Adaptation, clonal interference, and frequency-dependent interactions in a long-term evolution experiment with Escherichia coli

Twelve replicate populations of Escherichia coli have been evolving in the laboratory for >25 years and 60,000 generations. We analyzed bacteria from whole-population samples frozen every 500 generations through 20,000 generations for one well-studied population, called Ara−1. By tracking 42 known mutations in these samples, we reconstructed the history of this population’s genotypic evolution over this period. The evolutionary dynamics of Ara−1 show strong evidence of selective sweeps as well as clonal interference between competing lineages bearing different beneficial mutations. In some cases, sets of several mutations approached fixation simultaneously, often conveying no information about their order of origination; we present several possible explanations for the existence of these mutational cohorts. Against a backdrop of rapid selective sweeps both earlier and later, two genetically diverged clades coexisted for >6000 generations before one went extinct. In that time, many...

十二个重复大肠杆菌（Escherichia coli）种群已在实验室中持续演化超过25年，共计历经60000个世代。针对其中一株被深入研究、命名为Ara⁻¹的种群，我们对其每500个世代冻存一次、截至第20000个世代的全种群样本中的细菌开展了分析。通过追踪这些样本中的42个已知突变，我们重构了该种群在此时间段内的基因型演化历程。Ara⁻¹种群的演化动力学展现出强烈的选择性清除（selective sweep）信号，以及携带不同有益突变的竞争谱系间发生的克隆干涉（clonal interference）现象。在部分情形中，多组突变可同时接近固定，这类情况往往无法反映其起源的先后顺序；我们针对这类突变群的存在提出了多种可能的解释。在早期与晚期均存在快速选择性清除的背景下，两个遗传分化的演化支共存了超过6000个世代，直至其中一支最终灭绝。在此期间，诸多……