Population genomics of yeast
The yeasts are an excellent model system for studies in genomics as they have small genomes, dense with genes and other interesting features, and therefore easy to study, and studies on yeast often precede those on larger, more complex organisms, including humans. Saccharomyces paradoxus is a wild, undomesticated relative of S. cerevisiae (bakers yeast; the best known eukaryote) and in studying it we can exploit the genetic tools and knowledge available from S. cerevisiae. We have established a collection of strains from one population, here at Silwood Park, which have now been sequenced both in our lab and in collaboration with the Sanger Institute of genomic studies (http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/index.shtml). We have been analysing sequences from an entire chromosome from several strains of S. paradoxus, to find out how different regions of the genome evolve during the short-term micro-evolutionary scale. For example, comparisons of sequences from different populations reveal that the centromeres, the points of chromosome attachment to the spindle that pulls the two homologues apart during mitosis and meiosis, are among the fastest evolving parts of the chromosome. This is somewhat unexpected in view of the universal and conserved role of centromeres among eukaryotes. We have also been looking at the patterns of mutational and recombinational diversities along the genome, repeatability of evolutionary patterns across populations, patterns of selection in various features of the genome, etc.
Molecular ecology of yeast
Ecology is the organism's way of life, and we cannot evaluate the effects of particular genes in nature without knowledge of ecology. Despite the vast amounts of knowledge on the genetics of S. cerevisiae very little is known about yeasts in nature, and although we can readily isolate strains of S. paradoxus in nature we do not know where it grows, when, and how much, and so we have been undertaking studies to find out. Furthermore, isolates from different continents appear to represent divergent, phylogenetically independent clades, but is unclear whether or not intermediates remain to be found. We are also assaying for phenotypic differences among our strains to see if genetic differences will correlate with differences in the phenotypes.