I use mathematical and computational models to investigate evolutionary genetics phenomena, with a keen interest in mating system evolution; adaptation in different environments, and its potential costs; invasions and emergence of parasites; and creating statistics for genomic analysis.
Below is a selection of topics I’m either currently working on, or have worked on and still retain an interest in. However, I’m always interested to discuss potential projects, so please contact me if you have an idea that you’d like to discuss further.
Gene genealogies of facultative sexual organisms
Facultative sexual species are those that have distinct sexual and asexual stages to their life-cycle. Studying such organisms offer key insights into one of the biggest question in evolutionary theory: why has sex evolved? However, in some organisms it can be hard to tell visually when sex has occurred. Furthermore, due to their unusual life-cycles, such organisms harbour unusual distributions of genetic variation, which can obscure evidence of selection and environmental effects if relying on obligate-sex models to make comparisons.
To remedy this, I am currently extending coalescent models to consider how gene genealogies are affected when sex is rare, especially when one obtains multiple samples from a large geographic area. These models can then be used to determine the onset of sex and demography from genome sequences of facultative sexuals. In our single-locus analysis, we demonstrated how traditional evidence of rare sex – allelic sequence divergence – can be removed with low rates of gene conversion. The effects of background selection are also much stronger with infrequent rates of sex.
Hitchhiking of deleterious alleles under different mating systems
Adaptation is one of the major processes in evolution. If a new allele appears that offers a fitness advantage, then it will increase in frequency until it fixes. However, if a deleterious allele is also closely linked to the adaptive site, then it can also fix as well, reducing the selective advantage of the adaptive mutation.
I have investigated this process in a number of ways; firstly in a haploid model, in which myself and Sally Otto quantified the probability that deleterious alleles can fix with adaptations, and what effect this has on detecting adaptations in the genome. I then extended this work with Sylvain Glémin, to consider how this process affects the evolution of outcrossing or self-fertilisation, as potential mating strategies.
Evolutionary Epidemiology, and the emergence of new viral strains
One of the more immediate applications of emergence and adaptation theory is determining what causes the invasion and emergence of new infectious diseases. The mathematics underlying such outbreaks are similar to those affecting genetic adaptation, and it remains a key interest of mine to attempt to unify the two areas. Not only can such models have an impact on determining emerging epidemic outbreaks, but also on judging the probability that new strains can emerge from pre-existing infections, given the first strain immunises individuals. I have also worked on phylogenetic methods that detect possible genetic similarities between infectious disease outcomes.
The evolution of sex and recombination in large populations
The evolution of sex is one of the biggest – and controversial – topics in evolutionary biology. For my PhD with Peter Keightley, I investigated whether sex could overcome its inherent costs (having to find mates, a reduction in the number of offspring produced) if it affected large number of loci. The rationale being that recombination can create the fittest gene combinations, and if a large number of loci are affected, then this potential advantage can be substantial.
Our first results demonstrated how the presence of even a small amount of adaptive mutation can aid selection for recombination modifier alleles, if deleterious mutation was also present. We further determined how these demonstrated advantages to recombination can prevent asexual individuals from displacing an existing sexual population, if it was spread across several subdivided regions.