Investigating genome wide patterns of natural selection in eukaryotes

Gossmann, Toni Ingolf (2012) Investigating genome wide patterns of natural selection in eukaryotes. Doctoral thesis (PhD), University of Sussex.

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Abstract

Mutations are the ultimate source of new genetic information and they can be neutral,
harmful or beneficial. The ultimate fate of all mutations is either to be lost or to eventually
become fixed in a population. In this thesis I investigate genome wide traces of natural
selection in eukaryotes. I focus on the most common type of mutations, point mutations,
in protein coding genes.

I investigated whether there is adaptive evolution in 11 plant species comparisons by
applying an extension of the McDonald Kreitman (MK) test and found little evidence
of adaptive evolution. However, most of the investigated plant species have low effective
population sizes (Ne) and the rate of adaptive evolution is thought to be correlated to
Ne. I therefore extended my study using additional data from mammals, drosophilids
and yeast to investigate the relationship between the rate of adaptive evolution and Ne.
I found a highly significant correlation between the rate of adaptive evolution relative to
the rate of neutral evolution (!a) and Ne.

It has been proposed that evidence of adaptive evolution can be an artifact of fluctuating
selection. I simulated a model of fluctuating selection, in which the average strength
of selection acting upon mutations is zero. Under this model adaptive evolution is inferred
using MK-type tests. However, the mutations which become fixed are on average positively
selected. The signal of adaptive evolution is therefore genuine.

Ne can not only vary between species but also across genomes. However, how much
variation there is, and whether this affects the efficiency of natural selection, is unknown.
I analysed 10 species and show that variation in Ne is widespread. However, this variation
is limited, amounting to a few fold variation in Ne between most genomic regions. This is
never-the-less sufficient to cause variation in the efficiency of selection.

Item Type: Thesis (Doctoral)
Schools and Departments: School of Life Sciences > Biology and Environmental Science
Subjects: Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0447 Genes. Alleles. Genome
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0460 Mutations
Depositing User: Library Cataloguing
Date Deposited: 22 Jan 2013 13:08
Last Modified: 08 Sep 2015 13:23
URI: http://sro.sussex.ac.uk/id/eprint/43293

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