Fig. 1: Measuring mutational fitness effects.

A Timeline of evolution in the ara-2 LTEE population, showing mutation accumulation and diversification into S and L around 6k generations, then clone sampling at 6.5k generations; data from⁴⁷, jitter added to mutation fixation time for easier visualization. Hypermutator phenotype appeared around 2.5k generations⁵⁹. B Schematic of transposon mutagenesis process to generate barcoded libraries of REL606, 6.5k S and L, as well as experimental procedure to observe barcode dynamics. The erlenmeyer flask clipart (flask-2 icon by DBCLS) shown here is used and modified under a CC-BY- 4.0 creative commons license. C Barcoded knockout mutant frequency trajectories in the evolutionary condition for each genetic background, colored by estimated fitness. All barcodes within a gene were summed together; shown are the trajectories from replicate 1 in the evolutionary condition for each genetic background (monoculture for REL606, together at ecological equilibrium frequency for S and L; representative of both replicates). D Overall distributions of fitness effects in the evolutionary condition for each genetic background. The majority of knockouts were neutral, so only genes that were called as significantly non-neutral were included (see methods section “Probabilistic model of read count trajectories and fitness inference”). E Replicate–replicate correlation of estimated fitness effects. F Comparison of knockout fitness effects across genetic backgrounds, which are generally uncorrelated. Points with a blue interior correspond to genes that were mutated (excluding S-SNPs) in 6.5k S/L relative to REL606 (sequencing data from ref. ⁴⁶). Points with red outlines correspond to genes that were mutated in parallel in nonmutator LTEE populations (data from ref. ⁴⁷). The correlation coefficients decrease slightly if we recompute them, excluding likely neutral genes (ρ = 0.14, 0.03, 0.03; top to bottom). In panels E, F, knockouts with high measurement noise (σ_s > 0.3%) were excluded (except for labeled genes), ρ is the weighted pearson correlation coefficient, and error bars represent standard errors, as calculated in methods section “Probabilistic model of read count trajectories and fitness inference”. Also in panels E, F, the “cloud” of points around 0 mostly represents likely neutral knockouts.