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Myotis lucifugus, once among the most widespread and common bats in North America, has been forecast to be extirpated east of the Rockies in as few as 16 years by the spread of white-nose syndrome. Recent genetic research has demonstrated that this species is paraphyletic and part of a broader species complex; however, only one lineage (Myotis lucifugus lucifugus [M. l. lucifugus]) is present in eastern North America. I used molecular tools and niche modeling to validate this and investigate the role that historical biogeography has played in the phylogenetic and population genetic structure of this species to determine if the eastern subspecies represents an evolutionarily distinct population.To establish the genetic structure within M. l. lucifugus, I densely sampled maternity colonies in Minnesota and sequenced 182 individuals for a portion of cytochrome b. Phylogenetic reconstruction and a haplotype network were used to infer the relationships among mitochondrial haplotypes. Population growth statistics were calculated to determine if there was evidence of significant expansion, and an environmental niche model (ENM) was constructed based on conditions during the last glacial maximum (LGM) to illustrate potential glacial refugia. All individuals derived from a single mitochondrial lineage. Genetic evidence points to population growth starting approximately 18 kya. ENM results show that there was likely a single large southern refugium extending across the southeastern United States and possibly several isolated refugia in western North America. Myotis lucifugus lucifugus likely maintained both a large range and a large population during the peaks of the glacial cycles, and its population appears to have expanded following the retreat of the Laurentide ice sheet. This imperiled lineage likely diverged in isolation from other members of the M. lucifugus/western long-eared Myotis during the Pleistocene.

Bats face an unprecedented array of threats in the early 21st century, from traditional concerns such as habitat loss, to white nose syndrome and collisions with wind turbines. These growing challenges arise when the National Wildlife Refuge System, a system of public lands and waters that provides habitat for nearly every bat species in North America north of Mexico, is beginning its first revision cycle for its management plans, known as Comprehensive Conservation Plans. The U.S. Fish and Wildlife Service is thus uniquely positioned to assess its current contribution to sustaining viable populations of bats in the United States and incorporate those findings into the biological objectives that will guide Refuge management for the next 15 y. We present a review of the degree to which the first generation of Comprehensive Conservation Plans addresses bat conservation, and we provide recommendations to guide managers, planners, and partners in the development of the second generation of these Comprehensive Conservation Plans.