Data from: Tempo and mode of genome evolution in a 50,000-generation experiment

Adaptation by natural selection depends on the rates, effects and interactions of many mutations, making it difficult to determine what proportion of mutations in an evolving lineage are beneficial. Here we analysed 264 complete genomes from 12 Escherichia coli populations to characterize their dynamics over 50,000 generations. The populations that retained the ancestral mutation rate support a model in which most fixed mutations are beneficial, the fraction of beneficial mutations declines as fitness rises, and neutral mutations accumulate at a constant rate. We also compared these populations to mutation-accumulation lines evolved under a bottlenecking regime that minimizes selection. Nonsynonymous mutations, intergenic mutations, insertions and deletions are overrepresented in the long-term populations, further supporting the inference that most mutations that reached high frequency were favoured by selection. These results illuminate the shifting balance of forces that govern genome evolution in populations adapting to a new environment.

自然选择介导的适应性演化依赖于众多突变的发生速率、效应及其相互作用，这使得精准确定演化谱系内有益突变所占比例极具挑战性。本研究对12株大肠杆菌（Escherichia coli）种群的264个完整基因组展开分析，以刻画其历经50000代演化的基因组动态变化特征。保留祖先突变率的种群支持如下演化模型：绝大多数固定突变为有益突变，有益突变的比例随适应度（fitness）的提升而逐步降低，且中性突变以恒定速率累积。本研究还将上述种群与在最小化选择压力的种群瓶颈传代体系下演化的突变累积株系开展对比分析。非同义突变、基因间突变、插入突变与缺失突变在长期演化种群中占比偏高，进一步佐证了“多数达到高频率的突变均受到选择青睐”这一推论。本研究结果阐明了适应新环境的种群中，调控基因组演化的多种作用力的动态平衡格局。