Understanding variation in nucleotide diversity across the mouse genome
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Date
29/11/2018Author
Booker, Thomas Rhys
Metadata
Abstract
It is well known that nucleotide diversity varies across the genomes of eukaryotic
species in ways consistent with the effects of natural selection. However, the
contribution of selection on advantageous and deleterious mutations to the observed
variation is not well understood. In this thesis, I aim to disentangle the contribution of
background selection and selective sweeps to patterns of genetic diversity in the mouse
genome, thus furthering our understanding of natural selection in mammals. In chapter
1, I introduce core concepts in evolutionary genetics and describe how recombination
and selection interact to shape patterns of genetic diversity. I will then describe three
projects in which I examine aspects of molecular evolution in house mice. In the first
of these, I estimate the landscape of recombination rate variation in wild mice using
population genomic data. In the second, I estimate the distribution of fitness effects
for new mutations, based on the site frequency spectrum, then analyse population
genomic simulations parametrized using my estimates. In the third, I use a model of
selective sweeps to estimate and compare the strength of selection in protein-coding
and regulatory regions of the mouse genome. This thesis demonstrates that selective
sweeps are responsible for a large amount of the variation in genetic diversity across
the mouse genome.