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.Fitness_evolvedCompetitive fitness measurements for 46 evolved populations of Escherichia coli. Three replicate fitness assays were performed for each population. Founding genotypes are also indicated, as are numbers of high confidence substitutions (hc_fixed), polymorphisms (hc_poly), and total number of mutations (hc_total, the sum of hc_fixed and hc_poly).MICMeasurements of ciprofloxacin resistance for all strains and populations used in this study. Resistance is measured as the minimal inhibitory concentration (MIC), the concentration of antibiotic required to inhibit growth by 90% in an overnight culture. MIC is given both in absolute terms (ng/mL cup) and in terms of fold-increase over the susceptible ancestor MG1655.Data_by_progenitorData on progenitor strains and summaries for evolved populations by progenitor. See readme file for details.Mutation dataTable S1 from paper. All mutations found in whole genome sequencing of evolved populations.TableS1.xls