Conservation Genomics and Viromics of Sonoran Desert Felids

Abstract

Human population growth, urbanization, and reductions in critical wildlife habitats are drastically reducing biodiversity. Further, anthropogenic factors impact pathogen evolution, and emerging disease poses threats to wildlife, domestic animals, and humans. Small, threatened wildlife populations, which have less genetic diversity, are particularly vulnerable to further population decline related to disease or anthropogenic impacts. Therefore, conservation priorities should include studies of both disease threats and host genetic variability. In this dissertation, I present host and viral genomic studies of Sonoran Desert felids, highlighting important considerations for future wild felid management. In Appendix A, I describe three novel circovirus genomes detected in the feces of Sonoran felids. These genomes represent two distinct circovirus species, and the first to be described associated with felids. Circoviruses are associated with disease in other vertebrates, so future monitoring of these viruses in populations of Sonoran felids and their prey is of interest for promoting felid health and conservation. In Appendix B, I compare the DNA virome composition of pumas (Puma concolor) and bobcats (Lynx rufus) in Sonora, Mexico. I observed diverse circular DNA viruses in both species, and found pumas had greater levels of virome diversity, possibly due to bioaccumulation of pathogens in apex predators. I additionally found that, although there was considerable overlap in virome composition between the two species, there were significant differences that could be attributed to host species. This study contributes to the growing body of knowledge of wild felid viral diversity. In Appendix C, I combined SNP-based pedigree reconstruction with GPS data to test home range sharing among mother-daughter pairs of urban bobcats in the Tucson Mountains, Arizona. In this study, every mother identified as having at least one daughter shared home ranges with one daughter, while other confirmed daughters established adjacent home ranges. This study provides substantial support for female philopatry and male-biased dispersal, as well as for the mother-daughter home range sharing hypothesis and matrilineal land tenure. As human populations and urbanization continue to expand, it is crucial to investigate disease, behavioral, and genetic consequences to wildlife in anthropogenically altered habitats.