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Gene tree analyses as a means of investigating gene family evolution, species phylogenies, and hybridization in the plant subtribe Iochrominae
Molecular sequence data is a powerful source of information for understanding evolutionary processes. While the reconstruction of historical relationships with molecular sequence data is generally considered within the purview of reconstructing species phylogenetic relationships, recent advancements in phylogenetic and genomic methods have expanded the utility of phylogenies outside of categorizing species relationships. In this thesis I demonstrate the broad utility of DNA sequence phylogenies by first demonstrating how phylogenies may offer important insights into patterns of gene duplication that may be seen within a single species or few close relatives. I then demonstrate how the traditional interspecies phylogenetic framework can be expanded to included large amounts of DNA sequence from across the genome as a way of increasing the power of phylogenetic inferences that characterize species relationships. Finally, I show how large genomics datasets may be used to characterize not only species relationships but also patterns of hybridization that occur at deep evolutionary timescales. In this way I am able to demonstrate how molecular sequence data may be used to describe important evolutionary processes that occur within a single species (gene duplication) as well as processes that occur between species that do not explicitly result in a tree like relationship (hybridization). Both of these processes are aided by a rigorous understanding of the overall species relationships, which I also show is aided by large genomic datasets. Future studies working at the interface of gene duplication, species diversification, and hybridization will benefit greatly from the common phylogenetic framework that underlies rigorous insights into each of these areas of inquiry.^
Gates, Daniel J, "Gene tree analyses as a means of investigating gene family evolution, species phylogenies, and hybridization in the plant subtribe Iochrominae" (2016). ETD collection for University of Nebraska - Lincoln. AAI10245892.