Comparing the Utility of Microsatellites and Single Nucleotide Polymorphisms in Conservation Genetics: Insights from a Study on Two Freshwater Fish Species in France

Biodiversity is facing an unprecedented crisis and substantial efforts are needed to conserve natural populations, especially in river ecosystems. The use of molecular tools to guide conservation practices in rivers has grown in popularity over the last decades, but the amount of precision and/or biological information that would be gained by switching from the traditional short tandem repeats (STRs) to the increasingly used single nucleotide polymorphisms (SNPs) is still debated. Here, we compared the usefulness of STRs and SNPs to study spatial patterns of genetic variability in two freshwater fish species (Phoxinus dragarum and Gobio occitaniae) in southern France. SNPs were obtained from a pool-seq procedure and mapped to new genome assemblies. They provided much more precise estimates of genetic diversity and genetic differentiation than STRs, but both markers allowed the detection of very similar genetic structures in each species, which could be useful for delineating conservation units. While both markers provided similar outcomes, there were two discrepancies in genetic structures that could, nonetheless, be explained by unrecorded stocking events. Overall, we demonstrated that SNPs are not unconditionally superior to STRs in the context of large-scale riverscape genetic conservation, and that the choice of marker should primarily be based on research questions and resources available.