Towards Genomics-Informed Biodiversity Conservation: Case Studies on Environmental DNA, Fin Whales and Bobcats Genomics and the Distribution of Fitness Effects

Global biodiversity is declining at an alarming rate. Genetics approaches have been invaluable for conservation practices across scales, from identifying impacts of inbreeding in endangered species to mapping global biodiversity patterns. The rapid development of next-generation sequencing technologies and computational advances further enabled genomics-informed biodiversity conservation in the 21st century. Compared with a handful of genetic markers that could only be acquired in relatively high-quality genetic materials, genomics approaches generate data with whole genome coverage and allow analyses on environmental DNA (eDNA). Here I demonstrate the applications of genomics in biodiversity conservation in four case studies that encompass a wide spectrum of genetic material types, from eDNA to whole genome sequencing, and a wide spectrum of topics, from population genetics to landscape ecology. In the first chapter, I analyzed the landscape biodiversity pattern derived from eDNA metabarcoding using surface soil samples collected across California. Combining eDNA with environmental predictors, including remote sensing data, have capacity to model biodiversity at landscape scales and to create new biodiversity baselines that span the tree of life. In the second chapter, I analyzed the population genomics pattern in a pair of fin whale (Balaenoptera physalus) populations with contrasting demographic trajectories and whaling pressures. I was able to detect the severity of whaling in the Eastern North Pacific population and found that even low levels of migration are crucial to the sustenance of the small and isolated Gulf of California population. In the third chapter, I extended the single-species population genomics to a comparative framework and evaluated the extent of the Distribution of Fitness Effects variation in eight animal species with diverse phylogenetic relationships. I found that the DFE is more similar in more closely related species. In the appendix chapter, I provided another example of how genomics could aid conservation by describing a de novo genome assembly of the bobcat (Lynx rufus), an indicator species for landscape connectivity.Overall, this dissertation illustrates the promise and prospect of including genomics in conservation biology through four case studies