Date of Award


Document Type

Campus Access Dissertation


Biological Sciences

First Advisor

Robert Friedman


Comparative genomics reveals differences in gene order among species. In the genomes, genes are rearranged through inversion, transposition, translocation, and chromosome fission and fusion. Using gene order as a phylogenetic character has the potential to resolve previously unresolved species relationships. In this study, gene order data were used to resolve both shallow and deep relationships of prokaryotes and eukaryotes, including the genus Prochlorococcus, the methanogens, and five mammalian orders. A computational pipeline was developed to construct distance-based gene order trees. The resulting gene order phylogeny was consistent and congruent with the sequence-based trees. It also resolved the controversial branches within these lineages. For instance, the gene order phylogeny supported Rodentia as an outgroup of the Primate-Carnivora-Perissodactyla clade. Finally, a comparative phylogenetic approach compared the gene families between Prochlorococcus and Synechococcus and concluded that Prochlorococcus evolved towards genome reduction. Mapping various overlapping patterns to the ancestral genomes along the Prochlorococcus phylogeny, we found that formation of overlapping genes has evolved faster than their degradation, which could be a mechanism of reductive genome evolution of Prochlorococcus.


© 2010, Haiwei Luo