestion. Change “DNA barcoding is a useful tool for the identification of the family Scaridae in” to “DNA barcoding is a useful tool for the identification of the family Scaridae in Hainan.”
L 97. Please, include the period when the fish were captured.
Response: Thank you for your valuable suggestion. We've added them. Line 101: and buyers on October 5, 2018.
L 178-180 and L 217-218 contain similar information. I suggest deleting L 178-180.
Response: Thank you for your valuable suggestion. We have detected Line 178-180.
Specific remarks.
L 36. Consider replacing “that lives in tropical and subtropical coral reefs, and is” with “that live in tropical and subtropical coral reefs, and are”
Response: Thank you for your valuable suggestion. We have been modified. L 37: Change “that lives in tropical and subtropical coral reefs, and is” to “that live in tropical and subtropical coral reefs, and are”.
L 47. Consider replacing “body shape and bright color” with “body shapes and bright colors”
Response: Thank you for your valuable suggestion. We have been modified. L49: Change “body shape and bright color” to “body shapes and bright colors”
L 50. Consider replacing “its biomass” with “their biomass”
Response: Thank you for your valuable suggestion. We have been modified. L51: Change “its biomass” to “their biomass”
L 64. Consider replacing “morphologically identifying the Scaridae” with “morphological identification of the Scaridae”
Response: Thank you for your valuable suggestion. We have been modified. L64: Change “morphologically identifying the Scaridae” to “morphological identification of the Scaridae”
L 65. Consider replacing “its role” with “their role”
Response: Thank you for your valuable suggestion. We have been modified. L65: Change “its role” to “their role”
L 66. Consider replacing “its effects in coral reef ecosystems [9, 18]. The fish have the ability to” with “their effects on coral reef ecosystems [9, 18]. The fish have the ability to be”
Response: Thank you for your valuable suggestion. We have been modified. L66: Change “its effects in coral reef ecosystems [9, 18]. The fish have the ability to” to “their effects on coral reef ecosystems [9, 18]. The fish have the ability to be”
L 71. Consider replacing “information of” with “information about”
Response: Thank you for your valuable suggestion. We have been modified. L72: Change “information of” to “information about”
L 73. Consider replacing “small specimens of otoliths” with “small otoliths”
Response: Thank you for your valuable suggestion. We have been modified. L73: Change “small specimens of otoliths” to “small otoliths”
L 79. Consider replacing “techniques is” with “techniques are”
Response: Thank you for your valuable suggestion. We have been modified. L80: Change “techniques is” to “techniques are”
L 85. Consider replacing “is accurate” with “are accurate”
Response: Thank you for your valuable suggestion. We have been modified. L86: Change “is accurate” to “are accurate”
L 120. Consider replacing “parrotfishes” with “parrotfish”
Response: Thank you for your valuable suggestion. We have been modified. L123: Change “parrotfishes” to “parrotfish”
L 128. Consider replacing “Based on Kimura” with “Based on the Kimura”
Response: Thank you for your valuable suggestion. We have been modified. L132: Change “Based on Kimura” to “Based on the Kimura”
L 179. Consider replacing “(Wu et al., 2017)” with “[16]”
Response: Thank you for your valuable suggestion. We have been modified. Change “(Wu et al., 2017)” to “[16]”
L 197. Consider replacing “53 times” with “53 times higher than”
Response: Thank you for your valuable suggestion. We have been modified. L 164: Change “53 times” to “53 times higher than”
L 218. Consider replacing “are the same species” with “are the same species [16]”
Response: Thank you for your valuable suggestion. We have been modified. L227: Change “are the same species” to “are the same species [16]”
L 246. Consider replacing “researchers in China” with “researchers from China”
Response: Thank you for your valuable suggestion. We have been modified. L253: Change “researchers in China” to “researchers from China”
Author Response File: Author Response.pdf
Reviewer 3 Report
This manuscript is introducing a tool for DNA barcoding scarid fishes. Then, why do you need to show overall nucleotide composition, divergence time etc. The English and logic are far below the standard,
Author Response
Dear reviewer,
Thank you very much for your comments and professional advice. These opinions help to improve academic rigor of our article. Based on your suggestion and request, we have made corrected modifications on the revised manuscript. Meanwhile, the manuscript had be reviewed. We hope that our work can be improved again. Furthermore, we would like to show the details as follows:
This manuscript is introducing a tool for DNA barcoding scarid fishes. Then, why do you need to show overall nucleotide composition, divergence time etc. The English and logic are far below the standard.
Response: Thank you for your valuable suggestion. We have been modified.
Author Response File: Author Response.pdf
Round 2
Reviewer 3 Report
L.73-: Why otoliths? I don't understand why you would use a complex factor such as otoliths as a comparison for species identification.
L.130: what is redundant sequences?
L.144: Why do you need nucleotide compositions for species identification?
L.159: 1% should be 0.01
Figure 2 must be Table
L.209: Again nucleotide compositions. What is the point of stating averages?
L.214-218: This statement is quite normal. It does not seem necessary.
L.228-: Why do you need infer divergence history for species identification?
Author Response
Dear reviewer,
Thank you very much for your comments and professional advice. These opinions help to improve academic rigor of our article. Based on your suggestion and request, we have made corrected modifications on the revised manuscript. Meanwhile, the manuscript had be reviewed. We hope that our work can be improved again. Furthermore, we would like to show the details as follows:
L.73-: Why otoliths? I don't understand why you would use a complex factor such as otoliths as a comparison for species identification.
Response: Thank you for your valuable suggestion. Studies have shown that the morphology of otoliths can be used to identify fish. The otoliths are widely used for taxonomic and biological studies in non-ostariophysan teleosts for many reasons: their typically large size, relative ease of access, opaque and translucent seasonal markings, morphological variation and resistance to digestion in the alimentary canal of predators.
References
Jawad, L.A. A comparative morphological investigation of otoliths of six parrotfish species (Scaridae) from the 340 Solomon Islands. J Fish Biol, 2018, 93, 1046-1058.
Assis C A. The lagenar otoliths of teleosts: their morphology and its application in species identification, phylogeny and systematics. Journal of Fish Biology, 2003, 62, 1268-1295.
Jawad LA. Comparative morphology of the otolith of the triplefins (family: Tripterygiidae). Journal of Natural History, 2008, 41, 901-924.
L.130: what is redundant sequences?
Response: Thank you for your valuable suggestion. Many copies of a gene appear on a chromosome. There are a large number of repeated sequences in the genome, which will interfere with the data during sequencing and alignment.
L.144: Why do you need nucleotide compositions for species identification?
Response: Thank you for your valuable suggestion. Molecular methods are useful in elucidating phylogenetic relationships, and evolutionary patterns for bio-logical ecology where classical morphological methods are not applicable.
L.159: 1% should be 0.01
Response: Thank you for your valuable suggestion. Change “1%” to “0.01”.
Figure 2 must be Table
Response: Thank you for your valuable suggestion. We have been modified. Supplementary data: table 1.
L.209: Again nucleotide compositions. What is the point of stating averages?
Response: Thank you for your valuable suggestion. The key point for the effective identification of species using CO I gene sequences is that the interspecific genetic distance must be greater than the intraspecific genetic distance, and the distances must differ by approximately 10 times. The average genetic distance expresses the difference among populations, which can more scientifically and effectively clarify the classification relationship among species.
L.214-218: This statement is quite normal. It does not seem necessary.
Response: Thank you for your valuable suggestion. The possible explanation for this result might be that the variation range of G + C content is directly related to the evolution rate of codons. The larger the variation range of G + C content, the faster the evolution rate of codons.
L.228-: Why do you need infer divergence history for species identification?
Response: Thank you for your valuable suggestion. By inferring the divergent history of species identification, we can prove that CO I is also suitable for identification at the genus level in the Scaridae.
Author Response File: Author Response.pdf
Round 3
Reviewer 3 Report
These authors have not responded adequately to any of my comments.
