We study evolutionary processes in genomes. We use this data to describe how genomes change, while maintaining the function of the molecular machinery of the cell and competing in a natural environment. We use a variety of laboratory and computational techniques, applying methods from molecular evolution, population genomics, comparative genomics, functional genomics (we also use also tinkering and plenty of thinking). We are open to exploring evolutionary genomics in a variety of species and timescales.
Most recently we have been working with the fission yeast Schizosaccharomyces pombe as a model. We begun the process of describing the evolutionary history, genetic and phenotypic diversity of this model. Our aim is to describe how the genome and variations in the genome create the variation in the species.
So far, we have described genomic diversity of all known wild strains, analysed more than 220 traits, described their heritability and conducted the first genome-wide association studies (GWAS) for this species (Nature Genetics 2015). We also showed these wild strains have potential in the winemaking industry. We then described structural variation in the genome (large duplications/deletions, inversions and translations). We showed that structural variants contribute considerably to heritable traits and some appear to be transient within populations (Nature Communications 2017).
The fission yeast dispersed throughout the world in within human history (~340 BCE)
It is feasible to conduct genome-wide association studies (GWAS) in fission yeast
Structural variants (such as duplications) can be transient and can influence quantitative traits
Origin and early evolution of life
Evolution of introns, from the early evolution of life to the factors that affect their loss
Genomic diversity and selective constraint in malaria parasites (Plasmodium species)