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.

中文翻译：

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基因树不一致是否解释了宏观进化模型与树形和分枝时间的经验模式之间的不匹配？

物种形成和灭绝的经典无效模型产生的系统发育与经验系统发育的分布不同。特别是，与常见的无效模型预测的系统发育相比，经验系统发育不太平衡，并且分支时间更接近根。这种差异可能是由于物种形成和灭绝过程的无效模型过于简单，或者由于经验数据集不能代表随机系统发育。第三种可能性的出现是因为系统发育重建方法通常推断基因树而不是物种树，从而在预测物种树模式的模型与考虑基因树的经验分析之间产生不一致。我们调查了在组合出生 - 死亡和多物种合并模型下基因树和物种树之间的差异可以解释经验树和出生 - 死亡物种树的差异的程度。我们模拟嵌入在模拟物种树中的基因树，并研究它们在树平衡和分枝时间方面的差异。我们观察到基因树不太平衡，并且通常比物种树具有更接近根的分支时间。TreeBase 中的经验树也不如我们模拟的物种树平衡，模型基因树可以解释与物种树相比高达 8% 的不平衡增加。然而，我们看到经验树的不平衡性增加了更多，大约 100%，这意味着额外的特征也必须导致经验树的不平衡性。