Data from: Uncovering the genetic signature of quantitative trait evolution with replicated time series data

The genetic architecture of adaptation in natural populations has not yet been resolved: it is not clear to what extent the spread of beneficial mutations (selective sweeps) or the response of many quantitative trait loci drive adaptation to environmental changes. Although much attention has been given to the genomic footprint of selective sweeps, the importance of selection on quantitative traits is still not well studied, as the associated genomic signature is extremely difficult to detect. We propose ‘Evolve and Resequence’ as a promising tool, to study polygenic adaptation of quantitative traits in evolving populations. Simulating replicated time series data we show that adaptation to a new intermediate trait optimum has three characteristic phases that are reflected on the genomic level: (1) directional frequency changes towards the new trait optimum, (2) plateauing of allele frequencies when the new trait optimum has been reached and (3) subsequent divergence between replicated trajectories ultimately leading to the loss or fixation of alleles while the trait value does not change. We explore these 3 phase characteristics for relevant population genetic parameters to provide expectations for various experimental evolution designs. Remarkably, over a broad range of parameters the trajectories of selected alleles display a pattern across replicates, which differs both from neutrality and directional selection. We conclude that replicated time series data from experimental evolution studies provide a promising framework to study polygenic adaptation from whole-genome population genetics data.自然种群中适应的遗传架构迄今尚未阐明：尚不清楚有益突变的扩散（选择性清除，selective sweeps）或是众多数量性状基因座（quantitative trait loci）的响应，在多大程度上驱动了种群对环境变化的适应。尽管学界已对选择性清除的基因组印迹给予大量关注，但针对数量性状的选择的重要性仍未得到充分研究，因为其相关的基因组特征极难被检测到。我们提出将“进化与重测序（Evolve and Resequence）”作为一种颇具前景的工具，用以研究进化种群中数量性状的多基因适应。通过模拟重复时间序列数据，我们发现，种群对新的中间性状最优值的适应，在基因组层面上可体现为三个特征阶段：（1）等位基因频率向新的性状最优值发生定向改变；（2）当达到新的性状最优值后，等位基因频率趋于平稳；（3）随后重复实验间的等位基因频率轨迹出现分化，最终在性状值保持不变的情况下，导致等位基因的丢失或固定。我们针对相关的种群遗传学参数，对这三个阶段的特征展开探究，以期为各类实验进化研究设计提供预期参考。值得注意的是，在广泛的参数范围内，受选择等位基因的频率轨迹在重复实验中呈现出一种独特模式，该模式既不同于中性进化，也不同于定向选择。我们据此得出结论：实验进化研究所得的重复时间序列数据，为基于全基因组种群遗传学数据开展多基因适应研究提供了颇具前景的研究框架。