Title from PDF of title page (University of Missouri--Columbia, viewed on July 31, 2013). ; The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. ; Dissertation advisor: J. Chris Pires ; Includes bibliographical references. ; Vita. ; Ph. D. University of Missouri-Columbia 2012. ; "July 2012" ; [ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Ancient whole genome duplications (WGDs), which multiply copies of the entire genome within an organism, are ubiquitous throughout the evolutionary history of higher eukaryotic lineages. These events have been hypothesized to be the basis for major evolutionary transitions, including having provided the "building blocks" for the origin of novel traits and an important driver for the largest species radiations across plants, fungi, protozoa, and animals. Repeated rounds of WGDs, or polyploid events, have been best documented among the flowering plants, and tend to be phylogenetically localized near the origin of speciose clades. However, the exact mechanisms that promote speciation in plants and retain duplicate pathways (i.e. "building blocks") following whole genome duplications for millions of years have been poorly understood. We utilized a phylogenomic framework, which was constructed utilizing a novel next-generation sequencing approach to localize and date two ancient WGDs shared by the model plant Arabidopsis thaliana and investigate the impact these events have had on both the origin of novel traits and diversification rates. ; Includes bibliographical references.