Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates

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 suit 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 rates 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 dive...随着生命之树（tree of life）上的物种丰富度存在差异，学界对识别影响类群物种形成或灭绝速率的因素有着浓厚的研究兴趣。为此，理论生物学家开发了一系列系统发育比较方法（phylogenetic comparative methods），旨在识别系统发育（phylogeny）上多样化速率发生转移的位置，以及这些转移是否与某些性状相关联。借助这些方法，已有大量研究预测，物种形成与灭绝速率在生命之树上存在差异。本研究表明，序列进化速率不对称会导致推断出的系统发育产生系统性偏差，进而引发关于类群多样化模式的错误推断。研究结果显示，随着序列进化速率不对称性的增强，研究者更倾向于选择包含多样化速率转移可能性的更复杂模型。因此，这些结果表明，任何关于多样化速率转移的推断……