An Integrative Appraisal of the Diversity of the Genus Myotis (Chiroptera, Vespertilionidae) in Chile

The taxonomy of Chilean Myotis has long been contentious, particularly regarding the status of M. arescens relative to M. atacamensis and M. chiloensis . Here, we use an integrative framework combining genome‐wide single nucleotide polymorphisms (SNPs), morphometrics, and bioacoustics to reassess lineage boundaries and evolutionary relationships in Chilean Myotis . We analyzed 19,707 high‐quality SNPs from 80 specimens spanning the full latitudinal distribution of the group, 10 external and craniodental measurements from 123 specimens, and 825 echolocation pulses from free‐flying bats. Population genomic analyses revealed three genetic clusters, but only M. atacamensis formed a deeply divergent and well‐supported lineage, with no detectable recent gene flow to southern taxa. In contrast, M. arescens and M. chiloensis showed shallow genetic differentiation, strong asymmetric gene flow, and a latitudinal gradient of shared ancestry. Phylogenetic reconstruction based on SNPs failed to recover reciprocal monophyly between M. arescens and M. chiloensis , and process‐based species delimitation strongly supported a two‐lineage model comprising M. atacamensis and a single southern lineage ( M. chiloensis  +  M. arescens ). Morphometric and bioacoustics analyses mirrored these patterns: M. atacamensis was clearly differentiated in skull size and echolocation calls, whereas M. arescens and M. chiloensis formed overlapping morpho‐acoustic continua. Together, our results indicate that M. atacamensis is an independently evolving desert‐adapted lineage, while M. arescens represents a northern population within a geographically structured M. chiloensis . We therefore recommend recognizing only two Myotis species in Chile and interpreting M. arescens as a population‐level unit within M. chiloensis , with important implications for taxonomy, biogeography, and conservation assessments.