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.突变的适合度效应（fitness effects）取决于其所处的遗传背景，并由此影响进化种群的后续演化机遇。具体而言，在种群中固定的突变可能会改变后续突变的选择优势，进而产生历史偶然性。本研究聚焦于关键代谢基因pykF中的突变，对上述效应展开研究——这些突变在12个大肠杆菌（Escherichia coli）种群的长期进化实验历史早期独立发生。当8种不同的进化型非同义突变被转入祖先菌株时，均展现出约10%的相似适合度增益，且该增益高于缺失突变所带来的适合度增益。相较之下，当将这些相同的突变转入在20000代时从种群中分离得到的进化克隆时，其适合度效应差异极大，区间约为0%至25%。有两种被转入此类进化克隆的突变，在同一克隆内展现出相近的适合度效应，但在不同克隆间的效应却各不相同，这表明进化型pykF等位基因与各进化克隆中积累的其他突变之间存在上位性互作（epistatic interactions）。我们还在6种进化型pykF等位基因各自固定的种群中，于0至50000代之间的7个时间点，测定了这些等位基因的适合度效应。适合度效应的变异程度在中间时间点较高，在50000代时降至低位，此时平均适合度效应也处于最低水平。本研究结果证实，即便在同一基因内部，遗传背景对于不同有益突变的适合度效应的决定作用同样至关重要。