Styles, Pamela
(2010)
The evolution of transposable elements in humans and Drosophila.
PhD thesis, University of Nottingham.
Abstract
The different genomic environments in which transposable elements reside in the Great Apes and the Drosophila result in substantial differences between the evolution of transposable elements in these two groups of organisms. In the Great Apes, where deletion of transposable elements is relatively rare, elements tend to be retained in the genome to the extent that complete sets of elements belonging to a particular transposable element family can be obtained. In Drosophila, there is a rapid turnover of transposable elements, imposing strong selection pressure on transposable elements to be able to infect new hosts. This study investigates the evolution of transposable elements in these two genomic environments.
Complete sets of elements belonging to young Alu subfamilies in humans and closely-related species are used to investigate factors involved in their evolutionary history, such as mutation and gene conversion. The application of the master gene model, and other proposed models of the proliferation of young Alu subfamilies, are considered in light of the results obtained. The evolution of the AluYg, Yh and Yi lineages are investigated using a C++ program to simulate their evolutionary history. The results of the simulations are compared to statistics such as theta and pi, as well as the number of shared mutations and the proliferation time, in order to determine possible, and likely, values for parameters such as the retrotransposition rate and the number of source elements for each subfamily. The results suggest that although the master gene model may apply to some lineages, it is not the best model to explain the evolutionary history of all young Alu subfamilies.
The selection pressure on transposable elements in Drosophila results in a high level of horizontal transfer of these elements among species of the Drosophila genus. In this study, the twelve sequenced Drosophila genomes are used to investigate the frequency of horizontal transfer within these twelve species using a large dataset of transposable element sequences from the DNA transposons, as well as LTR, and non-LTR, retrotransposons. Horizontal transfer is inferred where identity between transposable elements of the same family in different species exceeds that between the coding regions of the Adh gene in the relevant species. Cases are further supported by evidence from the distribution of the transposable element family across the Drosophila genus, and phylogenetic incongruence, which in many cases elucidates likely directions of transfer. The results suggest that horizontal transfer may be even more common than previously thought, and appears to be most common for the LTR retrotransposons. The possibility that possession of the env gene may result in higher rates of horizontal transfer of LTR retrotransposons is investigated, and the env open reading frame is found to be under selective constraint.
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