Summary: Understanding what makes a species is fundamental to understanding evolutionary biology, yet there is so much about this process that still puzzles us. Until recently, mating between different species, or hybridization, was thought to be a rare event. With the advent of genome sequencing, biologists began to realize that hybridization is remarkably common throughout the tree of life. Despite this realization that hybridization is common, there is much we do not know about its evolutionary effects. In my dissertation work, I use a combination of genomic and computational techniques to ask how selection on hybrids shapes the genomes and evolution of hybrids and parental species. (Abstract shortened by ProQuest.).