Abstract
Despite their paramount importance in molecular ecology and conservation, genetic diversity and structure remain challenging to quantify with traditional genotyping methods. Next-generation sequencing holds great promises, but this has not been properly tested in highly mobile species. In this article, we compared microsatellite and RAD-sequencing (RAD-seq) analyses to investigate population structure in the declining bent-winged bat (Miniopterus schreibersii) across Europe. Both markers retrieved general patterns of weak range-wide differentiation, little sex-biased dispersal, and strong isolation by distance that associated with significant genetic structure between the three Mediterranean Peninsulas, which could have acted as glacial refugia. Microsatellites proved uninformative in individual-based analyses, but the resolution offered by genomic SNPs illuminated on regional substructures within several countries, with colonies sharing migrators of distinct ancestry without admixture. This finding is consistent with a marked philopatry and spatial partitioning between mating and rearing grounds in the species, which was suspected from marked-recaptured data. Our study advocates that genomic data are necessary to properly unveil the genetic footprints left by biogeographic processes and social organization in long-distant flyers, which are otherwise rapidly blurred by their high levels of gene flow.