Evolutionary rescue in a host–pathogen system results in coexistence not clearance

The evolutionary rescue of host populations may prevent extinction from novel pathogens. However, the conditions that facilitate rapid evolution of hosts, in particular the population variation in host susceptibility, and the effects of host evolution in response to pathogens on population outcomes remain largely unknown. We constructed an individual‐based model to determine the relationships between genetic variation in host susceptibility and population persistence in an amphibian‐fungal pathogen (Batrachochytrium dendrobatidis) system. We found that host populations can rapidly evolve reduced susceptibility to a novel pathogen and that this rapid evolution led to a 71‐fold increase in the likelihood of host–pathogen coexistence. However, the increased rates of coexistence came at a cost to host populations; fewer populations cleared infection, population sizes were depressed, and neutral genetic diversity was lost. Larger adult host population sizes and greater adaptive genetic variation prior to the onset of pathogen introduction led to substantially reduced rates of extinction, suggesting that populations with these characteristics should be prioritized for conservation when species are threatened by novel infectious diseases.