Molecular data have been used to date species divergences ever since they were described as documents of evolutionary history in the 1960s. Yet, an inadequate fossil record and discordance between gene trees and species trees are persistently problematic. We examine how, by accommodating gene tree discordance and by scaling branch lengths to absolute time using mutation rate and generation time, multispecies coalescent (MSC) methods can potentially overcome these challenges. We find that time estimates can differ – in some cases, substantially – depending on whether MSC methods or traditional phylogenetic methods that apply concatenation are used, and whether the tree is calibrated with pedigree-based mutation rates or with fossils. We discuss the advantages and shortcomings of both approaches and provide practical guidance for data analysis when using these methods.

自从将分子数据描述为1960年代的进化史以来，就一直使用分子数据来对物种的差异进行测算。然而，化石记录不足以及基因树和物种树之间的矛盾始终存在问题。我们研究了如何通过适应基因树的不一致性以及通过使用突变率和生成时间将分支长度缩放到绝对时间来实现多物种合并（MSC）方法如何潜在地克服这些挑战。我们发现，时间估计可能会有所不同-在某些情况下会有所不同-取决于使用的是MSC方法还是采用串联的传统系统发育方法，以及是否使用基于谱系的突变率或使用化石对树进行了校准。