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Abstract：
Identifying along which lineages shifts in diversification rates occur is a central goal of comparative phylogenetics; these shifts may coincide with key evolutionary events such as the development of novel morphological characters, the acquisition of adaptive traits, polyploidization or other structural genomic changes, or dispersal to a new habitat and subsequent increase in environmental niche space. However, while multiple methods now exist to estimate diversification rates and identify shifts using phylogenetic topologies, the appropriate use and accuracy of these methods are hotly debated. Here we test whether five Bayesian methods-Bayesian Analysis of Macroevolutionary Mixtures (BAMM), two implementations of the Lineage-Specific Birth-Death-Shift model (LSBDS and PESTO), the approximate Multi-Type Birth-Death model (MTBD; implemented in BEAST2), and the Cladogenetic Diversification Rate Shift model (ClaDS2)-produce comparable results. We apply each of these methods to a set of 65 empirical time-calibrated phylogenies and compare inferences of speciation rate, extinction rate, and net diversification rate. We find that the five methods often infer different speciation, extinction, and net-diversification rates. Consequently, these different estimates may lead to different interpretations of the macroevolutionary dynamics. The different estimates can be attributed to fundamental differences among the compared models. Therefore, the inference of shifts in diversification rates is strongly method dependent. We advise biologists to apply multiple methods to test the robustness of the conclusions or to carefully select the method based on the validity of the underlying model assumptions to their particular empirical system.
摘要：
确定多元化率发生的谱系变化是比较系统发育学的中心目标；这些变化可能与关键的进化事件相吻合，例如新的形态特征的发展，适应性性状的获得，多倍体化或其他结构基因组变化，或扩散到新的栖息地，并随后增加环境生态位空间。然而,虽然现在存在多种方法来估计多样化率并使用系统发育拓扑来识别变化，这些方法的适当使用和准确性引起了激烈的争论。在这里，我们测试了五种贝叶斯方法-宏观进化混合物的贝叶斯分析(BAMM)，血统特定的出生-死亡-转移模型(LSBDS和PESTO)的两种实现，近似多类型出生-死亡模型(MTBD；在BEAST2中实现)，和Cladogenetic多元化利率偏移模型(ClaDS2)-产生可比的结果。我们将这些方法中的每一种应用于一组65个经验时间校准的系统发育，并比较了物种形成率的推论，灭绝率,和净多元化率。我们发现这五种方法经常推断不同的物种形成，灭绝,和净多元化率。因此,这些不同的估计可能导致对宏观进化动力学的不同解释。不同的估计可以归因于比较模型之间的基本差异。因此,多元化率变化的推断与方法密切相关。我们建议生物学家应用多种方法来检验结论的稳健性，或者根据基础模型假设对其特定经验系统的有效性来仔细选择方法。
