Phylogenies of extant species are consistent with an infinite array of diversification histories
Phylogenies of extant species are consistent with an infinite array of diversification histories
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现存物种的系统发育与无数的多样化历史一致
DOI：
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发表时间：
2019
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通讯作者：
Matthew W. Pennell
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作者：
Stilianos Louca;Matthew W. Pennell
现存物种的时间校准分子系统发育（“现存时间树”）被广泛用于估计多样化率的动态（1-6）和测试这些率与环境因素（5,7）或物种特征(8)之间的关联。然而，在缺乏化石数据的情况下，围绕这些推断的可靠性一直存在相当大的争论（9-13），到目前为止，这个关键问题仍未得到解决。在这里，我们从数学上阐明了在广义出生-死亡模型下可以从现有时间树中提取的精确信息，这是大多数现有估计方法的基础。我们证明了对于一个给定的现存时间树和一个候选多样化方案，存在无限多个可能产生给定树的可选多样化方案。即使在存在无限数据的情况下，仅使用现有的时间树也不可能区分这些“一致”场景。重要的是，一致的多样化情景可以表现出明显不同但似乎合理的多样化动态，这表明许多先前的研究可能过度解释了系统发育证据。我们表明，可以使用复合变量唯一地描述全等模型集，其中包含有关过去多样化动态的所有可用信息（14）；这为从现存的时间树中了解过去提供了另一种范式。
Time-calibrated molecular phylogenies of extant species ("extant timetrees") are widely used for estimating the dynamics of diversification rates (1–6) and testing for associations between these rates and environmental factors (5, 7) or species traits (8). However, there has been considerable debate surrounding the reliability of these inferences in the absence of fossil data (9–13), and to date this critical question remains unresolved. Here we mathematically clarify the precise information that can be extracted from extant timetrees under the generalized birth-death model, which underlies the majority of existing estimation methods. We prove that for a given extant timetree and a candidate diversification scenario, there exists an infinite number of alternative diversification scenarios that are equally likely to have generated a given tree. These “congruent” scenarios cannot possibly be distinguished using extant timetrees alone, even in the presence of infinite data. Importantly, congruent diversification scenarios can exhibit markedly different and yet plausible diversification dynamics, suggesting that many previous studies may have over-interpreted phylogenetic evidence. We show that sets of congruent models can be uniquely described using composite variables, which contain all available information about past dynamics of diversification (14); this suggests an alternative paradigm for learning about the past from extant timetrees.