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...自然选择驱动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，这使得我们难以确定正在演化的谱系中有益突变所占的比例。本研究针对12个大肠杆菌（Escherichia coli）种群的264套完整基因组展开分析，以刻画其历经50000代演化后的动态变化规律。保留祖先突变率的种群支持如下模型：绝大多数固定突变均为有益突变，且有益突变的比例随适合度提升而逐渐下降，中性突变则以恒定速率累积。本研究还将上述种群与在最小化选择压力的种群瓶颈培养体系下演化得到的突变累积株系进行了对照分析。长期演化种群中，非同义突变、基因间区突变及插入缺失变异均呈现过度富集特征，进一步佐证了绝大多数达到高频率的突变均受选择青睐这一推论。上述研究结果阐明了调控基因组演化的多重作用力的动态平衡机制……