As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suite of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study we show that asymmetric rates of sequence evolution lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out. This article is protected by copyright. All rights reserved.

中文翻译：

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分子序列进化速率的异质性极大地影响了检测多样化速率变化的准确性

由于物种丰富度在生命之树上各不相同，因此人们对确定影响谱系形成或灭绝速度的因素非常感兴趣。为此，理论生物学家开发了一套系统发育比较方法，旨在确定系统发育过程中多样化率的变化发生在哪里，以及它们是否与某些特征相关。使用这些方法，许多研究预测物种形成和灭绝率在生命之树上各不相同。在这项研究中，我们表明序列进化的不对称速率导致推断的系统发育中的系统偏差，进而导致关于谱系多样化模式的错误推断。结果表明，随着序列进化速率的不对称性增加，选择更复杂模型的趋势也是如此，其中包括多样化率变化的可能性。因此，这些结果表明，任何关于多样化模式变化的推论都应该非常谨慎，至少在排除关于分子取代率的任何偏见之前。本文受版权保护。版权所有。