title: Population genomics reveals structure at the individual, host-tree scale and persistence of genotypic variants of the undomesticated yeast Saccharomyces paradoxus in a natural woodland.
abstract: Genetic diversity in experimental, domesticated and wild populations of the related yeasts, Saccharomyces cerevisiae and Saccharomyces paradoxus, has been well described at the global scale. 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 centimetres (microsites) to tens of metres? 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 Quercus alba) within 1 km2in 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 sequencing and genomic SNP analysis revealed five differentiated groups (clades) 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 different clades coexist at fine spatial scale and that population structure persists over at least a one-year interval in these wild yeasts, suggesting the efficacy of yearly sampling to follow longer term genetic dynamics in future studies.
authors.affiliation: Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada.
authors.forename: Wenjing
authors.initials: W
authors.lastname: Xia
authors.affiliation: Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Québec, QC, G1V 0A6, Canada.
authors.forename: Lou
authors.initials: L
authors.lastname: Nielly-Thibault
authors.affiliation: Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Québec, QC, G1V 0A6, Canada.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Charron
authors.affiliation: Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Québec, QC, G1V 0A6, Canada.
authors.forename: Christian R
authors.initials: CR
authors.lastname: Landry
authors.affiliation: Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada.
authors.forename: Dahlia
authors.initials: D
authors.lastname: Kasimer
authors.affiliation: Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada.
authors.forename: James B
authors.initials: JB
authors.lastname: Anderson
authors.affiliation: Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada.
authors.forename: Linda M
authors.initials: LM
authors.lastname: Kohn
mesh_terms: D065928:Forests; D005828:Genetics, Population; D009864:Ontario; D029963:Quercus / Q000382:microbiology*; D012440:Saccharomyces / Q000235:genetics*; D014197:Trees / Q000382:microbiology
keywords: SNPs; fungi; hybridization; microbial ecology; yeast