Inferring the parameters of a simple admixture scenario.

Using MS, we simulated 200 replicates of the admixture scenario depicted in Figure 2B. In 100 replicates, the gene flow occurred 400 generations ago, while in the other 100 replicates it occurred 200 generations ago. Our estimates of the four parameters are consistently close to the true values, showing that we are able distinguish the two histories by numerically optimizing the likelihood function.