Environmental DNA Detects Remaining Populations of Endangered Stream Salmon (Sichuan Taimen: Hucho bleekeri Kimura Salmonidae) in the Qinling Mountains

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The authors investigated the presence of Sichuan taimen within the Qinling Mountains through the application of an eDNA based qPCR assay with the additional support of a traditional method, creel netting. The topic of this paper is of a great interest for the community and can increase the efficiency of management plans. However, the presentation of the methodology and the results must be improved. They are a bit confusing. The two sections should be better organized, aiming for linearity and clarity. I put my suggestions directly on the manuscript. The abstract should be better re-organized according to the contents of the manuscript.

Comments for author File: Comments.pdf

Comments on the Quality of English Language

The authors should use the impersonal form. 

Author Response

Response to Reviewers Comments:

Specific comments: In order of referred line number (Revised line number):

List of Major Changes:
1) The title was changed to “Environmental DNA Detects Remaining populations of Endangered Stream Salmon (Sichuan Taimen: Hucho Bleekeri Kimura Salmonidae) in the Qinling Mountains”.

2) Abstract:

Revisions weremade on writing in this section.

3)Introduction:

Revisions weremade on writing in this section.

4) Materials and Methods:

Based on the suggestions, this section was reconstructed and major revisions were made on writing.

5) Result

According to comments, this section was reconstructed. Werewritten the results of eDNA Survey and added the Tab. S1 after the text as supplementary materials.

6) Discussion

The Discussion section was rewritten and reconstructed.The causal relationship between ‘Ct values of qPCR’ and ‘amount of DNA present in water samples’ was incorrectly stated in the original manuscript. This has been rectified. The authors are grateful to the referees for pointing out their error.

Response to Reviewer 1:

• I admit that our work requires more thoughtful analysis and considerable improvement in writing. Some grammar and spelling errors were corrected as suggestion. For example, 1) we rewrotethe genus, species and subspecies name in italics in the text and in references.2) We used passive voice where possiblein the manuscript to avoid the use of “we”.
• The abstract section was rewritten as suggestion. The description of “we designed a qPCR primer and probe set using the D-loop region” (line 25) was incorrectly stated in the original manuscript. This has been rectified. The authors are grateful to the referrer for pointing out their error.
• Line 19 (Line 18): ‘Sichuan’ was added before ‘taimen’.
• Line 24 (Line 23): ‘our’ was changed to ‘This’.
• Line 59 (Fig.1): Following the suggestion of the reviewer, geographical distributions of Sichuan taimen in China were added to Fig.1 to better locateour study area.
• Line 79 (Line 79):With regard to the reviewer’s doubt that how this experiment will enhance the detection probability of Sichuan taimen eDNA, we have recognized this problem.To clarify this issue, the description of “enhance the detection probability of Sichuan taimen eDNA”waschanged to “enhance the detection probability of Sichuan taimeneDNA via assessing the season’ effect”.
• Line 87 (Line 88):We consider Sichuan taimen as epibiotic species base on the literatures and the ref.17 was citedhere.
• Line 115 (Line 118):I admit that the ‘Materials and Methods’ section is poorly constructed. I hope that the revised ‘Materials and Methods’ is now suitable for publication.
• Line 118 (Line 120): ‘Sichuan taimen’ was added after‘targeted DNA of’.
• Line 118-120 (Line 119-123): Our teamdeveloped the protocol in Deng et al 2023 and we apply the protocol in this study. The description of “we developed a protocol” (line 118) was improperly stated in the original manuscript. This has been rectified here and in abstract.
• Line 124 (Line 125): ‘to be present recently’ was changed to ‘to be recently present’.
• Line 127 (Line 128): ‘sites 1-6, Figure 1’ was added after‘a 600-meter river section’.
• Line 128 (Line 129): ‘sites 8, Figure 1’ was added after‘the river was completely frozen’.
• Line 129 (Line 31): ‘sites 7, Figure 1’ was added after‘positive controls’.
• Line 129-136 (Line 131-138): The ponds which served as positive control were receiving water from the river where you collected water samples. We chose the ponds as positive control because it is the only Sichuan taimen farm in China.
• Line 141 (Line 146):The number (line ) are the sample ID listed in table 1. ‘six sites rearing pond’ was changed to ‘six sites and rearing pond’.
• Line 152-153 (Line 158-159): With regard to the reviewer’s doubt that how the optimal season for eDNA survey was determined, we changed the original sentence to “Finally, we calculated the detection rate of the target DNA at each sampling time, and then considered the season with highest detection rateas the optimal time for the following eDNA survey”.
• Line 162-163 (Line 165-167): The description of “TaqMan qPCR amplification procedure was optimized” (line 162) was improperly stated in the original manuscript. This has been rectified h.
• Line 167 (Line168): ‘our’ was changed to ‘This’.
• Line 187 (Line 200): The number are the sample ID listed in table 2.
• Line 193 (Line 206): ‘eDNA samples’ was changed to ‘water samples’.
• Line 235 (249): ‘16’ was added after ‘site’.
• Line 244 (Line 258):Following the suggestion of the reviewer, the ‘Materials and Methods’ section was reconstructed andFigure 4 used as supplementary materials.We prefer to group the date according the river for the reason that the habitat of Sichuan taimen in Qinlingmoutainswereseverely fragmented.
• Line246 (Line 247):Following the suggestion of the reviewer, Figure 4 was deleted in the text and used as supplementary materials.
• Line 250 (Line 260): ‘sites 5-10 and 13-18; see Figure 2’ was added.
• Line 251-257(Line 263-267): ‘cycle thresholds’ were changed to ‘Ct values’.
• Line 262 (Line 264): As suggested by reviewer, S1 was added as supplementary materials.
• Line 263-271(Line 274-283): I admit that this paragragh is poorly constructed and confusing.Wetempered the conclusion as it is high likely that Sichuan taimen is absent from those sites at this region. I hope that the revised manuscript is now suitable for publication.
• Line 289 (Line 302): ‘Sichuan’ was added before ‘taimen’.
• Line 331 (Line 352): ‘a space’ was added before ‘Yangtze River’.
• Line 335-250 (Line 325-332, Line 356-364): I admit that this paragragh is poorly constructed and confusing.I hope that the revised manuscript is now suitable for publication.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

I think this is a valuable and well-done paper which could be published. The authors are no so ambitious in the Discussion, but they made a good contribution to the study of a Red Book animal distribution. The success of eDNA method is demonstrated.

The only thing I can recommend is to replace the sub-chapter 2.1. Study species to Introduction, while the Introduction section must be shortened a bit.

Also the authors sometimes ignore the Italic in some genus and species epithets.

Few comments are in the file

Great success to the authors in their further studies!

Comments for author File: Comments.pdf

Author Response

Response to Reviewers Comments:

Specific comments: In order of referred line number (Revised line number):

List of Major Changes:
1) The title was changed to “Environmental DNA Detects Remaining populations of Endangered Stream Salmon (Sichuan Taimen: Hucho Bleekeri Kimura Salmonidae) in the Qinling Mountains”.

2) Abstract:

Revisions weremade on writing in this section.

3)Introduction:

Revisions weremade on writing in this section.

4) Materials and Methods:

Based on the suggestions, this section was reconstructed and major revisions were made on writing.

5) Result

According to comments, this section was reconstructed. Werewritten the results of eDNA Survey and added the Tab. S1 after the text as supplementary materials.

6) Discussion

The Discussion section was rewritten and reconstructed.The causal relationship between ‘Ct values of qPCR’ and ‘amount of DNA present in water samples’ was incorrectly stated in the original manuscript. This has been rectified. The authors are grateful to the referees for pointing out their error.

 

 

 

Response to Reviewer 2:

• I admit that our work requires more thoughtful analysis and considerable improvement in writing. Some grammar and spelling errors were corrected as suggestion. For example, 1) we rewrote the genus, species and subspecies name in italics in the text and in references.
• Line 3-15(Line 3-15)：‘Hucho bleekeri’ was written in italics and ‘Salmonidae’ was added after the species name.
• Line 34 (Line 34):‘expertise’ was added before the ‘expertise’; ‘Assessing species’ was changed to the ‘Species identification’.
• Line 43 (Line 43): ‘of’ was added after the ‘monitoring’.
• Line 56 (Line 54): ‘Hucho’ was changed to the ‘Salmonidae’.
• Line 84-113 (Line 85-116):The ‘Materials and Methods’ section was reconstructed as suggestion.We prefer to retain ‘study species’ and ‘study area’ in ‘Materials and Methods’ sectionfor reasons that it indicated the biological properties, geographical distribution and trends of Sichuan taimen of Qinling population in detail.
• Line 236 and line242 (Line 250 and line 257): ‘B. lenok tsinlingensis’ was written in italics.

 

 

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Minor suggestions attached

Comments for author File: Comments.pdf

Author Response

Dear reviewer,

 

Thanks for your comments and suggestions on our MS (fishes-2685688) which is entitled “Environmental DNA Detects Remaining populations of Endangered Stream Salmon (Sichuan Taimen) in the Qinling Mountains.” Thank you very much for proposing so helpful and positive comments on our manuscript. We appreciate you very much for your efforts. According to your suggestions, we checked entire MS, and made some revisions directly on the MS Word file by using a green font. Please check it. Thanks for your consideration for publication in Fishes.

 

With regards,

Dr. Wei Jiang

Shaanxi Key Laboratory of Qinling Ecological Security,

Shaanxi Institute of Zoology,

Xi’an, Shaanxi, 710032,

P. R. China

 

Response to Reviewer :

 

Specific comments: In order of referred line number (Revised line number):

 

• Line 121-122(Line 120)：As suggested by reviewer,the clause of ‘which was described in our previous study’ was deleted.
• Line 145-146 (Line 143-144): The serial numbers in map refer to sampling sites in season effect analysis. The map was rectified, and ‘the serial numbers indicate sampling sites and the green triangle indicates positive control.’ Was added as an illustration. I hope that the revised ‘Figure 1’ is now suitable for publication.
• Line 200 (Line 198-200): The serial numbers in map (figure 2) refer to table 1. ‘The serial numbers indicate survey sites and were also listed in corresponding table 1. The green triangle indicates positive control or negative c’ Was added as an illustration.
• Line 259(Line 259-260): The numbers in table heading refer to the number of species individuals caught.
• Line 272-273: Following the suggestion of the reviewer, figure 4 was deleted in the text and used as supplementary materials.

Author Response File: Author Response.pdf