Data from: Diverse phenotypic and genetic responses to short-term selection in evolving Escherichia coli populations

Beneficial mutations fuel adaptation by altering phenotypes that enhance the fit of organisms to their environment. However, the phenotypic effects of mutations often depend on ecological context, making the distribution of effects across multiple environments essential to understanding the true nature of beneficial mutations. Studies that address both the genetic basis and ecological consequences of adaptive mutations remain rare. Here, we characterize the direct and pleiotropic fitness effects of a collection of 21 first-step beneficial mutants derived from naïve and adapted genotypes used in a long-term experimental evolution of Escherichia coli. Whole-genome sequencing was able to identify the majority of beneficial mutations. In contrast to previous studies, we find diverse fitness effects of mutations selected in a simple environment and few cases of genetic parallelism. The pleiotropic effects of these mutations were predominantly positive but some mutants were highly antagonistic in alternative environments. Further, the fitness effects of mutations derived from the adapted genotypes were dramatically reduced in nearly all environments. These findings suggest that many beneficial variants are accessible from a single point on the fitness landscape, and the fixation of alternative beneficial mutations may have dramatic consequences for niche breadth reduction via metabolic erosion.有益突变通过改变生物体表型以提升其对环境的适配能力，进而推动适应性演化。然而，突变的表型效应往往依赖于生态背景，因此探究突变效应在多环境下的分布规律，对于厘清有益突变的本质至关重要。目前，同时解析适应性突变的遗传基础与生态效应的研究仍较为匮乏。本研究针对大肠杆菌（Escherichia coli）长期实验演化体系中的21株一阶有益突变体展开表征，这些突变体分别源自未适应的原始基因型与已驯化基因型，我们解析了它们的直接适合度效应与多效性适合度效应。全基因组测序可成功识别绝大多数有益突变。与既往研究不同，本研究发现：在单一环境中筛选得到的突变体具备多样的适合度效应，且遗传平行性案例极少。这些突变的多效性效应整体以正向为主，但部分突变体在替代环境中表现出极强的拮抗效应。此外，源自驯化基因型的突变体，其适合度效应在几乎所有环境中均出现显著衰减。本研究结果表明，诸多有益变异可从适合度景观的单一节点获得；而替代性有益突变的固定，可能通过代谢侵蚀过程导致生态位宽度大幅缩减。