FigureS2

FIGURE S2. The effects of species-specific positive selection on effective population size and divergence time estimates of the deep species tree model. Results are shown for (a-c), (d-f), (g-i), and (j-l) for simulated datasets consisting of 1-locus (a, d, g, j), 2-loci (b, e, h, k), and 10-loci (c, f, i, l). The mean (points) and standard deviation (error bars) of parameter estimates based on 200 replicates are shown for three different Species-AB divergence times: 0.001 (blue), 0.005 (black), and 0.009 (red). Each panel is split into two subpanels representing 5 (left of dotted line) or 20 (right of dotted line) haplotypes sampled per species. 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), strong (“S”, s = 0.10), and very strong (“VS”, s = 0.5) selection coefficients.