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ABSTRACT In our rapidly changing world, evolution is likely to play an important role in facilitating the resilience of wildlife populations. The Sierra Nevada yellow‐legged frog (Rana sierrae) provides a rare example of recovery following severe declines caused by the amphibian chytrid fungus (Batrachochytrium dendrobatidis). However, the role of evolution in facilitating this recovery remains circumstantial. In this study, we sought to gain insights into the potential role of evolution by comparing genomes of frogs from naive and recovering populations located in close proximity. Using multiple methods to scan frog genomes for signatures of selection, our study reveals several genomic variants associated with frog recovery. Specifically, we identify outlier gene variants across genes related to skin integrity and intracellular regulation, an interferon‐related gene and a recovery‐associated variant in RIN3—a gene that may play a critical role in disease defence and wound healing. Finally, we report no differences in genetic diversity between naive and recovering populations. Our study provides a rare example from natural populations that suggests that evolution can produce individuals that harbour adaptive alleles and allow population recovery in the presence of novel stressors. These findings complement recent research on rapid amphibian evolution in response to disease and provide mechanistic hypotheses for how individuals can prove resilient to disease outbreaks. 

Insights from conservation genomics have dramatically improved recovery plans for numerous endangered species. However, most taxa have yet to benefit from the full application of genomic technologies. The mountain yellow-legged frog species complex, Rana muscosa and Rana sierrae, inhabits the Sierra Nevada mountains and Transverse/Peninsular Ranges of California and Nevada. Both species have declined precipitously throughout their historical distributions. Conservation management plans outline extensive ongoing recovery efforts but are still based on the genetic structure determined primarily using a single mitochondrial sequence. Our study used two different sequencing strategies – amplicon sequencing and exome capture – to refine our understanding of the population genetics of these imperiled amphibians. We used buccal swabs, museum tissue samples, and archived skin swabs to genotype frog populations across their range. Using the amplicon sequencing and exome capture datasets separately and combined, we document five major genetic clusters. Notably, we found evidence supporting previous species boundaries within Kings Canyon National Park with some exceptions at individual sites. Though we see evidence of genetic clustering, especially in the R. muscosa clade, we also found evidence of some admixture across cluster boundaries in the R. sierrae clade, suggesting a stepping-stone model of population structure. We also find that the southern R. muscosa cluster had large runs of homozygosity and the lowest overall heterozygosity of any of the clusters, consistent with previous reports of marked declines in this area. Overall, our results clarify management unit designations across the range of an endangered species and highlight the importance of sampling the entire range of a species, even when collecting genome-scale data.