Data from: Effects of genotype on rates of substitution during experimental evolution

Rates of molecular evolution may vary widely between populations, yet the causes of this variation are still incompletely understood. Genetic differences between populations may make an important contribution to variation in rates of evolution, owing to differences in fitness, population size, mutation rates, or in the distribution of fitness effects (DFE) of available beneficial mutations. By whole genome sequencing of Escherichia coli populations experimentally evolved in the presence of a quinolone antibiotic, we found that rates of substitution varied by genotype, with evidence for a contribution from a genotype’s starting fitness. Subsequent targeted sequencing showed that genotypes with high average substitution rates were more likely to undergo the simultaneous fixation of several mutations, consistent with theoretical models of multiple mutation dynamics. Moreover, patterns of substitution were indicative of epistatic relationships between known resistance mutations.种群间的分子进化速率往往存在显著差异，但其背后的成因迄今仍未完全明晰。由于适合度、种群规模、突变率的差异，以及可获得有益突变的适合度效应分布（Distribution of Fitness Effects, DFE）各不相同，种群间的遗传差异可能对进化速率的变异起到重要推动作用。本研究通过对在喹诺酮类抗生素环境下经实验进化的大肠杆菌（Escherichia coli）种群开展全基因组测序，发现不同基因型的替换速率存在差异，且有证据表明基因型的初始适合度对替换速率存在贡献。后续靶向测序结果显示，平均替换速率较高的基因型更易发生多个突变的同步固定，这与多突变动态的理论模型相一致。此外，替换模式还揭示了已知耐药突变之间存在上位性关系。