Genetic insight into diversity and population structure provides hints for the conservation of the vulnerable South European roach Sarmarutilus rubilio (Leuciscidae)

Abstract The South European roach Sarmarutilus rubilio is a threatened freshwater fish, endemic to the Italian peninsula. Previous investigations revealed the presence of three mitochondrial haplogroups (namely HpA, HpB, and the highly divergent HpC) that originated in allopatry, despite currently coexisting at the margins of the species’ distribution. However, no information on S. rubilio contemporary genetic structure is available. In this study, we tested cross-amplification for 19 Leuciscidae-designed microsatellite loci, optimizing protocols for 12 of them that were used to analyze genetic variation, population structure, and demography in twelve S. rubilio populations representative of the species range. Our results revealed population structuring at the basin scale, which is more pronounced than differentiation revealed by mtDNA, indicating the role of local and relatively recent processes (e.g., isolation, habitat fragmentation, genetic drift, environmental selection) over ancient phylogeographic ones. Overall, we did not find evidence of compromised genetic diversity and strong bottlenecks, although in some sites a low effective population size was detected. In addition, microsatellites did not support the hypothesis of HpC as a cryptic species. These data provide practical indications to support the conservation and management of S. rubilio as required by the European Habitats Directive.