Data from: 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

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. 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 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 co-exist 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.

酿酒酵母（Saccharomyces cerevisiae）与帕氏酿酒酵母（Saccharomyces paradoxus，简称S. paradoxus）这两种近缘酵母的实验种群、驯养种群及野生种群的遗传多样性，已在全球尺度下得到充分表征。本研究针对小空间尺度下的局部种群开展群体基因组学研究，旨在解答两个核心科学问题：其一，帕氏酿酒酵母种群在从厘米级（微位点）到数十米的空间尺度内，是否存在基因组变异？其二，基因组变异的分布格局是否会随时间持续存在？本研究的样本包含2014年采集的42株帕氏酿酒酵母菌株，以及2015年采集的43株菌株；所有菌株均采集自安大略省南部一片混交硬木林内1平方千米范围内，依托红栎（Quercus rubra）与白栎（Quercus alba）这4株宿主树周边的72个相同微位点。此外，样本中还纳入了2015年从邻近枫树与山毛榉树上分离得到的6株额外帕氏酿酒酵母菌株。全基因组测序与基因组单核苷酸多态性（Single Nucleotide Polymorphism，SNP）分析显示，采样区域内存在5个分化显著的类群（进化枝clades）。2014至2015年间，基因型在其对应微位点内的留存信号极为显著。来自同一宿主树的分离株相较于不同宿主树的菌株，亲缘关系更为紧密，宿主树间的菌株扩散证据十分有限。生长试验结果显示，有1种基因型的迟滞期相较于其余菌株显著更长。本研究结果表明，不同进化枝可在精细空间尺度下共存，且这类野生酵母的种群结构至少可在一年的时间跨度内保持稳定；这提示未来研究中可采用年度采样方案，以追踪长期的遗传动态变化。