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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

Understanding the effect of individual differences on trophic interactions of upper-level predators, which can have disproportionate effects on an ecosystem, is imperative for successful management of populations. Marine mammals that prey on fish species of commercial and conservation importance are thus of particular interest. However, quantitatively monitoring and evaluating the impact of marine mammals on the environment is challenging because it is difficult to observe, capture, and collect repeated samples of individuals. Molecular genetic analysis of scat provides an inexpensive and feasible option to address these challenges. I developed an innovative non-invasive method for re-sampling individual marine mammals by collecting harbor seal (Phoca vitulina) scat at a haul-out in Cowichan Bay, B.C. I chose to study this species because it is the most abundant pinniped in the inland waters of the Pacific Northwest and a notable predator on fisheries stocks. In addition, a Python-based computer program for experimental design, incorporating genotyping error, was created to determine the sampling schemes needed to genetically track individuals of any taxa with site fidelity. My results demonstrate that non-invasive individual tracking via microsatellites can be successfully implemented in marine mammals. Furthermore, the optimum sampling scheme to track individuals over a given time frame at the study site requires 690 samples over 23 bouts (30 samples per bout). These genetic-tracking and sampling scheme methodologies can be applied to help answer several biological questions including diet, relatedness, population structure and impacts on species of interest.