Biology ETDs


Lijing Bu

Publication Date



Gene duplication is considered a major contributor to genome evolution and functional diversity. Differences in genomic features (such as structural resemblance, transcriptional orientation, and genomic location) between members of a gene duplicate pair may indicate the possible duplication mechanisms, as well as the evolutionary fates the paralogs may experience. In addition to these genomic features, molecular genetic features, such as differences in codon usage and expression levels may provide further insight into functional changes between paralogs. In this dissertation, multiple genomic analyses were conducted in order to evaluate the differences in genomic and genetic properties between duplicate copies in order to understand the effect duplication mechanisms may have on the divergence of duplicate pairs. Chapter Two focuses on differing patterns of sequence asymmetry, codon usage, and gene expression levels between the members of gene duplicate pairs belonging to two different populations of paralogs in Saccharomyces cerevisiae: ohnologs, which arose via a whole genome duplication (WGD), and small segmental duplication (SSD) paralogs. It is shown that ohnologs have more highly conserved gene order (synteny) relative to SSD paralogs, despite their greater evolutionary age. Within SSD pairs, the derived paralog (the copy with lower synteny) seems to evolve faster, simultaneously exhibiting a lower CIA value and lower expression levels relative to the ancestral copy. While synteny and evolutionary rate differences were not coupled in ohnolog pairs, the relationship between evolutionary rate asymmetry, CAI, and expression levels was similar to that observed in SSD pairs. These results indicate that codon usage contributes to rate asymmetry in the evolution of gene duplicates in both, ohnologs and SSD paralogs, while differences in synteny (as experienced by SSD pairs, but not very young ohnologs) only affects rate asymmetry in SSD pairs. This may imply relaxed selection on codon usage and the expression of derived copies, potentially leading to the acquisition of novel functions over time. Chapters Three and Four focus on the effects of structural resemblance and other genomic features on young gene duplicate pairs within the Homo sapiens (human) and Pan troglodytes (chimpanzee) genomes. The results imply that the majority of gene duplicates in both species are structurally complete duplications, encompassing the entire coding region of a gene. The chimpanzee genome additionally contains a large fraction (46%) of retrotransposed young gene duplicates relative to the human genome (13%) which may be due to differences in genome architecture, such as mobile element content between the two genomes. While RNA-mediated processes lead to a majority of inter-chromosomal paralogs, DNA-mediated paralogs reside largely on the same chromosome, in which case inter-paralog distance does not increase over time. These results in conjunction with results of previous studies in nematodes, yeast, and flies, suggest that the structural resemblance types and location of duplicates are closely linked to the duplication mechanism by which paralog pairs arise. This is also true for closely related species, as illustrated by the comparison of the human and chimpanzee genomes. The above studies illustrate the relationship duplication span (as illustrated in Chapter Two) and mechanisms (illustrated in Chapters Three and Four) have on the location, synteny, structural resemblance types, and functionality of gene duplicates in different genomes. The findings imply that differences in mechanisms between species can have significant effects on the genome evolution and divergence between even closely related taxa.




Evolution, Genetic variation, Mutation rate, Codon usage, Synteny, Computational biology, Saccharomyces cerevisiae, Structural resemblance, duplication span, synonymous divergence, human, chimpanzee, Gene duplication

Document Type


Degree Name


Level of Degree


Department Name

UNM Biology Department

First Advisor

Katju, Vaishali

First Committee Member (Chair)

Bergthorsson, Ulfar

Second Committee Member

Long, Jeffrey

Third Committee Member

Natvig, Donald