PONE-D-23-37840Spatial population genetic structure of Caquetaia kraussii (Steindachner, 1878) evidenced by species-specific microsatellite loci in the middle and low basin of the Cauca River, ColombiaPLOS ONE

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Reviewers' comments:

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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: Partly

Reviewer #2: Yes

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

Reviewer #1: No

Reviewer #2: Yes

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

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Reviewer #1: No

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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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: Comments to: “Spatial population genetic structure of Caquetaia kraussii (Steindachner, 1878) evidenced by species-specific microsatellite loci in the middle and low basin of the Cauca River, Colombia” by IC Tenorio, CD Joya and EJ Márquez.

This MS describe population genetic structure and genetic diversity of a cichlid species. Using variability of 16 microsatellite loci the authors found high genetic diversity and four genetic clusters.

The MS is well written and easy to follow. I have comments.

1.- The manuscript is not in the format of the journal. Authors should consider the submission instructions for their papers.

2.- MS lacks page number and line numbers

Introduction

3.- Page 1 introduction. Please add a reference to: “Moreover, individuals that migrate and reproduce with distant populations exhibit gene flow and, thus, high genetic diversity.”

4.- “Particularly, this study aimed to provide a response to C. kraussii genetic diversity and

structure related questions between 2020 and 2022”. I cannot find where the authors used date (2020-2022) in the analysis. Please explain or delete.

Materials and methods

5.- “Furthermore, a discriminant analysis of principal components (DAPC) was

performed using the R-package Adegenet (Jombart, 2008), with six principal components

retained.” How the authors selected 6 PCA? How many DL were used? The authors used de a-score?

6.- “Other approach included a Bayesian analysis in STRUCTURE 2.3.4 (Pritchard et al., 2000), with 1,000,000 Monte Carlo Markov chains with 100.000 regarded as the burn-in period.” The authors used the admixture model? The authors used correlated or uncorrelated allele frequencies?

7.- “BayeScan v2.1 (Foll & Gaggiotti, 2008) was used for loci detection under selection.” BayeScan could be used before all analysis.

8.- “Lastly, GENECLASS2 (Piry et al., 2004) was used for testing whether an individual resides in the sampled site or is immigrant from another section. To this end, L_home/L_max rate was used for first generation migrant detection.” Why you expect first generation migrant? Please use other methods (e.g. BayesAss).

Results:

9.- “Genetic diversity showed a decreasing gradient from the lower to the middle section of the Cauca River (S8>S7>S6>S5>S4)” Please add a figure for this result.

10.- “for both He (R: -0.970, p: 0.001) and Ar (R: 1.000, p: 0.000)”. Please, never a p-value = 0. Probability in this case could be p < 0.0001.

11.- Table 2.: please careful with p-value. Change from 0.0000 to <0.0001.

12.- Table 2: Change from “PHWE: statistical significance tests of departure from Hardy-Weinberg equilibrium.” To PHWE: p-value for the departure from Hardy-Weinberg equilibrium. Same for FIS p-value

13.- “Furthermore, Bayescan posterior probability (PO) values for the loci detection under selection (Supplementary Table 4) evidenced that the only paired comparison showing one locus under selection (Ckra 21; reference value > 0.76) was S4-S5 v. S6-S7-S8. Moreover, another parameter found, Alpha, had a value of 1.234 which suggests the existence of balancing or purifying selection. It is important in the analysis this detection? Do you erase these loci? No words in discussion about that?

14.- “(Supplementary Figure 2)”: I cannot find this figure.

Discussion

Please re-write this section considering a whole discussion follow the main goal of the study. Discussion about each method used cannot be useful for readers. For example, main results are about population genetic structure. Thus, what about the respective role of the barriers and fish behavior, etc.

Discussion about Ne is poor. Please improve this section comparing with other species.

Conclusion

Please re-write considering main results.

References

Please change “Referencias” to “References”

Change format to plosone

Figures

Change quality (300 dpi)

Reviewer #2: The manuscript contains an interesting study on the genetic diversity and populations structure of the cichlid Caquetaia Krausii located in the basin of the Causa River. The topic is worthy of investigation, and the manuscript is particularly interesting in that it investigates the effect of Ituango hydroelectric project on the genetic structure of the species.

In principle, the experimental design is appropriate, except that the study of EPSC stock does not fit in. The objective of the manuscript is to determine the genetic diversity of the species and the genetic structure of the population. In my opinion, the main factor in examining the genetic structure is the impact of the hydroelectric project on the natural populations, and the farm stock does not correspond to the natural stock.

The structure of the introduction is appropriate; however, I suggest including a paragraph on the hydroelectric project and the effect of such projects on the genetic diversity of cichlids.

The description of the methodology needs some corrections:

Please add sample sizes in the materials and methods. They could be found only in Table 2 in the results.

The 16 microsatellite markers were selected from 30 “according to their polymorphism level” – this means that 14 were monomorphic, or that the PIC value was not enough high?

Please add the description of the Mantel test to the materials and methods.

Please add the proportion of SMM in TPM, the variance of TPM and the number of iterations for the Wilcoxon signed rank test.

Results:

The authors give a negative correlation between Ar and geographical distance, but the value of R is 1.000 (based on the figure, this does not seem realistic). Please revise it.

In Table 2, are the values means of the 16 markers? If yes, then please include SD also. Was there a statistical comparison between populations? If yes, significant differences should be marked and taken into account in the diversity gradient in the text.

The resolution of Figure 2 is low, making the figure difficult to interpret.

Additionally to the first-generation migrant detection, I suggest calculating the relative directional migration network by the method based on Jost's D using divMigrate-online software (Sundqvist et al., 2016). In addition to a statistical assessment of one-way migration, this also provides a good and easy-to-understand chart to illustrate the extent of migration.

I recommend running the mantel test without the farm stock, as it is expected to improve the correlation. Moreover, it might be also useful to calculate only the stocks under the hydroelectric project separately, taking into account its strong impact.

Discussions should focus less on the reproductive features of the species and more on the habitat characteristics that may cause differences in population size and diversity of subpopulations. This is particularly valid for the hydroelectric project (founder effect, relatedness, migration rate, etc.).

Nevertheless, after the necessary corrections, the manuscript could provide valuable results for the population genetics of Cichlid fishes.

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Reviewer #1: No

Reviewer #2: No

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PONE-D-23-37840R1Spatial population genetic structure of Caquetaia kraussii (Steindachner, 1878) evidenced by species-specific microsatellite loci in the middle and low basin of the Cauca River, ColombiaPLOS ONE

Dear Dr. Márquez,

Thank you for submitting your revised 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.

Please submit your revised manuscript by May 27 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Sven Winter

Academic Editor

PLOS ONE

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Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Additional Editor Comments:

The manuscript has greatly improved, and the reviewers were mostly satisfied with the changes. Before acceptance, however, I would like a more detailed reply to the open question regarding the inclusion of the EPSC stock, as this was repeatedly criticized by reviewer 2. 

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: (No Response)

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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

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: 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: No

Reviewer #2: Yes

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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

Reviewer #2: Yes

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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: the authors answered all my questions. the authors performed new analyses, corrected typos and rewrote the discussion

Reviewer #2: The authors have made significant changes to the manuscript, taking into account most of my suggestions. I accept the methodology and justification for the migration estimation. However, I still see no justification for including the EPSC stock in the analysis, as it is a farm stock, not a natural one. As a basis for comparison (as explained by the authors), I can only accept it if the genetic characteristics of the PHI (above dam) stock are compared with those of the EPSC stock, since it was assumed that isolation is observed for both stocks. However, this would require more data on the EPSC stock (how long it has been bred in isolation, what founder stock size it started with, etc.), and would then give a good indication of what the dam construction has caused in the PHI stock in comparison. This was partly done in the discussion, it is worth highlighting the changes in more detail.

In addition, Figure 3 showing the STRUCTURE analysis results is missing from the uploaded manuscript.

Nevertheless, with the above suggestions, I consider the manuscript publishable.

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Reviewer #1: No

Reviewer #2: No

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Spatial population genetic structure of Caquetaia kraussii (Steindachner, 1878) evidenced by species-specific microsatellite loci in the middle and low basin of the Cauca River, Colombia

PONE-D-23-37840R2

Dear Dr. Márquez,

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.

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Sven Winter

Academic Editor

PLOS ONE

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