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 more than 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 over 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个重复的大肠杆菌（Escherichia coli）种群已在实验室中持续进化超过25年，历经60000代。针对一个被深入研究的命名为Ara–1的种群，我们对其每500代冻存的全种群样本中的细菌进行了分析，直至第20000代。通过追踪这些样本中42个已知突变，我们重构了该种群在此期间的基因型进化历程。Ara–1种群的进化动力学显示出强烈的选择扫荡（selective sweeps）证据，以及携带不同有益突变的竞争谱系之间存在克隆干涉（clonal interference）现象。在部分情形中，多组突变会同时接近固定状态，通常无法推断其起源顺序；针对这类突变群的存在，我们提出了多种可能的解释。在早期与后期均存在快速选择扫荡的背景下，两个遗传分化的演化支（clade）共存了超过6000代，直至其中一支灭绝。在此期间，最终占据优势的演化支中又积累了诸多额外突变。我们证实，这两个演化支演化出了频率依赖型相互作用，这一作用避免了任一演化支被立即竞争性排除，但随着优势演化支积累有益突变，该相互关系最终瓦解。即便在最简单的微生物种群中，也可能出现克隆干涉与频率依赖现象。此外，频率依赖作用所产生的动力学效应，可延长仅靠克隆干涉所能维持的共存时长。