Data from: Effects of beneficial mutations in pykF gene vary over time and across replicate populations in a long-term experiment with bacteria

The fitness effects of mutations can depend on the genetic backgrounds in which they occur and thereby influence future opportunities for evolving populations. In particular, mutations that fix in a population might change the selective benefit of subsequent mutations, giving rise to historical contingency. We examine these effects by focusing on mutations in a key metabolic gene, pykF, that arose independently early in the history of 12 Escherichia coli populations during a long-term evolution experiment. Eight different evolved nonsynonymous mutations conferred similar fitness benefits of ~10% when transferred into the ancestor, and these benefits were greater than the one conferred by a deletion mutation. By contrast, the same mutations had highly variable fitness effects, ranging from about 0 to 25%, in evolved clones isolated from the populations at 20,000 generations. Two mutations that were moved into these evolved clones conferred similar fitness effects in a given clone, but different effects between the clones, indicating epistatic interactions between the evolved pykF alleles and the other mutations that had accumulated in each evolved clone. We also measured the fitness effects of six evolved pykF alleles in the same populations in which they had fixed, but at seven time points between 0 and 50,000 generations. Variation in fitness effects was high at intermediate time points, and declined to a low level at 50,000 generations, when the mean fitness effect was lowest. Our results demonstrate the importance of genetic context in determining the fitness effects of different beneficial mutations even within the same gene.

突变的适应度效应（fitness effects）往往取决于其所处的遗传背景（genetic backgrounds），并由此影响进化种群的后续演化机遇。具体而言，在种群中发生固定的突变可能会改变后续突变的选择效益（selective benefit），进而催生历史偶然性（historical contingency）这一现象。本研究聚焦于关键代谢基因pykF中的突变，基于12个大肠杆菌（Escherichia coli）种群的长期进化实验展开分析——这些突变在实验早期便于各种群中独立出现。8种不同的进化型非同义突变（nonsynonymous mutations）在被转入祖先菌株时，均展现出约10%的相似适应度增益，且该效益高于1种缺失突变（deletion mutation）所带来的适应度变化。与之形成鲜明对比的是，当上述突变被转入20000代时分离得到的进化菌株（evolved clones）中时，其适应度效应差异悬殊，区间范围约为0至25%。两类被转入进化菌株的突变，在同一宿主菌株中展现出相似的适应度效应，但在不同宿主菌株间的效应差异显著，这表明进化型pykF等位基因（alleles）与各进化菌株中积累的其他突变之间存在上位性相互作用（epistatic interactions）。本研究还测定了6种进化型pykF等位基因（alleles）在其发生固定的种群中，于0至50000代的7个时间节点下的适应度效应。适应度效应的变异程度在中间代际时处于较高水平，而在50000代时降至低位——此时平均适应度效应达到最低值。本研究结果证实，即便针对同一基因内的不同有益突变，遗传背景在决定其适应度效应的过程中仍发挥着至关重要的作用。