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Understanding the causes of population variation in host response to disease, and the mechanisms of persistence, can serve as vital information for species conservation. One such mechanism of population persistence that has gained support is the demographic process of compensatory recruitment. Host populations may persist by increasing recruitment to compensate for reduced survival due to infection, thus limiting the negative effects of the disease on population trajectories. However, high‐elevation populations are inherently vulnerable to stochastic processes and may be limited in their ability to exhibit compensatory recruitment relative to lower elevation populations. We use long‐term mark–recapture data from five populations of boreal toads Anaxyrus boreas boreas, across an elevational gradient in Colorado, before and after pathogen arrival to assess whether populations can persist with Batrachochytrium dendrobatidis (Bd) via compensatory recruitment. Prior to pathogen arrival, we found a life‐history trade‐off between survival and recruitment across elevations, where high‐elevation toads have high survival but lower recruitment and vice versa at lower elevations. Pathogen arrival had a strong negative effect on apparent annual survival and recruitment leading to negative population growth rates and dramatically reduced host abundances. The data did not support the occurrence of compensatory recruitment. Synthesis and applications. Our unique dataset indicates that demographic responses to pathogens may be environmentally (i.e. elevationally) context dependent and highlights the value of long‐term monitoring. We recommend that practitioners verify that potential persistence mechanisms occur across multiple populations and relevant environmental gradients to counter any assumptions of the mechanism existing species‐wide. Quantifying variation in population responses to disease will aid in understanding the bounds of such persistence mechanisms and identify particularly vulnerable populations where mechanisms are nonexistent.

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Catastrophic population declines due to disease often lead to fragmented remnant populations and loss of gene flow. Managers are left to determine appropriate conservation actions to recover and maintain population persistence. The recent utilization of genomic data to assist in species recovery now allows us to combine genome-wide surveys of differentiation and diversity with the identification of potentially adaptive regions to develop conservation plans that incorporate ecological and evolutionary processes. The unprecedented global decline of amphibian populations due to the pathogen Batrachochytrium dendrobatidis has increased the need to apply genomic tools to amphibian conservation practices. We show here how understanding genetic characteristics of remnant frog populations affected by disease can be applied directly to restoration efforts. Cascades frogs (Rana cascadae) occur in the mountainous regions of the Pacific northwestern United States and have declined dramatically at the southern edge of their range in California. We conducted genome-wide surveys within this region to inform conservation and reintroduction efforts. We found strong north-south genetic differentiation between Oregon and California and novel spatial structure within California. Genetic diversity was lower in California than Oregon and genetic drift was the most important driver of genetic diversity and population structure in California, making conservation efforts aimed at boosting overall genetic diversity most urgent. Spatial genetic structure of populations within California suggests that reintroductions to Lassen Volcanic National Park, where they were recently extirpated, should use remaining source populations south of the park. Our findings support the treatment of California's R. cascadae populations separately from the rest of their range and highlight the importance of conservation genomics in applied species conservation.