Phylogenetic analyses are increasingly being performed with datasets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences on divergence time estimation has not been fully investigated. Using a series of simulation experiments and empirical analyses, we demonstrate that when topological incongruence between gene trees and the species tree is not accounted for, the temporal duration of branches in regions of the species tree that are affected by incongruence is underestimated, whilst the duration of other branches is considerably overestimated. This effect becomes more pronounced with higher levels of topological incongruence. We show that this pattern results from erroneous estimation of the number of substitutions along branches in the species tree, although the effect is modulated by the assumptions inherent to divergence time estimation, such as those relating to the fossil record or among-branch-substitution-rate variation. By only analysing loci with gene trees that are topologically congruent with the species tree, or only taking into account the branches from each gene tree that are topologically congruent with species tree, we demonstrate that the effects of topological incongruence can be ameliorated. Nonetheless, even when topologically congruent gene trees or topologically congruent branches are selected, error in divergence time estimates remains. This stems from temporal incongruences between divergence times in species trees and divergence times in gene trees, and more importantly, the difficulty of incorporating necessary assumptions for divergence time estimation.

中文翻译：

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基因树和物种树拓扑之间不一致对分歧时间估计的影响

系统发育分析越来越多地使用包含数百个基因座的数据集进行。由于不完全的谱系分类、杂交和水平基因转移，这些位点的基因树可能经常具有彼此不同的拓扑结构以及与物种树不同的拓扑结构。这些拓扑不一致对发散时间估计的影响尚未得到充分研究。通过一系列模拟实验和实证分析，我们证明了当不考虑基因树和物种树之间的拓扑不一致时，受不一致影响的物种树区域中分支的时间持续时间被低估，而持续时间其他分支的数量被大大高估了。随着拓扑不一致的程度越高，这种效应变得越明显。我们表明，这种模式是由于对物种树中分支的替换数量的错误估计造成的，尽管这种影响受到发散时间估计固有的假设的调节，例如与化石记录或分支间替换有关的假设率变化。通过仅分析与物种树拓扑一致的基因树的基因座，或仅考虑每个基因树中与物种树拓扑一致的分支，我们证明可以改善拓扑不一致的影响。尽管如此，即使选择了拓扑一致的基因树或拓扑一致的分支，分歧时间估计的误差仍然存在。