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Rates of emerging infectious diseases are increasing globally. Impacts of emerging diseases on wildlife populations have been identified as major drivers to species declines and extinctions. Species loss due to disease has necessitated prioritizing disease mitigation in wild populations. In particular, amphibians have been disproportionately affected by the disease, chytridomycosis, caused by a fungal pathogen Batrachochytrium dendrobatidis (Bd). Decades of amphibian species being on the brink of extinction has accelerated the need to interrogate amphibian-Bd interactions. In this dissertation, I focus on an emblematic example of amphibian-Bd dynamics. The mountain yellow-legged frog (Rana muscosa/sierrae), a high alpine species of the Sierra Nevada of California, have declined across more than 90% of their historical range with Bd being a major driver to their decline. While many populations have been lost, there are some remaining frog populations persisting even with Bd present. This devastating loss of a species juxtaposed to potential hope for recovery presents an excellent opportunity to investigate host-pathogen dynamics as well as refining conservation strategies to bolster remaining populations. In this dissertation, I explore this host-pathogen system by integrating a genomic perspective to both species and disease management. For Chapter 2, I focus on a region of the frog species range that is under intensive conservation efforts and used genetic samples from both extant and extirpated populations to inform management actions. In Chapter 3, I take a pathogen perspective and use similar genetic tools in a comparative approach to investigate underlying evolutionary histories of Bd in the Sierra Nevada of California and Central Panama. In Chapter 4, I expand our genomic efforts to the entire mountain yellow-legged frog species range to create an explicit framework for species recovery and management. Together, my work weaves topics of conservation genetics, disease ecology, and evolutionary biology to highlight the use of genomics for applied conservation and builds novel frameworks for addressing species declines in the face of persistent threats.

Supplemental Methods, Figures(S1-7), and References