Fig. 5: Fitness effects of beneficial genes are correlated with evolutionary outcomes.

We explored if genes with beneficial knockout fitness effects are correlated with A establishment of a mutation in a gene, and B changes in gene expression over evolutionary time, relative to neutral knockouts. A Slopes from logistic models, with presence of a mutation in a gene as the response variable. The fitness effects were normalized by the median beneficial fitness effect, so that coefficients can be interpreted as the average difference in log-odds establishment between neutral knockouts and the ‘typical’ beneficial knockout. REL606 beneficial knockout fitness is positively correlated with gene establishment probability for most environments, but in different time intervals, potentially pointing to shifting targets of selection. Error bars represent standard errors, which were calculated as detailed in methods section “Genome evolution”. FDR-corrected p-values were obtained from the logistic regression model. B We compared the distributions of log-fold change in expression between genes with neutral knockout fitness effects, less beneficial effects (lower 50%), and more beneficial effects (upper 50%). We used the change in expression from 0k gens (REL606) to 40k gens (L), from 6.5k gens (S) to 40k gens (S), and from 6.5k gens (L) to 40k gens (L) for the REL606, 6.5k S, and 6.5k L panels, respectively. The expression change between ancestor and 40k L (left) is nearly identical to the expression change between ancestor and 40k S as well as other timepoints (Fig. S25). Beneficial knockout fitness in REL606 is generally positively correlated with increasing gene expression over time. In S and L, fitness in several environments--including the ecological equilibrium and acetate and glucose growth--is correlated with decreasing gene expression. The center line of the boxplot is the median; the limits of the box represents the first and third quartiles; the whiskers extend to one times the inter-quartile range; outliers are not shown. FDR-corrected Mann–Whitney U tests were used to compare conditions. Asterisks denote coefficients/comparisons that are significantly different from 0 (FDR correction; *p < 0.05, **p < 0.01, ***p < 0.001).