Whole-genome resequencing of black-tailed prairie dogs that survived or died from plague infection
Introduced infectious diseases are a major threat to biodiversity, and outbreaks caused by novel pathogens can devastate wildlife populations. Pathogens exert strong selection on surviving hosts, sometimes eliciting the evolution of immunity in the host population. The bacterial pathogen causing sylvatic plague, Yersinia pestis, was introduced to North America in the early 1900s and caused widespread population declines in prairie dogs (genus Cynomys), which experience >95% mortality during epizootics. In 2013, survival from plague was documented in a small number of black-tailed prairie dogs (C. ludovicianus) in natural populations in Boulder, Colorado (USA). We performed whole-genome sequencing on all 7 individuals that survived infection with plague and 7 individuals that likely died. Our objective was to use genome-wide association tests, FST outlier tests, and other inferences of selection to infer SNPs under selection from plague. We aim to determine the degree to which parallel evolution occurs at the level of gene classes in addition to individual genes across the genus and broader taxonomic groups including humans. Understanding the genomic basis of immunity can enable genetically-informed management actions such as targeted relocation to protect grassland species. Moreover, understanding how rapid adaptation to pathogens occurs can help us predict the time frame and spatial scale at which adaptation may occur, during which other interventions are needed.