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.

图S5　选择对中等物种树模拟的物种树估计的影响。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的后验概率（posterior probability，PABC，蓝色）与错误拓扑结构的后验概率（PBCA，黄色）的分布情况，均值以黑色标记表示；实验数据集分别包含1个位点（底部行）、2个位点（中部行）与10个位点（顶部行），所有数据集均在每个物种种群采样5个个体（左侧列）或20个个体（右侧列）的条件下，基于3种不同的物种AB分化时间进行模拟：从左至右分别为0.0001（蓝色）、0.0005（黑色）与0.0009（红色）。本研究采用从白色到深灰色的色阶来表征受选择位点的占比：0%（中性进化，白色）、10%、20%、50%与100%（深灰色）。对于带有选择作用的模拟实验，我们设置了不同的选择强度：弱选择（"W"，选择系数s=0.01，浅红色）、强选择（"S"，选择系数s=0.10，中红色）以及极强选择（"VS"，选择系数s=0.5，深红色）。