FigureS3

FIGURE S3. The effects of species-specific positive selection on posterior probabilities of species hypotheses of the shallow and moderate-depth species tree models. Results are shown 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.图S3。物种特异性正向选择（species-specific positive selection）对浅深度与中等深度物种树模型（species tree models）的物种假说（species hypotheses）后验概率（posterior probabilities）的影响。本结果基于三类模拟数据集生成，分别包含单基因座（1-locus，对应子图a、d、g、j）、双基因座（2-loci，对应子图b、e、h、k）以及十基因座（10-loci，对应子图c、f、i、l）。针对物种AB的三类不同分化时间——近期分化（蓝色）、中等分化时长（黑色）与古老分化（红色），本图展示了基于200次重复实验得到的参数估计值均值（点标记）与标准差（误差棒）。每个主图均被一条虚线划分为两个子分区，分别代表每个物种采样5个单倍型（haplotype，虚线左侧）与20个单倍型（虚线右侧）。本图采用从白色到深灰色的颜色梯度，以表征受选择基因座的不同占比：0%（中性选择，白色）、10%、20%、50%与100%（深灰色）。在开展带选择的模拟实验时，我们设置了不同的选择强度：弱选择（"W"，选择系数s=0.01）、强选择（"S"，选择系数s=0.10）以及极强选择（"VS"，选择系数s=0.5）三类选择系数。