FigureS6

FIGURE S6. The effects of selection on species tree estimates for the deep 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): 0.001 (blue), 0.005 (black), and 0.009 (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.

图S6：选择作用对深度物种树模拟中物种树推断结果的影响。小提琴图（violin plot）展示了200次重复实验中，正确有根物种拓扑结构（rooted species topology）的后验概率（posterior probability）（PABC，蓝色）与错误拓扑结构（PBCA，黄色）的分布，其中黑色线条表示均值。本图的数据集分别为单基因座（locus，底部）、两基因座（loci，中部）与十基因座（loci，顶部），这些数据集均以每个物种5个样本（左侧面板）或20个样本（右侧面板）进行模拟，并设置了三种不同的物种AB分化时间（从左至右依次为0.001（蓝色）、0.005（黑色）与0.009（红色））。我们采用从白色到深灰色的颜色梯度，表征受选择基因座的占比：0%（中性进化，白色）、10%、20%、50%与100%（深灰色）。针对带有选择作用的模拟实验，我们设置了三类不同的选择强度：弱选择（"W"，选择系数s=0.01，浅红色）、强选择（"S"，s=0.10，中红色）以及极强选择（"VS"，s=0.5，深红色）的选择系数（selection coefficient）。