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Abstract
Numerous mechanisms have played a part in generating the patterns of biodiversity we observe today. Understanding these drivers by examining genetic diversity within and between species is a goal of many evolutionary biologists. In this dissertation I contribute an addition to our understanding of evolutionary divergence and generation of biodiversity, by looking at two biogeographic examples including a geographic isolation of freshwater biota and a deeper examination of a known genetic cline along a latitudinal environmental gradient for a coastally distributed species. Further I examined how a gene family has evolved across vertebrates with interesting patterns of duplication among Actinopterygian fish. In addition to addressing questions of evolution I have also developed several genetic resources that can be used for further studies including a complete mitochondrial genome sequence for the yellowfin shiner, Notropis lutipinnis, a de novo transcriptome assembly for the barnacle Notochthamalus scabrous, as well as the first genome wide analyses of population divergence for four non-model freshwater fishes. The studies presented here expand our understanding of divers of divergence that generate diversity such as geographic isolation, environmental selection pressures, and genome evolution.