PONE-D-23-06704GBS-obtained data highlighted the necessity of an updated action plan for wild stocks management of Salmo caspius in the Caspian SeaPLOS ONE

Dear Dr. Jafari,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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ACADEMIC EDITOR:

Reviewer 1

Dear Authors

I had a chance to act as a reviewer of the ms PONE-D-23-06704 entitled: GBS-obtained data highlighted the necessity of an updated action plan for wild stocks management of Salmo caspius in the Caspian Sea submitted to PlosOne.

This is a study on the genetic diversity of Salmo caspius from a breeding center in the southern Caspian Sea basin. The authors have analysed four different groups of individuals based on the Genotyping-by sequencing (GBS) method. The results are new and interesting. Its publication in Plos One is highly recommended, however, after a significant revision of the present manuscript.

I have made most of the comments and edits in the attached pdf file, but a few main issues are listed below:

1- There are too many knowledge gaps in the introduction section (see the comments), which need further clarifications.

2- The sampling section needs improvement. As a reader, I have no idea what the four study groups are (NCP, NCPLY, CO, and CP). The authors need to explain these groups in more detail, and also explain the rationale for this grouping. This part needs to be explained carefully and comprehensively, since the whole study seems to be based on it.

3- Finally, there is a bias in the sampling. The CO and NCP groups are represented by 4 and 3 individuals respectively, whereas this is contrasted by the fact that in a standard population genetic analysis each population/group must be represented by at least 10 individuals. If possible, the number of analyzed samples should be increased for these two groups.

Sincerely Yours

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PlosOne

Thanks for considering me as a reviewer of the ms PONE-D-23-06704 entitled: GBS-obtained data highlighted the necessity of an updated action plan for wild stocks management of Salmo caspius in the Caspian Sea submitted to PlosOne.

This is a study on the genetic diversity of Salmo caspius from a breeding center in the southern Caspian Sea basin. The authors have analysed four different groups of individuals based on the Genotyping-by sequencing (GBS) method. The results are new and interesting. Its publication in Plos One is highly recommended, however, after a significant revision of the present manuscript.

I have made most of the comments and edits in the attached pdf file, but a few main issues are listed below:

1- There are too many knowledge gaps in the introduction section (see the comments), which need further clarifications.

2- The sampling section needs improvement. As a reader, I have no idea what the four study groups are (NCP, NCPLY, CO, and CP). The authors need to explain these groups in more detail, and also explain the rationale for this grouping. This part needs to be explained carefully and comprehensively, since the whole study seems to be based on it.

3- Finally, there is a bias in the sampling. The CO and NCP groups are represented by 4 and 3 individuals respectively, whereas this is contrasted by the fact that in a standard population genetic analysis each population/group must be represented by at least 10 individuals. If possible, the number of analyzed samples should be increased for these two groups.

Reviewer 2

The manuscript by Jafari et al. deals with population genetic analysis of a few groups from a hatchery in the south Caspian Sea basin that can provide data for stock augmentation purposes. Based on a fast review of the manuscript, I found major problems with taxonomic aspects, data analyses and also the claims made in the manuscript. I could not see and statistical support for the claims of the authors. The most important analysis for a conservation oriented work is the analysis of molecular variance (AMOVA) which is lacking. Or the genetic distance that is used has is not a good choice due to small sample sizes used in this study. Apparently, authors were not familiar with genomic works performed on the Caspian Sea trout in recent years and ignored them completely. Further, the manuscript needs language check by a native English speaking person.

Overall, I cannot accept the manuscript for publication in its current form. I suggest major revisions and resubmission.

My comments are listed bellow:

The title should be revised, may be: Genome-wide data suggest a revision in management of the Caspian Sea trout Salmo caspius

Abstract

Line 29: provide also authorship at first mention of the scientific names!

Line 34: GBS-obtained SNP variants: replace with genome-wide single nucleotide polymorphisms (SNP)

Line 36: admixture

38: critically endangered? It is not even listed in IUCN redlist. Please check it!

Introduction

Line 43: families

Line 45: consequence

Lines 45-47: no! Salmo trutta is the Atlantic trout! All natural populations of brown trout in the southern Caspian Sea basin are Salmo caspius: resident and sea-run forms are only ecological forms, but not species! Please rather than using general checklists, have a look at recent papers published on population genomics of Salmo caspius using the same approach used here:

Hashemzadeh Segherloo, I., Tabatabaei, S.N., Abdoli, A. et al. Biogeographic insights from a genomic survey of Salmo trouts from the Aralo-Caspian regions. Hydrobiologia 849, 4325–4339 (2022). https://doi.org/10.1007/s10750-022-04993-8

Hashemzadeh Segherloo, I., Freyhof, J., Berrebi, P., Ferchaud, A.L., Geiger, M., Laroche, J., Levin, B.A., Normandeau, E. and Bernatchez, L., 2021. A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?. Molecular Phylogenetics and Evolution, 162, p.107204.

Tabatabaei, S.N., Abdoli, A., Hashemzadeh Segherloo, I., Normandeau, E., Ahmadzadeh, F., Nejat, F. and Bernatchez, L., 2020. Fine-scale population genetic structure of Endangered Caspian Sea trout, Salmo caspius: implications for conservation. Hydrobiologia, 847, pp.3339-3353.

Tabatabaei, S.N., Abdoli, A., Ahmadzadeh, F., Primmer, C.R., Swatdipong, A. and Segherloo, I.H., 2020. Mixed stock assessment of lake-run Caspian Sea trout Salmo caspius in the Lar National Park, Iran. Fisheries Research, 230, p.105644.

Lines 47-49: I could not see any genetic work in references, which are cited (checklists). Please use references dealing directly with the Caspian sea trout using robust data. It is clear that resident form of the Caspian trout or any other member of Salmo trutta species-complex is morphologically different from lake- or sea-run forms. Please see the above mentioned references.

Lines 62-65: I guess these are not morphotypes, are they? They should be temporal ecotypes, which migrate during different seasons. Please clarify!

Line 76: please provide the complete terms at the first mention and then use only abbreviations: Next Generation Sequencing (NGS)

Lines 76-77: please provide references.

Line 79: only two citations show the wide use of the approach in population genetics and aquaculture? Please provide examples!

Line 84: breeding center or centers across the southern Caspian Sea basin? If more than one breeding center is considered, please indicate. In m&m section authors indicate only one breeding center!

Material and Methods

Lines 87-91: it is not clear how these fish were selected? where the fish had been caught from? Were they all from the same population? What was the relationship of different groups? What does it mean “new candidate parents”, “candidate parents last year”, “candidate offspring”, and “captured parents”? please clarify! How many specimens from each group? …

Line 97: not guideline, but protocol or manual

Line 98: please provide webpage of the manufacturer.

Line 102: please refer to citations properly! Jafari et al.

Line 103: webpage for BGI co.

Line 114: hired? Used?

Lines 135-138: as sample sizes used in this study are small, it is suggested to use other metrics like allele frequency differences to avoid problems related to small sample size. Fst is sensitive to small sample sizes.

Line 139: taken or calculated?

Results:

There are no details on proportion of missing data and how it was managed! Please clarify!

Lines 142-148: which K was selected in Structure analysis? Please clarify and provide statistical evidence.

The work aims at conservation, but one of the most important statistical analyses which is mostly used in conservation genetics works is missing: I expected to see AMOVA analysis of the data to see statistical support for population structure …

Line 179: Fig. 4a? appears to be 5a

Discussion

Lines 186-189: please see my previous comments: it is not the first genomic work on the Caspian Sea trout. There had been other studies!

Line 194: structure analysis

Lines 196-199: Fst is prone to small sample sizes, see previous comments!

Line 218: based

220-224: What is the mating scheme in the noted hatchery? The reduced diversity may be a result of breeding scheme! What was the sex ratio? How many brood fish had been used? And so on. All these are important factors which must be clarified.

Lines 226-227: It is not listed in the redlist as I searched! Please check!

Data availability

Line 248: data should be deposited in public databases like SRA or VCF files can be uploaded to Dryad …

Ethics:

Lines 251-252: Was there a licence issued by the Ethics committee? Pleas provide

References

References do not follow a standard and unified format. In some cases they are incomplete and details are missing!

Figure 1 why members of the same cluster (NCP) are distributed all around the graph? Is there any justification?

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Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: No

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: No

Reviewer #2: No

**********

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Dear Authors

I had a chance to act as a reviewer of the ms PONE-D-23-06704 entitled: GBS-obtained data highlighted the necessity of an updated action plan for wild stocks management of Salmo caspius in the Caspian Sea submitted to PlosOne.

This is a study on the genetic diversity of Salmo caspius from a breeding center in the southern Caspian Sea basin. The authors have analysed four different groups of individuals based on the Genotyping-by sequencing (GBS) method. The results are new and interesting. Its publication in Plos One is highly recommended, however, after a significant revision of the present manuscript.

I have made most of the comments and edits in the attached pdf file, but a few main issues are listed below:

1- There are too many knowledge gaps in the introduction section (see the comments), which need further clarifications.

2- The sampling section needs improvement. As a reader, I have no idea what the four study groups are (NCP, NCPLY, CO, and CP). The authors need to explain these groups in more detail, and also explain the rationale for this grouping. This part needs to be explained carefully and comprehensively, since the whole study seems to be based on it.

3- Finally, there is a bias in the sampling. The CO and NCP groups are represented by 4 and 3 individuals respectively, whereas this is contrasted by the fact that in a standard population genetic analysis each population/group must be represented by at least 10 individuals. If possible, the number of analyzed samples should be increased for these two groups.

Sincerely Yours

Reviewer #2: The manuscript by Jafari et al. deals with population genetic analysis of a few groups from a hatchery in the south Caspian Sea basin that can provide data for stock augmentation purposes. Based on a fast review of the manuscript, I found major problems with taxonomic aspects, data analyses and also the claims made in the manuscript. I could not see and statistical support for the claims of the authors. The most important analysis for a conservation oriented work is the analysis of molecular variance (AMOVA) which is lacking. Or the genetic distance that is used has is not a good choice due to small sample sizes used in this study. Apparently, authors were not familiar with genomic works performed on the Caspian Sea trout in recent years and ignored them completely. Further, the manuscript needs language check by a native English speaking person.

Overall, I cannot accept the manuscript for publication in its current form. I suggest major revisions and resubmission.

My comments are listed bellow:

The title should be revised, may be: Genome-wide data suggest a revision in management of the Caspian Sea trout Salmo caspius

Abstract

Line 29: provide also authorship at first mention of the scientific names!

Line 34: GBS-obtained SNP variants: replace with genome-wide single nucleotide polymorphisms (SNP)

Line 36: admixture

38: critically endangered? It is not even listed in IUCN redlist. Please check it!

Introduction

Line 43: families

Line 45: consequence

Lines 45-47: no! Salmo trutta is the Atlantic trout! All natural populations of brown trout in the southern Caspian Sea basin are Salmo caspius: resident and sea-run forms are only ecological forms, but not species! Please rather than using general checklists, have a look at recent papers published on population genomics of Salmo caspius using the same approach used here:

Hashemzadeh Segherloo, I., Tabatabaei, S.N., Abdoli, A. et al. Biogeographic insights from a genomic survey of Salmo trouts from the Aralo-Caspian regions. Hydrobiologia 849, 4325–4339 (2022). https://doi.org/10.1007/s10750-022-04993-8

Hashemzadeh Segherloo, I., Freyhof, J., Berrebi, P., Ferchaud, A.L., Geiger, M., Laroche, J., Levin, B.A., Normandeau, E. and Bernatchez, L., 2021. A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?. Molecular Phylogenetics and Evolution, 162, p.107204.

Tabatabaei, S.N., Abdoli, A., Hashemzadeh Segherloo, I., Normandeau, E., Ahmadzadeh, F., Nejat, F. and Bernatchez, L., 2020. Fine-scale population genetic structure of Endangered Caspian Sea trout, Salmo caspius: implications for conservation. Hydrobiologia, 847, pp.3339-3353.

Tabatabaei, S.N., Abdoli, A., Ahmadzadeh, F., Primmer, C.R., Swatdipong, A. and Segherloo, I.H., 2020. Mixed stock assessment of lake-run Caspian Sea trout Salmo caspius in the Lar National Park, Iran. Fisheries Research, 230, p.105644.

Lines 47-49: I could not see any genetic work in references, which are cited (checklists). Please use references dealing directly with the Caspian sea trout using robust data. It is clear that resident form of the Caspian trout or any other member of Salmo trutta species-complex is morphologically different from lake- or sea-run forms. Please see the above mentioned references.

Lines 62-65: I guess these are not morphotypes, are they? They should be temporal ecotypes, which migrate during different seasons. Please clarify!

Line 76: please provide the complete terms at the first mention and then use only abbreviations: Next Generation Sequencing (NGS)

Lines 76-77: please provide references.

Line 79: only two citations show the wide use of the approach in population genetics and aquaculture? Please provide examples!

Line 84: breeding center or centers across the southern Caspian Sea basin? If more than one breeding center is considered, please indicate. In m&m section authors indicate only one breeding center!

Material and Methods

Lines 87-91: it is not clear how these fish were selected? where the fish had been caught from? Were they all from the same population? What was the relationship of different groups? What does it mean “new candidate parents”, “candidate parents last year”, “candidate offspring”, and “captured parents”? please clarify! How many specimens from each group? …

Line 97: not guideline, but protocol or manual

Line 98: please provide webpage of the manufacturer.

Line 102: please refer to citations properly! Jafari et al.

Line 103: webpage for BGI co.

Line 114: hired? Used?

Lines 135-138: as sample sizes used in this study are small, it is suggested to use other metrics like allele frequency differences to avoid problems related to small sample size. Fst is sensitive to small sample sizes.

Line 139: taken or calculated?

Results:

There are no details on proportion of missing data and how it was managed! Please clarify!

Lines 142-148: which K was selected in Structure analysis? Please clarify and provide statistical evidence.

The work aims at conservation, but one of the most important statistical analyses which is mostly used in conservation genetics works is missing: I expected to see AMOVA analysis of the data to see statistical support for population structure …

Line 179: Fig. 4a? appears to be 5a

Discussion

Lines 186-189: please see my previous comments: it is not the first genomic work on the Caspian Sea trout. There had been other studies!

Line 194: structure analysis

Lines 196-199: Fst is prone to small sample sizes, see previous comments!

Line 218: based

220-224: What is the mating scheme in the noted hatchery? The reduced diversity may be a result of breeding scheme! What was the sex ratio? How many brood fish had been used? And so on. All these are important factors which must be clarified.

Lines 226-227: It is not listed in the redlist as I searched! Please check!

Data availability

Line 248: data should be deposited in public databases like SRA or VCF files can be uploaded to Dryad …

Ethics:

Lines 251-252: Was there a licence issued by the Ethics committee? Pleas provide

References

References do not follow a standard and unified format. In some cases they are incomplete and details are missing!

Figure 1 why members of the same cluster (NCP) are distributed all around the graph? Is there any justification?

==============================

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Kind regards,

Ishtiyaq Ahmad, Ph.D

Academic Editor

PLOS ONE

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Reviewer #1: No

Reviewer #2: No

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Attachments

Attachment

Submitted filename: PONE-D-23-06704_Reviewer_Comments.pdf

Genome-wide data suggest a revision in management of the Caspian Sea trout Salmo caspius

PONE-D-23-06704R1

Dear Dr. Jafri,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Ishtiyaq Ahmad, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Authors have adreesed all queries as per reviewer suggestions. So, I recommend your paper for publication.

Comments to the Author

Reviewer #1: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Dear Authors

I had a chance to review the revised version of the ms PONE-D-23-06704R1, entitled "Genome-wide data suggest a revision in management of the Caspian Sea trout Salmo caspius". It seems that you have implemented the comments/corrections based on the reviewer's comments.

I found it very interesting and now it can be considered for publication.

However, journal formatting should be done.

Best

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: Yes: Prof. Hamid Reza Esmaeili

**********