<p> Minimizing inbreeding depression and maintaining genetic diversity are central goals of conservation programs, including the Greenback Recovery Program (GRP), an interagency effort to protect the lineage of trout native to the South Platte River drainage in Colorado. The last remaining population of greenback cutthroat trout consists of about 700 individuals found in a three-mile stretch of stream in the Arkansas drainage, outside its native range. The GRP is committed to reintroducing the greenback into its native range in the South Platte. To do so, they are using a hatchery stock founded by 46 wild individuals. Both wild and hatchery populations have limited genetic diversity and deformities are common in the hatchery population. </p><p> Recovering the fitness of the hatchery population of greenbacks requires variation in fitness upon which selection can act. I performed crosses between individuals to quantify any remaining variation in fitness. The population had high variation in egg production and fertilization but very little variation in overall offspring survival. This suggests that the hatchery managers should consider alternative sources of genetic diversity, such as individuals from the wild or from other subspecies.</p><p> I used a crossing experiment between greenback cutthroat trout and a related subspecies to describe the genomic patterns of recovery of fitness. When greenbacks are crossed with another subspecies, the hybrid offspring have much higher fitness than the pure greenback offspring. I found that the probability of survival has a strong genetic component and that relatedness between the parents is a strong predictor of offspring survival, with offspring from less related greenback parents having higher fitness. This research will help managers decide whether outcrossing is a viable strategy to increase genetic diversity in cutthroat trout.</p><p> I explored the barriers to implementing evolutionary restoration tools, which include a reluctance to disrupt the taxonomic integrity of species. Evolutionary restoration is analogous to ecological restoration: both fields face the challenge of choosing appropriate restoration baselines and setting realistic restoration goals. Active interventions to increase gene flow should be considered as a complement to habitat protection and ecological restoration to prevent species decline.</p><p> I developed a teaching case study based on cutthroat trout research. The case study gives upper division biology students practice in applying evolutionary concepts to a real-world conservation problem by making evidence-based decisions accounting for uncertainty in real data sets. I used the case of cutthroat trout in Colorado because it requires a fundamental understanding of evolutionary processes such as speciation and hybridization and raises questions about the value of native species and the goals of conservation efforts.</p>

<p> This project aims to develop a panel of sequence capture baits to use for SNP genotyping for pedigree analysis in Wood Ducks (<i>Aix sponsa </i>) as well as for general population genetic analysis within species in the family Anatidae. SbfI RAD libraries were prepared with samples comprising five duck species (N = 96). Sequenced libraries were aligned to the Mallard (<i>Anas platyrhynchos</i>) reference genome and screened for 120bp regions proximal to the SbfI cutsite that contained SNPs conserved collectively in each species. A series of screenings identified regions which were used to produce 2,508 custom sequence capture baits. These baits were tested in novel individuals from the same species used to design the baits as well as novel species representing different taxonomic ingroup and outgroup levels within Aves. These baits delineate species at various taxonomic scales, even above the taxonomic level that was originally targeted and will prove useful for analyses of population and comparative genetics for species of Anatidae and perhaps more broadly.</p><p>