In order to identify expressologs (orthologs exhibiting the highest expression profile ranking) among a variety of plant species, bioinformatic methods were used in order to first identify sequence orthologs and subsequently to rank these orthologs based on expression profile similarity. Analyses conducted on these data suggested that expressologs exhibited greater functional equivalency. A comparison of drought response in A. thaliana and Populus showed that expressologs exhibited a higher correlation when computed using stress data as opposed to developmental data. This suggested that the use of condition-specific data sets is more appropriate when examining specific conditions. Analysis was conducted in order to investigate the hypothesis that neutral evolution was a predominant factor in gene expression divergence. Some evidence was found for selection acting on expression pattern maintenance. Further analysis will be required in order to confirm the type of selection acting to maintain expression patterns across species.

In order to identify expressologs (orthologs exhibiting the highest expression profile ranking) among a variety of plant species, bioinformatic methods were used in order to first identify sequence orthologs and subsequently to rank these orthologs based on expression profile similarity. Analyses conducted on these data suggested that expressologs exhibited greater functional equivalency. A comparison of drought response in A. thaliana and Populus showed that expressologs exhibited a higher correlation when computed using stress data as opposed to developmental data. This suggested that the use of condition-specific data sets is more appropriate when examining specific conditions. Analysis was conducted in order to investigate the hypothesis that neutral evolution was a predominant factor in gene expression divergence. Some evidence was found for selection acting on expression pattern maintenance. Further analysis will be required in order to confirm the type of selection acting to maintain expression patterns across species.

Genes present in multiple copies and genes that contain regions of repetitive sequences can undergo concerted evolution, which results in homogenization of the nucleotide sequence of the genes or repetitive regions. In regions of tandem repeats, this occurs through misalignment of repeat units followed by unequal crossover, which generates two products with differing numbers of repeat units. Gene conversion is thought to lead to one of these products becoming fixed in a species. The homogenous sequence of previously studied genes that have been thought to undergo this process has made it difficult to determine the exact models involved. Here I examine concerted evolution in SM50, a sea urchin gene that encodes a protein involved in biomineralization. The repetitive region in the SM50 gene varies in length between species, and there is variability in each repeat unit as well. I examine the codon usage in SM50 in a variety of species, and discuss how purifying selection, substitutions, concerted evolution, and selection at the level of DNA sequence have played a role in the evolution of this gene. I also examine the structure and sequence of the repeat units, and purpose models that have led to the evolution of the repeat pattern seen in the different species examined. Finally, I have found variation in the number of repeat units within several species. This has allowed us to deduce the specific models of unequal crossover that led to this variation. The unique variation in the repetitive region of SM50 has enabled us to describe a model of how substitutions affect the model of misalignment and unequal crossover.

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