Figure 1.

Complex demographic scenarios in which selective sweeps, due to a novel selection pressure acting upon at least one population from time T _s onward, can be masked or misinterpreted. In each scenario, sampling before (1), during (2), and after (3) T _s provides a time series of allele frequencies in populations A, B, and C, providing more power to infer the true evolutionary history. Allele frequencies are indicated by coloring of branches. i. Positive selection for a derived (red) allele in population B at time T _s drives it to high frequency, differentiating population B from populations A and C, but this differentiation at this locus is later masked by introgression from population B into population C. ii. The same evolutionary history as in i., except this time recent introgression of the ancestral allele (blue) from population A into population B masks the ancestral selection on the derived allele. iii. Parallel selection acts upon the derived allele at time T _s in both populations B and C. Three population selection tests such as the Population Branch Statistic can misinterpret this pattern of differentiation of A from both B and C as that of selection on the ancestral (blue) allele in population A (see Mathieson 2019 for an example of this type of scenario and selection on loci within the FADS gene in humans).