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.

尽管它们在分子生态学和保护中至关重要，但遗传多样性和结构仍然难以用传统的基因分型方法进行量化。下一代测序技术前景广阔，但尚未在高度流动的物种中进行适当的测试。在本文中，我们比较了微卫星和 RAD 测序 (RAD-seq) 分析，以研究数量下降的弯翅蝙蝠 ( Miniopterus schreibersii)的种群结构) 在整个欧洲。这两个标记都恢复了弱范围分化的一般模式，很少有性别偏见的扩散，以及与三个地中海半岛之间重要遗传结构相关的距离强烈隔离，这可能是冰川避难所。微卫星在基于个体的分析中证明没有信息，但基因组 SNP 提供的分辨率阐明了几个国家内的区域子结构，殖民地共享不同祖先的迁移者而没有混合。这一发现与该物种的交配地和饲养地之间明显的亲属关系和空间划分是一致的，这是从标记重新捕获的数据中怀疑的。