Variant call file for mountain yellow-legged frog (MYLF) selection analysis

Vast alteration of the biosphere by humans is causing a sixth mass
extinction. Adaptation to modified environments often is the only means
for species to persist, but the extent to which such "evolutionary
rescue" can prevent or reverse biodiversity loss is largely unknown.
Using results from genomic analyses, a 15-year reintroduction effort, and
population modeling, we provide a compelling example of evolution
reversing the declines of an imperiled amphibian and allowing the
reestablishment of extirpated populations. The once-common mountain
yellow-legged (MYL) frog is threatened with extinction by the
human-facilitated emergence of a lethal fungal pathogen (Batrachochytrium
dendrobatidis; "Bd"). Although most MYL frog populations are
extirpated following disease outbreaks, some persist and eventually begin
to recover. Using an exome capture approach, we show that MYL frogs have
undergone substantial evolutionary change following disease outbreaks.
Moreover, in naturally recovering populations observed changes in immune
function loci are associated with increased resistance/tolerance to Bd
infection. Large-scale reintroduction of frogs from rescued populations
resulted in the establishment of reproducing populations despite ongoing
disease. In addition, results from viability modeling suggest that
established populations have a low probability of extinction over 50
years. Collectively, these results provide a rare example of how
evolutionary rescue and the reintroduction of resistant/tolerant
individuals can allow the landscape-scale recovery of disease-impacted
species. This example has potentially broad implications for the many taxa
worldwide that are threatened with extinction by anthropogenic stressors.