FigureS5

FIGURE S5. The effects of selection on species tree estimates for the moderate species tree simulations. Violin plots show the distribution of posterior probabilities of the correct rooted species topology (PABC, blue) and incorrect topology (PBCA, yellow) across 200 replicates (mean shown in black) for datasets consisting of 1-locus (bottom), 2-loci (middle), and 10-loci (top) that were simulated with either 5 (left) or 20 samples per species (right) under three different Species-AB divergence times (from left to right): 0.0001 (blue), 0.0005 (black), and 0.0009 (red). A color gradient ranging from white to dark gray is used to indicate the different percentages of loci under selection: 0% (neutral, white), 10%, 20%, 50% and 100% (dark gray). For simulations with selection, we varied the strength of selection: weak (“W”, s = 0.01, light red), strong (“S”, s = 0.10, medium red), and very strong (“VS”, s = 0.5, dark red) selection coefficients.