Data from: Does gene tree discordance explain the mismatch between macroevolutionary models and empirical patterns of tree shape and branching times?

Classic null models for speciation and extinction give rise to phylogenies that differ in distribution from empirical phylogenies. In particular, empirical phylogenies are less balanced and have branching times closer to the root compared to phylogenies predicted by common null models. This difference might be due to null models of the speciation and extinction process being too simplistic, or due to the empirical datasets not being representative of random phylogenies. A third possibility arises because phylogenetic reconstruction methods often infer gene trees rather than species trees, producing an incongruity between models that predict species tree patterns and empirical analyses that consider gene trees. We investigate the extent to which the difference between gene trees and species trees under a combined birth–death and multispecies coalescent model can explain the difference in empirical trees and birth–death species trees. We simulate gene trees embedded in simulated species trees and investigate their difference with respect to tree balance and branching times. We observe that the gene trees are less balanced and typically have branching times closer to the root than the species trees. Empirical trees from TreeBase are also less balanced than our simulated species trees, and model gene trees can explain an imbalance increase of up to 8% compared to species trees. However, we see a much larger imbalance increase in empirical trees, about 100%, meaning that additional features must also be causing imbalance in empirical trees. This simulation study highlights the necessity of revisiting the assumptions made in phylogenetic analyses, as these assumptions, such as equating the gene tree with the species tree, might lead to a biased conclusion.

用于物种形成与灭绝的经典零模型（null models）所生成的系统发育树，其分布特征与经验系统发育树存在显著差异。具体而言，相较于常见零模型预测的系统发育树，经验系统发育树的平衡性更弱，且分支时间更靠近根节点。

该差异可能源于两类诱因：一是物种形成与灭绝的零模型过于简化，二是经验数据集并非随机系统发育树的代表性样本。第三种可能性则在于，系统发育重建方法通常仅能推断基因树（gene trees）而非物种树（species trees），这会导致预测物种树模式的模型，与基于基因树开展的经验分析之间存在不一致性。

本研究探讨了：在联合生灭-多物种溯祖模型下，基因树与物种树之间的差异，能够在多大程度上解释经验树与生灭物种树之间的分歧。我们对嵌入模拟物种树的基因树进行了模拟，并针对树的平衡性与分支时间开展了差异分析。结果显示，相较于物种树，基因树的平衡性更弱，且分支时间通常更靠近根节点。

来自TreeBase数据库的经验树同样比我们模拟得到的物种树平衡性更弱，且本模型生成的基因树，相较物种树可解释最高达8%的不平衡性增幅。然而，我们在经验树中观察到的不平衡性增幅要大得多，约为100%，这意味着还存在其他特征同样会导致经验树的平衡性失衡。

本模拟研究强调了重新审视系统发育分析中各项假设的必要性——诸如将基因树等同于物种树这类假设，可能会导致分析结论产生偏差。