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Cryptic species diversity is known to be common in bats but remains challenging to study in these mammals, whose natural history traits render their sampling and monitoring challenging. For these animals, indirect genetic approaches provide a powerful tool to gain insight into the evolutionary history and ecology of cryptic bat species. The speciation history of the polyphyletic Chaerephon pumilus species group (Molossidae) is poorly understood, including those found on western Indian Ocean islands. Two species in this complex have been identified in the Comoros: C. pusillus and C. leucogaster. Here, we aim to genetically characterize these two species and investigate their spatial population genetic structure. Analyzing five nuclear microsatellite markers from 200 individuals and one mitochondrial DNA gene (Cyt‐b) from 161 (out of the 200) individuals sampled on Madagascar and the Comoros, our findings indicated that these species are genetically differentiated. We observed mitonuclear discordance in numerous individuals (33% of the 161 mtDNA‐sequenced individuals). Based on ABC analyses, we found that this pattern could potentially be the result of asymmetric introgressive hybridization from C. leucogaster to C. pusillus and calls for further studies on the demographic history of these species. Moreover, at the intra‐specific level, analyses of the microsatellite loci suggested the evidence of a more pronounced, although weak, geographically based genetic structure in C. pusillus than in C. leucogaster. Altogether, our findings provide preliminary insights into the eco‐evolutionary aspects of this species complex and warrant further research to understand hybridization dynamics and mechanisms responsible for mitonuclear discordance. [ABSTRACT FROM AUTHOR]

Fine-scale spatial genetic structure of populations results from social and spatial behaviors of individuals such as sex-biased dispersal and philopatry. However, the demographic history of a given population can override such socio-spatial factors in shaping genetic variability when bottlenecks or founder events occurred in the population. Here, we investigated whether socio-spatial organization determines the fine-scale genetic structure for both sexes in a Mediterranean mouflon ( Ovis gmelini musimon × Ovis sp.) population in southern France 60 years after its introduction. Based on multilocus genotypes at 16 loci of microsatellite DNA ( n = 230 individuals), we identified three genetic groups for females and two for males, and concurrently defined the same number of socio-spatial units using both GPS-collared individuals ( n = 121) and visual resightings of marked individuals ( n = 378). The socio-spatial and genetic structures did not match, indicating that the former was not the main driver of the latter for both sexes. Beyond this structural mismatch, we found significant, yet low, genetic differentiation among female socio-spatial groups, and no genetic differentiation in males, with this suggesting female philopatry and male-biased gene flow, respectively. Despite spatial disconnection, females from the north of the study area were genetically closer to females from the south, as indicated by the spatial analysis of the genetic variability, and this pattern was in accordance with the common genetic origin of their founders. To conclude, more than 14 generations later, genetic signatures of first introduction are not only still detectable among females, but they also represent the main factor shaping their present-time genetic structure. [ABSTRACT FROM AUTHOR]