Comparison of the percentage of introgressed sites inferred by PhyloNet-HMM versus two lower bounds on simulated data sets.

The percentage of sites is the number of sites for which , based on Eq. (2), is , divided by the total number of sites in the simulated genomes, which is 100,000. The lower bounds on the true percentage of introgressed sites are based on the frequency that one of the two lineages from population A coalesced with lineages in population B between times and . (See Materials and Methods for additional discussion.) Six model conditions are shown, encompassing three migration rates and two different dates of migration. A migration rate corresponds to a pure isolation model, whereas a migration rate corresponds to an isolation-with-migration model. Standard error bars are shown, and the number of replicates for each model is .