| Although the evolutionary significance of gene duplication has long been appreciated, the issue of what factors determine gene duplicability remains unresolved. In this dissertation I perform a systematic assessment of this relationship. I show that a gene's functional characteristics, including role in metabolic processes, cellular localization, and network connectivity, influences its duplicability at different taxonomic levels. In a study of Saccharomyces cerevisiae (yeast) and Escherichia coli genomes, I find that genes in the central metabolic pathways and in the catabolic pathways have higher gene duplicability than other genes, whereas anabolic pathways largely consist of single-copy genes (singletons). The functional bias of gene duplicability is also evident between proteins with different cellular localization in yeast, where proteins that interact with external environments have a higher gene duplicability than proteins localized within intracellular compartments. Functional bias in gene duplicability is also revealed in the yeast protein-protein interaction network, where greater protein connectivity corresponds to lower rates of gene duplication. Finally, I investigate functional bias and gene family size distribution of genes in vertebrates relative to those in invertebrates. Most vertebrate proteins that can be found in invertebrate genomes form multigene families, while those that cannot be found in other non-vertebrate genomes are predominantly singletons. The proteins of the former also tend to evolve more slowly than those of the latter. Vertebrate gene families belonging to regulation, signal transduction, multicellular organismal development or protein modification functional groups are expanded, while vertebrate gene families involved in metabolic processes, are contracted. Together, these results suggest that many aspects of gene function are important to understand the role of duplication in genome evolution. |
