Clonal interference and the periodic selection of new beneficial mutations in Escherichia coli

Abstract

The conventional model of adaptation in asexual populations implies sequential fixation of new beneficial mutations via rare selective sweeps that purge all variation and preserve the clonal genotype. However, in large populations multiple beneficial mutations may co-occur, causing competition among them, a phenomenon called "clonal interference." Clonal interference is thus expected to lead to longer fixation times and larger fitness effects of mutations that ultimately become fixed, as well as to a genetically more diverse population. Here, we study the significance of clonal interference in populations consisting of mixtures of differently marked wild-type and mutator strains of Escherichia coli that adapt to a minimal-glucose environment for 400 generations. We monitored marker frequencies during evolution and measured the competitive fitness of random clones from each marker state after evolution. The results demonstrate the presence of multiple beneficial mutations in these populations and slower and more erratic invasion of mutants than expected by the conventional model, showing the signature of clonal interference. We found that a consequence of clonal interference is that fitness estimates derived from invasion trajectories were less than half the magnitude of direct estimates from competition experiments, thus revealing fundamental problems with this fitness measure. These results force a reevaluation of the conventional model of periodic selection for asexual microbes.

Figure 1.

Trajectories of log₁₀ (Ara⁺/Ara⁻) ratios of all 53 populations that were not founded by ancestral clones that already contained a fixed mutation. (A) mut⁺Ara⁺/mut⁺Ara⁻ populations. (B) mutSAra⁺/mut⁺Ara⁻ populations.

Figure 2.

Average fitness improvement (S) over 400 generations of a single clone from both the invading and the declining subpopulation (containing different Ara markers) of all 53 populations of Figure 1 measured in competition against the ancestor. The dotted line is the line of equality. Circles indicate mut⁺Ara⁺/mut⁺Ara⁻ and crosses for mutSAra⁺/mut⁺Ara⁻ populations.

Figure 3.

Trajectory of log₁₀ (Ara⁺/Ara⁻) vs. time and best-fitting linear step model (see text) of a representative (mutSAra⁺/mut⁺Ara⁻) population that shows the typical features of many trajectories. These include a lag period, followed by one or more seemingly linear slopes of the change of log₁₀ (Ara⁺/Ara⁻) over time (a₁, a₂, and a₃).

Figure 4.

(A) Time-averaged rate of subpopulation invasion (see text) vs. fitness improvement (S) over 400 generations of a clone from the invading subpopulation for the 47 populations that allowed regression analysis. The straight line gives the expected relationship between fitness effect of invading mutation and rate of invasion, given that the invading mutation is the only one present in the population; the dotted and dashed lines give the observed relationships for mut⁺/mut⁺ (circles) and mutS/mut⁺ populations (crosses), respectively. (B) Fitness improvement (S) of the total population vs. time-averaged rate of subpopulation invasion. No significant relationship is apparent for either strain combination (symbols as in A).

Figure 5.

Fitness improvement (S) of subpopulations derived from competition experiments of evolved clones against the ancestor vs. fitness improvement derived from the slopes of the log (Ara⁺/Ara⁻) trajectories. The analysis was done for both subpopulations of the 47 populations that allowed regression analysis. The dashed line is the line of equality; circles indicate mut⁺, and crosses indicate mutS subpopulations.