Joint distributions of P values for CNV stratification (x axis, Mann-Whitney U), archaic introgression (fD statistic, top two rows), and positive selection (population branch statistic, bottom row) tests. The archaic reference sequences used in the calculations of fD are Neanderthals (top row) and Denisovans (middle row), respectively. CNVs that show signatures of both positive selection and archaic introgression (red circles) are distinguished from loci that show signatures of introgression only (orange circles).