Conservation Genomics of the Endangered Mexican Wolf and De Novo SNP Marker Development in Pumas using Next-Generation Sequencing

Traditionally, conservation genetics has examined neutral-marker (e.g microsatellite) surveys to inform the conservation and management of species. The field expanded together with the expansion of molecular biology, primarily enabled by polymerase chain reaction (PCR) and DNA sequencing technologies. Recently, advances in genomics and bioinformatics, notably next-generation sequencing (NGS), have demonstrated the ability to further enhance conservation genetic assessments. As a result, conservation genetics is rapidly transforming into a field of conservation genomics. Although complete genome sequencing and analysis is still beyond the reach of many conservation genetic projects, researchers can benefit by producing large amounts of genetic data quickly for their species of interest, or by exploiting existing genomic data for a closely related species. The research presented below serves as an example of these two different approaches. First, I review the current state of conservation genomics, utilizing examples when appropriate to illustrate different techniques and approaches. Next, I describe the development of a tool using NGS that is useful for the rapid genetic analysis of pumas (Puma concolor) called PumaPlex. This work details the methods involved and will be useful for anyone interested in working with a species where little genomic data is available. The last three chapters focus on using an existing genomic tool for the domestic dog to analyze admixture, quantify inbreeding, and identify potential adaptive variation in the endangered Mexican wolf (Canis lupus baileyi). The results demonstrated the Mexican wolf has no significant recent ancestry from domestic dogs, and that several loci may potentially be effective in increasing fitness in the reintroduced population