Comparing the Utility of Microsatellites and Single Nucleotide Polymorphisms in Conservation Genetics: Insights from a Study on Two Freshwater Fish Species in France
Round 1
Reviewer 1 Report
The manuscript 'Comparing the utility of microsatellites and single nucleotide polymorphisms in conservation genetics: insights from a study on two freshwater fish species in France' (diversity-2353976) compares the use of STRs and SNPs in conseration genetics and try to answer if these two types of markers differ in estimating genetic diversitiy, genetic differentiation and spatial patterns in genetic variation.
In sum, I found the question relevant to this special issue, data quality good and methods well performed, but few efforts may need to improve the quality of this ms.
Introduction: this part looks somehow simple for me. I didn’t get any information about previous studies on this topic (ie, comparing STRs and SNPs) in other system. The authors only introduced the limitations of STRs and described the asset of SNPs. It will be more clear if the authors can write a new paragraph to introduce two focal species in this study. I will also suggest the authors add one sentence to alert the readers that two new reference genomes (though low quality) were generated in this study which definitely are useful for the community.
Line 51: I do not know why the author say SNPs ‘less informative than STRs’, please clarify the statement.
Materials and Methods: The authors claimed 42 sites were search but inds information was absent. Usually we should show sampling information in a table presenting the sample size of each site which matches the map. Also, the pipeline generating SNPs is too simple. The authors could summarize the brief procedures to produce SNPs in the case of citing another method paper. Parameters and programs used were not given. 3039 SNPs were obtained in gudgeons but 3000 SNPs were ‘radomly chosen’, please give details how to get the reduced SNPs set (e.g., only one SNPs from 39 loci which have two or more SNPs was kept). He was used a proxy of genetic diversiy in this study but I think the author need explaination for only selecting this index as we also use many other parameters such as inbreeding coefficient FIS and allelic richness, Ar).
Figure 1: figure captions says ‘the 41 sampled sites’ but in the text says 42 (Line 95)? please check which number is true.
Results：My main concern in this part is Figure 5. I would suggest the authors revise this figure (C) and (D) to compare the patterns revealed by SNPs and STRs.
Line 215-217: Figure 2A didn’t show evidence as stated ‘He was about one order of magnitude (i.e., ~10-fold) higher with SNPs than with STRs’. From Figure 2A, I would say ~3 -fold rather than 10. Please clarify why ~10-fold higher.
Line 242-243: same question as Line 215-217.
Line 245: mean±SD instead of max value of d should be shown.
Figure 5: (C), (D) actually visualized the ‘spatial’ genetic structure rather than genetic structure.
Discussion: The key pitfall of this study was that samples used for STRs were not identical with SNPs. From the perspective of conservation, absolute values of any genetic parameters would be nonesense unless in a comparative way. I would suggest the authors not focus on absolute values but relative ones. Regarding to the two discrepancies between STRs and SNPs, the authors can check if there are gene flow between suspected populations using STRUCTURE or ADMIXTURE. The scenario proposed seems unpossible (stock and extirpation events would be required to happen at the same time).
Minor revision in some sentences to be more clear.
Author Response
Please see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
The paper of Prunier et al constitutes an interesting study dealing with the comparison of the performance between STRs an SNPs in unravel several issues regarding diversity in organisms. Authors test this comparison in two freshwater fish species inhabiting in southwestern France. This study is very relevant due to the ongoing incorporation of genomics as a tool in conservation practices, and therefore, the need of improving and standarize methodologies and protocols. So far, although it exist, there are a few studies comparing these two kind of markers in different organisms, suggesting that any of them outperform the other in investigating genetic parameters, as is also shown by these authors. But of course each of them has its own advantages and handicaps over the other.
Authors here go one step further and also evaluate the spatial patterns of genetic variability. The biological models chosen for the study are adequate, as they can evaluate how markers works in two different species with different history lifes.
I consider this paper is suitable for being published in Diversity. Just I found some minor questions that would request to be solved before publication:
lines 108-109. It is a little bit confuse to me how is written. Do authors mean that they discarded the whole population? But what does it mean considering 90% missing data? As a whole? Individuals? Please clarify better this filter.
line 109: Does it mean that all analyzed SNPs had zero missing data?
line 111-112: this approach is adequate to uniform dataset to the same number of SNPs in order to make results comparable in both species. Please, clarify how random SNP selection was done.
I would like to see in the manuscript some analysis similar to Structure or Admixture as other way to check genetic structure based on both kind of markers.
I congratulate authors for such interesting and useful study
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
