Fine-scale phylogeny using a mathematical model of the dynamics of rDNA repeat sequence evolution

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Ever since Charles Darwin introduced his theory for evolution, biologists have been interested in reconstructing the Tree of Life, the tree representing the evolutionary history of all present-day species (http://www.phylo.org/). This is an extremely ambitious goal, and so biologists usually concentrate on constructing evolutionary trees for small sub-collections of present-day species. In the past, the construction of such trees was based on particular characteristics of the species, such as properties of their skeleton or anatomy. However, now that we are able to sequence parts of genomes, or in some cases whole genomes, it is now commonplace for biologists to construct evolutionary trees using DNA data. Consequently, in recent years a whole new theory has grown around building such trees called 'Phylogenetics'. The most important DNA sequence used in phylogenetics is that of the ribosomal DNA repeat unit which has been used to construct the universal tree-of-life. Thanks to recent large-scale genome sequencing projects we now have enough data available to construct far more detailed phylogenies. Thanks to recent advances in computational biology we also now have the means to build rapid and efficient tools to achieve this goal. The aim of this project is to build a mathematical tool to analyse rDNA sequence variation and dynamics at the most basic level. The tool will be applied to yeast and plant data, allowing much finer phylogenies to be constructed than hitherto possible. Yeast genomes provide excellent models for understanding genome dynamics in plants and indeed other eukaryotic genomes, including humans.

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