A gzipped archive of some data table associated with this project.

We evolved an outbred diploid sexual population of budding yeast with weekly episodes of recombination in the presence of five different stressors along with YPD for 21 weeks. We culled populations in which asexual cheaters evolved, and pool-sequenced two replicate populations per drug at six timepoints (weeks 1, 5, 9, 13, 16 and 21). Given that the base population used to begin the experiment was derived from a collection of 18 known founder strains, we were able to estimate founder haplotype frequencies throughout the genome from the poolseq data and examine haplotype change over time. For the first 16 weeks of the experiment, evolution is extremely repeatable between replicates within a drug, but different between drugs. For all populations the entire genome shows haplotype frequency change, either due to direct or indirect selection acting on variation in the base population, despite high rates of recombination and un-recombined haplotype block sizes of less than 100kb. Haplotype trajectories are dominated by an early purging of the dominant local haplotype, followed by a single replacement haplotype quickly increasing in frequency and then changing very little. The new equilibrated haplotype frequencies occur long before fixation in most cases, supporting a trait-based model of phenotypic evolution. Throughout the genome a consistent pattern of change is that one of the 18 local haplotypes changes a great deal, with the others changing very little. We finally repeat the analysis of the experiment ignoring founder haplotype information, focusing instead on directly ascertained frequency changes at SNPs. When we only employ directly ascertained SNP frequencies many of the above patterns observed are not easily detected.

本研究构建了远交二倍体有性酿酒酵母种群，在5种不同胁迫因子与YPD培养基共存的条件下，开展了为期21周、每周一次重组事件的演化实验。我们剔除了演化出无性欺骗型菌株的种群，并针对每种胁迫因子的两个重复种群，在6个时间节点（第1、5、9、13、16和21周）开展混池测序。由于本实验起始的基础种群源自18株已知奠基菌株的集合，我们可通过混池测序数据估算全基因组范围内的奠基单倍型（haplotype）频率，并追踪单倍型频率随时间的变化。实验的前16周内，同一胁迫因子下的重复种群间演化模式高度一致，但不同胁迫因子间的演化模式存在显著差异。尽管重组频率较高且未重组单倍型区块的长度均小于100kb，但所有种群的全基因组均出现单倍型频率变化，这一现象源于基础种群中存在的遗传变异受到直接或间接选择作用。单倍型频率动态整体呈现以下模式：早期先清除优势本地单倍型，随后某一替代单倍型频率快速上升，之后变化幅度极小。多数情况下，新的平衡单倍型频率会在等位基因固定前很早就达到，这一结果支持基于性状的表型演化模型。全基因组范围内存在一致的频率变化模式：18种本地单倍型中仅有一种发生显著频率变化，其余单倍型的频率几乎无波动。最后，我们开展了重复分析：在忽略奠基单倍型信息的前提下，仅聚焦于直接检测得到的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点频率变化。若仅使用直接检测得到的SNP频率数据，则难以复现上述多数演化模式。