Immunogenetic profiling of little brown myotis

White nose syndrome (WNS) has devastated populations of several species of bats in North America, leading to emergency conservation listings for several species including the previously ubiquitous little brown myotis (Myotis lucifugus). However, some bat populations near the epicenter of WNS panzootic may be stabilizing after initial precipitous declines, which could reflect a selective immunogenetic sweep in some populations. To investigate this hypothesis, we developed a novel, high-throughput sequence capture assay targeting 138 adaptive, intrinsic, and innate immunity genes of putative adaptive significance, as well as their respective regulatory regions (~370-kbp of genomic sequence per individual). We used the assay to explore baseline immunogenetic variation in M. lucifugus, and to investigate whether particular immune genes are associated with short-term survival of WNS, as predicted under an evolutionary rescue scenario. Our assay also detected 1,038 putatively neutral single-nucleotide polymorphisms to characterize contemporary population structure, providing context for the identification of local immunogenetic adaptation. Sequence capture provided a cost-effective, ‘all-in-one’ assay to test for genetic structure and patterns of local adaptation, revealing fine-scale, baseline immunogenetic differentiation between sampling sites <600 kilometers apart. We also identified functional immunogenetic variants in M. lucifugus associated with short-term WNS survival, indicating a theoretical potential for evolutionary rescue that requires further investigation. This study lays the foundations for future investigations of range-wide immunogenetic adaptation to WNS in M. lucifugus, and provides a blueprint for studies of evolutionary rescue in other host-pathogen systems.