FigureS1

FIGURE S1. The effects of species-specific positive selection on effective population size and divergence time estimates of the shallow (top) and moderate-depth (bottom) species tree models. 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: recent (blue), medium (black), and ancient (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.

补充图S1. 物种特异性正向选择对浅层次（上图）和中深度（下图）物种树模型的有效种群规模及分化时间估计值的影响。本结果对应(a-c)、(d-f)、(g-i)及(j-l)四组模拟数据集，各组分别包含1个位点（对应a、d、g、j）、2个位点（对应b、e、h、k）以及10个位点（对应c、f、i、l）。基于200次重复实验得到的参数估计值，我们展示了其均值（以点表示）与标准差（以误差棒表示），并覆盖三类不同的物种AB分化时间：近期（蓝色）、中等（黑色）与远古（红色）。每个主图面板均划分为两个子面板：虚线左侧为每个物种采样5条单倍型（haplotype），右侧则为20条单倍型。采用从白色到深灰色的色阶来表征受选择位点的不同占比：0%（中性进化，白色）、10%、20%、50%及100%（深灰色）。针对含选择作用的模拟实验，我们设置了三种不同的选择强度：弱选择（"W"，选择系数s=0.01）、强选择（"S"，s=0.10）以及极强选择（"VS"，s=0.5）。