Oral Comprehensive Exam Details
Bioinformatics Research in Whole Genome Duplication
| Author: | Julian Catchen |
|---|---|
| Date: | June 11, 2007 |
| Time: | 11:00 |
| Location: | 220 Deschutes |
| Committee: | John Conery (Chair) John Postlethwait Virginia Lo Yannis Smaragdakis |
Abstract
Evolution advances the fitness of an organism through a series of small, incremental changes over long periods of time. In contrast to this slow, stochastic process, the theory of whole genome duplication proposes a means for rapid evolutionary change and diversification. This theory, first proposed in the early 1970's, was considered controversial until recently. Now, however, with the availability of a number of fully sequenced genomes, these duplications are known to have occurred a number of times and in a variety of different organisms, from the single-celled paramecium, to the zebrafish. This paper will focus on three areas of research in the field of Bioinformatics including the methods, algorithms, and techniques that are critical to the study of whole genome duplication. We will examine sequence alignment, a process of comparing genes from different organisms, or within the same organism to identify relationships between those genes. Phylogenetics, the second major set of methods we will examine, uses a tree representation to determine evolutionary relationships such as the ordering of speciation for a set of organisms, or the appearance or loss of novel features in a gene. Third, we will discuss nonsynonymous and synonymous mutation rates, an analysis which allows us to infer the rates at which a set of related genes are changing. Finally, this paper will examine genome duplications, covering the theory behind them in detail as well as a review of past and current empirical evidence supporting them.