Evolution of Tandemly Repeated Sequences

Type of content
Theses / Dissertations
Publisher's DOI/URI
Thesis discipline
Mathematics
Degree name
Master of Science
Publisher
University of Canterbury. Mathematics & Statistics
Journal Title
Journal ISSN
Volume Title
Language
Date
2009
Authors
Snook, Michael James
Abstract

Despite being found in all presently sequenced genomes, the evolution of tandemly repeated sequences has only just begun to be understood. We can represent the duplication history of tandemly repeated sequences with duplication trees. Most phylogenetic techniques need to be modified to be used on duplication trees.

Due to gene loss, it is not always possible to reconstruct the duplication history of a tandemly repeated sequence. This thesis addresses this problem by providing a polynomial-time locally optimal algorithm to reconstruct the duplication history of a tandemly repeated sequence in the presence of gene loss.

Supertree methods cannot be directly applied to duplication trees. A polynomial-time algorithm that takes a forest of ordered phylogenies and looks for a super duplication tree is presented. If such a super duplication tree is found then the algorithm constructs the super duplication tree. However, the algorithm does not always find a super duplication tree when one exists.

The SPR topological rearrangement in its current form cannot be used on duplication trees. The necessary modifications are made to an agreement forest so that the SPR operation can be used on duplication trees. This operation is called the duplication rooted subtree prune and regraft operation (DrSPR). The size of the DrSPR neighbourhood is calculated for simple duplication trees and the tree shapes that maximize and minimize this are given.

Description
Citation
Keywords
duplication trees, tandemly repeated sequences, phylogenetics, rooted subtree prune and regraft, rSPR, supertree, rooted binary tree
Ngā upoko tukutuku/Māori subject headings
ANZSRC fields of research
Rights
Copyright Michael James Snook