Data from: 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 additional mutations arose in the clade that eventually prevailed. We show that the clades evolved a frequency-dependent interaction, which prevented the immediate competitive exclusion of either clade, but which collapsed as beneficial mutations accumulated in the clade that prevailed. Clonal interference and frequency dependence can occur even in the simplest microbial populations. Furthermore, frequency dependence may generate dynamics that extend the period of coexistence that would otherwise be sustained by clonal interference alone.

12株大肠杆菌（Escherichia coli）复现种群已在实验室中持续演化超过25年，历经60000个世代。我们针对其中一个被深入研究的命名为Ara⁻¹的种群，对每500代冻存一次的全种群样本中的细菌开展了分析，采样覆盖至第20000个世代。通过追踪这些样本中的42种已知突变，我们重构了该种群在此期间的基因型演化历程。Ara⁻¹种群的演化动力学展现出强烈的选择扫荡（selective sweep）证据，以及携带不同有益突变的竞争谱系间存在的克隆干扰（clonal interference）现象。在部分场景中，多组突变可同时接近固定，且通常无法推断其起源先后顺序；我们针对这类突变群的存在提出了数种可能的解释。在早期与后期均存在快速选择扫荡的背景下，两个遗传分化的进化枝（clade）共存了超过6000个世代，直至其中一支灭绝。在此期间，最终占优的进化枝中产生了诸多额外突变。我们发现，两个进化枝演化出了频率依赖型互作，这使得二者不会被立即竞争性排除，但随着占优进化枝积累了有益突变，该互作最终瓦解。即便在最简单的微生物种群中，也可能出现克隆干扰与频率依赖现象。此外，频率依赖效应可产生动力学过程，延长仅靠克隆干扰所能维持的共存时长。