Fig. 3.

FREQ-Seq² allele frequency and fitness trajectories over time for the evolved Ara${}^{-}$ strain. The Ara${}^{-}$ strain competed with the ancestral Ara${}^{+}$ strain, and their frequencies were measured at several time points over 2,000 generations. a) Ara${}^{-}$ allele frequency and b) relative fitness across eleven generations of the competition assay measured using both FREQ-Seq² and manual colony counting. The blue and red dots represent the mean allele frequency or relative fitness at each time point. In a), the dotted lines correspond to the initial Ara${}^{-}$ frequency before the strains were conducted and the solid lines correspond to the Ara${}^{-}$ frequency after competing. The line and curves show the fit of a linear, hyperbolic, and power law model to the initial frequencies, post-competition frequencies, and fitnesses, respectively. Note that the higher magnitude of the Ara${}^{-}$ frequencies for colony counting are due to the higher initial frequencies. The green line is the mean allele frequency measured using FREQ-Seq² for sixteen independent target 50/50 negative controls. The shaded regions represent 95% confidence intervals based on the standard error of the mean.