How do Bacterial Genomes Accumulate Mutation?

We are interested in understanding evolution in host-pathogen and other biological systems by developing mathematical models and statistical methods for analysing data. These projects would suit students interested in microbial evolution who would like to develop their skills in bioinformatics, computing and/or data analysis. Alternatively, you might be a student with a background in quantitative sciences such as maths, statistics, computing, physics or engineering and curiosity about how viruses and bacteria evolve. These projects can be tailored to fit the academic background, research interests and career goals of individual students

The post-genomic era has delivered a deluge of delicious DNA data. With unprecedented genetic resolution we can examine how populations of bacteria change over time. As studies of local bacterial populations begin to appear, we are faced with the challenge of making sense of the observed patterns of variation. Single nucleotide polymorphisms (SNPs) can occur between genes or within genes. When they appear in genes they can be synonymous (no change to the translated protein) or nonsynonymous (translated protein is different from the ancestor). Why are nonsynonymous SNPs sometimes highly abundant? Is it because natural selection has not yet purged the population of these variants or is it because natural selection favours these variants that are on their way to fixation in the population? Or are these SNPs selectively neutral random mutations?

This project aims to address these questions by 1) analysing data from recent bacterial whole-genome-sequencing studies and 2) developing a computational model of mutation and selection in bacteria.

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