PONE-D-23-37221Temporal analysis of genetic diversity and gene flow in the threatened catfish Pseudoplatystoma magdaleniatum from a dammed Neotropical RiverPLOS ONE

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I have now received comments from two reviewers on this manuscript. They both agree that the manuscript is technically sound but they both recommended minor revisions to the text before it can be recommended for publication. Reviewer 1 also made edits directly on two pdf files that are attached. I think that the authors should incorporate all of the reviewers' comments as this will greatly improve the quality of the manuscript.

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This study was supported by a grant framed under the Project “Variabilidad genética de un banco de peces de los sectores medio y bajo del río Cauca” (CT-2019-000661, Empresas Públicas de Medellín and Universidad Nacional de Colombia, Sede Medellín). Funders do not play any role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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This study was supported by a grant framed under the Project “Variabilidad genética de un banco de peces de los sectores medio y bajo del río Cauca” (CT-2019-000661, Empresas Públicas de Medellín and Universidad Nacional de Colombia, Sede Medellín). Funders do not play any role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Additional Editor Comments:

I have now received comments from two reviewers on this manuscript. They both agree that the manuscript is technically sound but they both recommended minor revisions to the text before it can be recommended for publication. Reviewer 1 made edits directly on two pdf files that are attached. I think that the authors should incorporate all of the reviewers' comments as this will greatly improve the quality of the manuscript.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

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: Yes

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

Reviewer #1: Yes

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: No

Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: Striped catfish Psuedoplatystoma magdalineatum is an important, fished species in the Magdalena drainage of Columbia. It has declined to the point that it is listed as endangered. Hence, assessment of population genetic variation is pertinent to gain an understanding of its genetic viability, to gain insights into its recent demographic history, and to delineate populations as units for fishery management, Garcia-Castro and Marquez screened 13 species-specific microsatellite DNA markers and applied a battery of standard population genetic tests to old and new samples collected from the lower Magdalena-Cauca basin. They found considerable genetic diversity, one panmictic population, and evidence of a recent genetic bottleneck, findings which will inform management. The authors appropriately called for population genetic assessment at a larger spatial scale. The study design is straightforward, and the statistical tests and interpretations are appropriate. The findings can be presented more crisply as suggested below. I’ve marked the manuscript to guide revision of the English prose; I hope the authors find my marks constructive.

Methods. – At line 135, I believe the authors do not mention site S1 in error.

Results. – The paragraph starting on line 231 should mention whether any particular loci or populations presented frequent departures from Hardy-Weinberg equilibrium.

At lines 245-246, the authors oversell the likelihood of the infinite alleles model (IAM) applying to their data. Most frequently, it is the two-phase mode that best applies to microsatellite data, often with about 80% stepwise mutation and 20% non-stepwise mutation. Why say anything about the likelihood of the IAM applying best? Why not simply report the results obtained, that IAM yielded a significant test result and the other models did not? The authors have a low M Garza and Williamson (2001) metric, and the cognizant reader will make their own judgement of there having been a recent bottleneck.

At line 261, the authors should strike the word “not”. Infinite estimates of Ne do not provide evidence that the population IS very large.

The authors should not make a big deal over the recent samples having a larger estimated Ne than the old samples. The confidence intervals overlap, which should be mentioned at line 265.

I marked the sentence at line 266 to read of genetically effective migration. Now that I have had an hour to reflect on that, I realize that GeneClass2 does not show genetically effective migration, so the authors should not make that change.

At line 275, I think that the authors intend to write within POPULATIONS. A word seems to be missing.

Discussion. – At line 308, the point of the sentence can be sharpened as: environmental and anthropogenic pressures threaten the demographic and genetic viability of the species, particularly those recognized as having some degree of vulnerability.

At line 326, the change in estimated Ne should be characterized as a non-significant increase. The confidence intervals are large, the estimates are imprecise and rather comparable, so the change should not be oversold.

At line 336, the minimum Ne estimates of 414 SUGGEST LONG-TERM evolutionary risks for this POPULATION OF the species.

References. – The literature citations are reasonably clean, but I did mark a few minor issues.

Reviewer #2: The manuscript reports the genetic diversity and population structure of the endangered fish Pseudoplatystoma magdaleniatum, using microsatellite loci. It is well written and presents data worthy of publication in PlosOne. However, there are some points that must be clarified and others that should be modified to improve the article. See my comments and suggestions below.

Line 39-40. Reword as suggested: basin showed healthy genetics after molecular analyses.

Line 44. If it was previously molecularly analysed, please complete the sentence with this information.

Line 65. Reword as suggested: large migratory fish and the most important fishing resource of Colombia

Line 69-71. All these sentences must be reworded. See my suggestion below.

P. magdaleniatum in the middle and lower sectors.... showed high genetic diversity and absence of populational structuring when analysed by microsatellites (quoted reference).

Line 71-74. Reword the entire paragraph since, similarly, these mentioned species did not show genetic structuring. In addition, data on inbreeding or genetic diversity (e.g. Ra, He, Ho) are not reported for all mentioned species.

Line 97. Change "above" to "mentioned"

Line 104-106. Reword as suggested: … genetic monitoring emerges as an alternative to estimate the threat status and potential changes in genetic diversity of wild populations over time, mainly of those species with some degree of conservation concern and subjected to disturbances in its ecosystem (Laikre et al., 2010; Schwartz et al., 2007).

Line 107-108. Delete “Ex-ante and Ex-post, since this information must be provided in the Material and Methods.

Line 110-11: I suggest rephrase this sentence as suggested below:

The expectations of this work were to find high genetic diversity and no population structuring in P. magdaleniatum of the Cauca River, based on the findings previously reported by...

Line 117. Change "Ex-ante and Ex-post samples" to "sampling"

Line 197 - . Rephrase as suggested below:

To explore genetic changes on a temporal scale of the population of this species, genotypes previously obtained for individuals collected during the years 2010 - 2014 (Ex-ante sample) in sectors of the middle and lower sites of the Magdalena-Cauca basin, using the same set of microsatellite loci and the same methodology for genotyping them (see García-Castro et al., 2021), were included in the analysis, totaling of 311 individuals of P. magdaleniatum.

Line 219-220. Make clear how stuttering effects were corrected.

Line 232-233. Reword as suggested: no locus evidenced deviation from equilibrium in S4-S5 and just one locus (Psm18)…

Line 234. Explain what false positive means in that context.

Line 238. Correct to: to only one locus (Psm24).

Line 315. Please quote some more recent biblio. references on this subject.

Line 358-36. Reword as suggested: In conclusion, our results indicate that P. magdaleniatum has high genetic diversity and is not genetically structured along the Cauca River, although preserving evidence of recent reductions in its population size.

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Reviewer #1: No

Reviewer #2: Yes: Patrícia Domingues de Freitas

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Attachments

Attachment

Submitted filename: Garcia-Castro and Marquez 1.pdf

Attachment

Submitted filename: Garcia-Castro and Marquez 2.pdf

Temporal analysis of genetic diversity and gene flow in the threatened catfish Pseudoplatystoma magdaleniatum from a dammed Neotropical River

PONE-D-23-37221R1

Dear Dr. Marquez,

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Kind regards,

Jesus E. Maldonado, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

The authors have adequately addressed all of the reviewers' comments. The manuscript is now much improved and meets the publication criteria in PlosOne.

Reviewers' comments: