| This dissertation is an investigation of the differences in evolutionary patterns across large plant gene families, and the importance of genome context in gene family evolution. The dissertation includes an aggregate analysis of 50 large gene families in Arabidopsis thaliana, as well as close analyses in Arabidopsis of the major latex protein family, the chlorophyll a/b binding protein family, the proteasome 20S subunit family, the apyrase gene family in three legume genomes, and the NBS-LRR disease resistance gene family in a wide range of taxa. The dissertation also describes software that I have developed to aid in gene family analysis. This includes (1) pipeline software to manage many analysis steps involved in sequence management, alignment, and phylogenetic reeonstructions; (2) software to identify genomic duplications within a genome or between related genomes; and (3) software to integrate information about gene position, genomic duplications, and gene family phylogenies and to infer which gene duplications in a phylogeny originated through local or large-scale segmental duplications. Together, this software helps to identify dominant evolutionary modes and evolutionary patterns in gene families, making use of the context and additional information provided by information about genomic position, internal genomic duplications, and species phylogenies. Families are found to be organized differently within the genome, and to have different rates of turnover (gene birth and death) that is associated with organization. Families are also found to respond differently to large-scale genomic duplications or losses.*; *This dissertation is a compound document (contains both a paper copy and a CD as part of the dissertation). The CD requires the following system requirements: Internet Browser; Adobe Acrobat; Microsoft Office. |
