In order to complete their life cycles, vertebrates require oxygen and water. However, environments are not always forgiving when it comes to constantly providing these basic needs for vertebrate life. The annual killifish Austrofundulus limnaeus is possibly the most well described extremophile vertebrate and its embryos have been shown to tolerate extremes in oxygen, salinity, and water availability. This phenotype is likely a result of the annual killifish life history, which includes periods of temporary habitat desiccation and oxygen deprivation, and requires the production of stress-tolerant embryos that depress metabolism in a state of suspended animation, known as diapause. Over the past several decades, the basic morphology and physiology of annual killifish development has become better characterized. However, there are still basic cellular processes that remain to be described in annual killifish such as A. limnaeus. Specifically, changes in DNA structure, expression, and copy number are known to have profound impacts on the phenotype and survival of an organism. Little is known as to how A. limnaeus maintains genome integrity during cell stress, nor how the A. limnaeus nuclear and mitochondrial genomes may have evolved under the unpredictable conditions in which A. limnaeus thrive. Early annual killifish embryonic development is also characterized by a complete dispersion and subsequent reaggregation of embryonic blastomeres prior to formation of the embryonic axis. This unusual period of v ACKNOWLEDGEMENTS My completion of this dissertation required support from many people. I would like to thank my mentor and advisor Jason Podrabsky for his never-ending support and invaluable insight throughout my entire graduate experience. This document and the scientific publications derived from it would not exist without his expertise and belief in my ability to succeed. I thank my graduate committee: Suzanne Estes, Justin Courcelle, Deborah Lutterschmidt, and Gwen Shusterman for taking the time and effort to ensure my research, and myself as a scientist, could reach my potential. I thank Charmain Courcelle and Kim Brown for their advice and for allowing me to use their lab equipment. I am appreciative of the support of my colleagues,