Figure 2.

Trajectories of the same quantitative trait locus in multiple replicates after a change to a new intermediate trait optimum show three distinct phases. Quantitative trait simulations for 500 independent replicates were performed with the default parameter settings, that is, 5 unlinked, free recombining loci with equal effect sizes (that is, 0.1 for each allele) and starting frequencies of 0.05, N_e=1000 and a Gaussian fitness function with mean 0.4, standard deviation of 0.2 and fitness ranges from 0.5 to 1.5 (for details see Table 1). Plots show trajectories of a single locus across replicates. Three phases can be recognized: (1) strong, highly reproducible frequency change in each replicate (red), (2) plateauing (yellow), (3) divergent trajectories with a highly stochastic outcome across replicates (blue). The remaining time period (white) indicates that the focal locus has become monomorphic in each replicate. (a) The trajectory of a single locus in 500 replicate simulations is summarized in violin plots, black dots indicate the median. Note, over time the median returns to zero as with an optimum of 0.4 a focal locus only fixes in 40% of the replicates, whereas the mean allele frequency remains at 0.4. (b) Example trajectories at a single locus in 10 independent replicates.