Evolution of 12 populations at 1000 loci were simulated. For each locus, each of the 12 populations starts at the same allele frequency and evolves independently, as shown in the upper left plot of allele frequency for a single locus. On the bottom, we see the current allele frequency for all loci at this generation, stratified by selection type and strength. Black dots mark the ancestral allele frequency and a vertical line marks the locus shown in the upper left plot. In the upper right, we attempt to estimate the ancestral allele frequency by taking the mean of the current allele frequencies of all 12 populations. A circle highlights the locus that appears in the upper left plot.

There are only 2 alleles for each locus: red or blue. The allele frequency changes in each generation via 2 mechanisms: drift and selection. For each locus, drift is the same: Freq[N+1]=rbinom(1000,Freq[N])/1000, since simulated population size is 1000. Selection depends on the color of the population, and the type of selection. For loci not under selection (NEU) and populations of neutral color, there is no allele frequency update (since presumably there is no selective pressure). For loci under positive selection (POS), blue alleles will be favored in blue populations, and disfavored in red populations. For loci under balancing selection (BAL) it is advantageous to have both a blue and red allele in a population that is either blue or red.