Saccharomyces paradoxus Genome sequencing

Genetic diversity in experimental, domesticated and wild populations of the related yeasts, Saccharomyces cerevisiae and S. paradoxus has been well described at the global scale. Knowing (a) how yeast populations are structured in the field at the local scale and (b) how structure may change over time is prerequisite to testing hypotheses about how such populations evolve under the effects of mutation, selection, drift, recombination, and migration. We investigated the population genomics of a local population on a small spatial scale to address two main questions. First, is there genomic variation in a S. paradoxus population at a spatial scale spanning centimeters (microsites) to tens of meters? Second, does the distribution of genomic variants persist over time? Our sample consisted of 42 S. paradoxus strains from 2014 and 43 strains from 2015 collected from the same 72 microsites around four host trees (Quercus rubra and Q. alba) within 1km2 in a mixed hardwood forest in southern Ontario. Six additional S. paradoxus strains recovered from adjacent maple and beech trees in 2015 are also included in the sample. Whole-genome Illumina sequencing and genomic SNP analysis revealed five differentiated groups within the sampled area. The signal of persistence of genotypes in their microsites from 2014 to 2015 was highly significant. Isolates from the same tree tended to be more related than strains from different trees, with limited evidence of dispersal between trees. In growth assays, one genotype had a significantly longer lag phase than the other strains. Our results indicate that genomically differentiated groups co-exist at fine spatial scale and that population structure persists over time in these wild yeasts.