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