Fine-scale maternal structure and high nuclear connectivity in the French populations of the Geoffroy's Bat (Myotis emarginatus)

The Geoffroy's bat (Myotis emarginatus) is a sedentary species increasingly threatened by habitat alteration. Here, we assessed genetic diversity and population structure in 760 individuals from 18 French maternity colonies using 34 microsatellite markers and mitochondrial D-loop sequences. Mitochondrial data revealed subtle regional structure, consistent with female philopatry, and a broader phylogeographic split between Western Europe and the Greater Middle East, reflecting historical isolation. In contrast, microsatellites showed high nuclear diversity and minimal population structure across France, with weak isolation by distance and kin clustering, indicating extensive male-mediated gene flow. Moreover, demographic inference suggested population stability, consistent with both marker types. This nuclear homogeneity and demographic stability are strikingly similar to the patterns observed in Rhinolophus ferrumequinum populations sampled at the same colonies, suggesting that reproductive aggregation can maintain connectivity even in sedentary species. Overall, M. emarginatus functions as a largely connected population at the national scale, although localized maternal lineages suggest the presence of functional phylopatric units around key maternity sites that warrant protection. Future genome-wide studies could refine conservation strategies by integrating fine-scale female philopatry with male-mediated connectivity.