Extended Data Fig. 3 |. MPL performs well in the presence of recombination.
a, Classification performance of MPL is robust to variation in per locus recombination probability, r. Results are shown for n = 100 independent Monte-Carlo runs. The lower and upper edge of the boxplot correspond to the 25th to 75th percentiles, the bar corresponds to the median while the top and bottom whiskers show the maximum and minimum value within 1.5× the interquartile range from the boxplot. Linkage effects in the data decrease as the recombination probability increases. As a measure of the linkage disequilibrium in the data, we plot the histograms (b) of the covariance (xij − xixj) of mutant allele frequencies integrated over time (300 generations) for a range of recombination probabilities. The number of mutant pairs with strong pairwise covariance values decrease with increasing values of r, indicating lower linkage disequilibrium. Simulation parameters. Same as those of simple scenario used in Fig. 2, that is, L = 50 loci with two alleles at each locus (mutant and WT): ten beneficial mutants (s = 0.025), 30 neutral mutants (s = 0), and ten deleterious mutants (s = −0.025). Mutation probability μ = 10−4, population size N = 103, r = {0, 10−5, 10−4, 10−3}. The initial population begins with all WT sequences, evolved over T = 300 generations.