Environmental adaptation and evolution through gene duplication and divergence

• Main Author: Ames, Ryan
• Other Authors: Lovell, Simon
• Published: University of Manchester 2012
• Subjects: 576.8
• Online Access: http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.553475

A key process in evolution is the adaptation of a species to a new environment that can be achieved by the gain of an advantageous novel function. The importance of gene duplication in generating functional innovation is currently being revealed. In order to determine whether gene duplication plays a role in environmental adaptation it is necessary to show that duplicate retention is dictated by the environment. Furthermore, investigating the genetic mechanisms of duplicate divergence will further our understanding of how these genes develop new functions and contribute to adaptation. In this thesis I examine the extent of gene duplication in yeast and investigates the mechanisms by which these duplicates diverge. Identifying gene duplicates in multiple yeast strains reveals that there are large differences in duplicate gene content between the strains. Interestingly, the retention of genes in duplicate is not random and correlates with a strain's natural environment. Next, parsimony and maximum likelihood methods are developed for determining the duplication and loss events in the evolution of {\it Drosophila} gene families. The performance of these methods is tested and their strengths and weaknesses are characterised. Duplicate divergence is also considered. Firstly, by examining transcription factor binding sites that may indicate divergence of expression between duplicates. Here, there is evidence of high rates of change in binding sites, which is consistent with positive selection and may indicate functional innovation. Interestingly, it is possible to find large differences in binding site gain and loss between the strains that can be rationalised by analysing their natural environments, suggesting a role for duplicate divergence in environmental adaptation. Secondly, duplicate divergence through changes in specificity of physical interactions is considered. Here, I show that as duplicates age they share fewer interactions. I develop a method to predict whether changes in interface regions will alter specificity and show that changes in specificity are best explained by examining functional atom contacts between residues. The investigations of duplicate divergence highlight the genetic mechanisms that lead to changes in expression and interactions through subfunctionalisation or neofunctionalisation, that could potentially lead to functional innovation. The correlation of duplicate retention with natural environment indicates that selection is shaping genome content. I argue that this has important implications for environmental adaptation and speciation.