Lupinus.online.FigureS2.04.26.11

SUPPLEMENTARY FIGURE S2. Net diversification rates (r = lineages/million years) in Lupinus estimated under the MEDUSA birth–death likelihood model. MEDUSA analyses were conducted using 1000 trees randomly selected from the posterior distribution of constrained pure–birth Bayesian MCMC tree searches in BEAST, pruned to the infrageneric skeleton topology in Figure 3 of the main text. Histograms show the frequency (ƒ) of estimates from replicate MEDUSA likelihood runs: a) ΔAIC scores for pure–birth versus birth–death models; b) background rates of net diversification in Lupinus; c) ΔAIC scores for a rate shift in eastern South America; d) net diversification rates in eastern South America; e) ΔAIC scores for a rate shift in western North America; f) net diversification rates in western North America; g) ΔAIC scores for a rate shift in Mexico/Andes; h) net diversification rates in Mexico/Andes. ΔAIC scores indicated that a pure–birth model was strongly favored over a model incorporating extinction (Fig. S2a). The strongest support for a primary rate shift was recovered in western North America (Fig. S2e), although the fastest rates were estimated in the Mexican/Andean clade (Fig. S2h).

补充图S2。基于MEDUSA出生-死亡似然模型估算的羽扇豆属（Lupinus）净多样化速率（r = 类群/百万年）。本次MEDUSA分析选取了BEAST约束纯生贝叶斯MCMC树搜索后验分布中随机抽取的1000棵树，并将其修剪至正文图3所示的属内骨架拓扑结构。直方图展示了重复MEDUSA似然运行所得估算值的频率（ƒ）：a) 纯生模型与出生-死亡模型的ΔAIC（赤池信息准则差值）得分；b) 羽扇豆属的背景净多样化速率；c) 南美东部区域速率转变的ΔAIC得分；d) 南美东部区域的净多样化速率；e) 北美西部区域速率转变的ΔAIC得分；f) 北美西部区域的净多样化速率；g) 墨西哥/安第斯地区速率转变的ΔAIC得分；h) 墨西哥/安第斯地区的净多样化速率。ΔAIC得分结果显示，相较于纳入灭绝参数的模型，纯生模型获得了显著支持（图S2a）。北美西部区域的一级速率转变得到了最强的统计支持（图S2e），尽管最快的净多样化速率被估算于墨西哥/安第斯演化支中（图S2h）。