Since the release of the human genome sequence in 2003, decreasing costs of DNA sequencing and advances in laboratory techniques have allowed scientists to study demography, admixture, and evolution for a growing diversity of taxa beyond humans. The work I present in this dissertation is part of the continued expansion of genomics. In particular, I present the assembly and analysis of whole genome data of extant and extinct species to study the evolutionary processes and consequences of population reduction.

My first chapter looks at the effects of habitat loss in the puma, whose range is the largest of any felid in the Western Hemisphere. I present a genome assembly of a puma from the Santa Cruz Mountains, and resequencing data for a panel of pumas from across their current range. I learn about the genomic health of the species, uncover Central American ancestry in present-day Florida pumas, and present a new model for the demographic history of the species.

In my second chapter, I present an assembly of the genome of the sole bear species to inhabit South America, the spectacled bear. The spectacled bear is the closest living relative to the extinct giant short-faced bears that roamed North America during the last Ice Age. I use the genome of the spectacled bear as a reference for mapping the genome of the extinct giant short-faced bear, and analyze both genomes to learn their population histories and relationships to extant ursids.

In my third chapter, I focus on another extinct bear, the California grizzly bear. Having gone extinct in the early 1900s due to overhunting, the California grizzly bear is an example of the detrimental results humans impose on their environment. Using genomic data from two preserved California grizzly bears, as well as the genomes of several modern brown bears, I characterize the genetic diversity among extant brown bears and explore the diversity of California grizzly bears.

Together, the research that comprises my dissertation presents a significant contribution to the growing body of literature for non-model organisms and provides resources relevant to the conservation of top predators.