Low‐Coverage Whole‐Genome Analysis of Population Structure, Bottlenecks, and Selection in Indiana Bats Before and After White‐Nose Syndrome

Conservation successes for the endangered Indiana bat (Myotis sodalis) in the early 2000s were largely reversed by white-nose syndrome (WNS), a novel fungal disease that emerged in North America in 2006. Impacts have been variable among Indiana bat colonies leading to uncertainty regarding the full impact of WNS on this species. However, many colonies maintain negative population growth, threatening long-term viability. Adaptive evolution could allow populations to persist despite disease, as has happened for other species; however, the evolutionary potential of Indiana bats remains unclear. Here, we perform low-coverage whole-genome sequencing to identify population structure, test for potential population bottlenecks, and scan for signatures of selection by comparing bat tissue samples from four states before and after WNS emergence. We found evidence of high connectivity across the Indiana bat range, but reduced gene flow to the colony from Northern New York. There was little evidence of a population bottleneck relating to WNS, suggesting disease-driven mortality has not significantly altered demographics in this species. Similarly, we found little evidence of parallel selection occurring across the sample set. However, 3 genes contained outlier loci within every state, and several SNPs showed signs of parallel selection within subsets of locations. Finally, although non-parallel allele frequency changes within a location are difficult to directly link to WNS, we found that groups of genes containing outlier loci in individual states were associated with immune, metabolic, and neural functions with a potential relationship to WNS pathophysiology.