|dc.contributor.author||Lewis, Samuel Howard||
|dc.description.abstract||The RNA interference (RNAi) mechanism is a conserved system of nucleic acid manipulation, based on
the interaction between small RNA guide molecules and Argonaute effector proteins. RNAi pathways
are found in the vast majority of eukaryotes, and have diversified into a broad array of functions including
gene regulation, antiviral immunity and transposable element (TE) suppression. Many of these
functional innovations coincide with duplication of Argonaute genes, suggesting that gene duplication
may be a key driving force in the diversification of RNAi. However, few studies have explicitly investigated
Argonaute evolution after duplication. In this thesis, I focused on the impact of gene duplication
on the evolution of Argonaute genes.
Argonaute genes in different species exhibit a broad array of functions; however, most of our knowledge
of Argonaute function in the arthropods is based on studies in D. melanogaster. To compare the
rate of duplication and its evolutionary effect between different Argonaute subclades, I quantified gene
turnover rates and evolutionary rate change in Argonaute genes from 86 Dipteran species (Chapter 2).
I find that duplication rate varies widely between subclades and lineages, and that duplication drives
an increase in evolutionary rate, suggesting that functional divergence after Argonaute duplication is
prevalent throughout the Diptera.
In the obscura group of Drosophila I identified a series of recent duplications of Argonaute2 (Ago2),
which has antiviral and anti-TE functions in D. melanogaster. To quantify the extent of functional divergence
between these paralogues, I measured the expression of paralogues from three species (D.
subobscura, D. obscura and D. pseudoobscura), in different tissues and under viral challenge (Chapter
3). I find that the majority of Ago2 paralogues have specialised to a derived testis-specific role, potentially
to suppress TE activity or meiotic drive. While CRISPR-Cas9 mediated knockout of these genes
ultimately proved unsuccessful (Chapter 5), the selective importance of their derived function is suggested
by its multiple independent origins.
Functional novelty, as appears to have evolved in the obscura group Ago2 paralogues, is often driven by
strong selection. To quantify the evolutionary rate and positive selection on these paralogues, I gathered
intraspecies polymorphism data for all paralogues in D. subobscura, D. obscura and D. pseudoobscura,
combining this with publicly-available population genomic data for D. pseudoobscura (Chapter 4). I
find that the majority of paralogues in all species have extremely low diversity, indicative of recent selection,
and identify recent selective sweeps on three paralogues in D. pseudoobscura. This suggests
that the majority of Ago2 paralogues in the obscura group are evolving under strong positive selection.
In this thesis I have aimed to quantify the effect of gene duplication on Argonaute evolution. I find that
Argonaute genes duplicate frequently in some lineages, resulting in the evolution of derived functions
that may be driven by positive selection. This suggests that functional diversification is prevalent in
eukaryotic RNAi, and is likely to coincide with expansion of the Argonaute gene family.||en
|dc.contributor.sponsor||Natural Environment Research Council (NERC)||en
|dc.publisher||The University of Edinburgh||en
|dc.relation.hasversion||E. Schnettler, H. Tykalová, M. Watson, M. Sharma, M. G. Sterken, D. J. Obbard, S. H. Lewis, M. McFarlane, L. Bell-Sakyi, G. Barry, S. Weisheit, S. M. Best, R. J. Kuhn, G. P. Pijlman, M. E. Chase- Topping, E. A. Gould, L. Grubhoffer, J. K. Fazakerley, and A. Kohl, “Induction and suppression of tick cell antiviral rnai responses by tick-borne flaviviruses.,” Nucleic Acids Research, vol. 42, no. 14, pp. 1–11, 2014.||en
|dc.relation.hasversion||Samuel H Lewis and Darren J Obbard, Recent insights into the evolution of innate viral sensing in animals, Current Opinion in Microbiology 2014, 20:170–175. http://dx.doi.org/10.1016/j.mib.2014.05.010||en
|dc.rights||Attribution-NonCommercial-ShareAlike 4.0 International||*
|dc.title||Evolution of Dipteran Argonaute genes through duplication, selection and functional specialisation||en
|dc.type||Thesis or Dissertation||en
|dc.type.qualificationname||PhD Doctor of Philosophy||en