Biology ETDs

Publication Date



We analyze duplicate genes in a yeast, Saccharomyces cerevisiae with the aim of determining a genes history and to observe that gene in its genomic context. In Chapter 2 we show that the fate of a duplicate gene pair is in part determined by its genome location. Moreover, we show that for two classes of duplicate genes, resulting from either small-scale duplication or whole-genome duplication, this fate can often be assessed by measuring the patterns of asymmetry in the sequence divergence of the genes in question. In Chapter 3 we study duplicate genes in the context of their local environments by comparing the patterns of evolution in the coding sequences of duplicate genes for ribosomal proteins with their upstream non-coding sequences. We found that while the coding sequences show strong evidence of recent gene conversion events, similar patterns are not seen in the non-coding regulatory elements. These duplicated ribosomal proteins are not functionally redundant despite their very high degree of protein sequence identity. This analysis confirms that the duplicated proteins have diverged considerably in expression despite their similar protein sequences. In Chapter 4 we analyze the structure of the transcriptional regulation network and characterize the molecular evolution of both its transcriptional regulators and their regulated genes. We found that both subfunctionalization and neofunctionalization of transcription factor binding play a role in divergence.

Project Sponsors

Department of Energy's Computational Science Fellowship




Saccharomyces cerevisiae, gene duplication

Document Type


Degree Name


Level of Degree


Department Name

UNM Biology Department

First Committee Member (Chair)

Werner-Washburne, Margaret

Second Committee Member

Miller, Rober

Third Committee Member

Conant, Gavin