Data from: Detecting evolutionarily significant units above the species level using the Generalized Mixed Yule Coalescent method

1. There is renewed interest in inferring evolutionary history by modelling diversification rates using phylogenies. Understanding the performance of the methods used under different scenarios is essential for assessing empirical results. Recently we introduced a new approach for analysing broadscale diversity patterns, using the Generalized Mixed Yule Coalescent (GMYC) method to test for the existence of evolutionarily significant units above the species (higher ESUs). This approach focuses on identifying clades as well as estimating rates and we refer to it as clade-dependent. However, the ability of the GMYC to detect the phylogenetic signature of higher ESUs has not been fully explored, nor has it been placed in the context of other, clade-independent approaches. 2. We simulated >32,000 trees under two clade-independent models: constant-rate birth-death (CRBD) and variable-rate birth-death (VRBD), using parameter estimates from nine empirical trees and more general parameter values. The simulated trees were used to evaluate scenarios under which GMYC might incorrectly detect the presence of higher ESUs. 3. The GMYC null model was rejected at a high rate on CRBD-simulated trees. This would lead to spurious inference of higher ESUs. However, the support for the GMYC model was significantly greater in most of the empirical clades than expected under a CRBD process. Simulations with empirically derived parameter values could therefore be used to exclude CRBD as an explanation for diversification patterns. In contrast, a VRBD process could not be ruled out as an alternative explanation for the apparent signature of hESUs in the empirical clades, based on the GMYC method alone. Other metrics of tree shape, however, differed notably between the empirical and VRBD-simulated trees. These metrics could be used in future to distinguish clade-dependent and clade-independent models. 4. In conclusion, detection of higher ESUs using the GMYC is robust against some clade-independent models, as long as simulations are used to evaluate these alternatives, but not against others. The differences between clade-dependent and clade-independent processes are biologically interesting, but most current models focus on the latter. We advocate more research into clade-dependent models for broad diversity patterns.1. 学界重新燃起了利用系统发育（phylogenies）构建分化速率模型以推断演化历史的研究兴趣。明晰不同场景下所用方法的表现，对评估实证研究结果至关重要。近期我们提出了一种分析大尺度多样性格局的新方法：借助广义混合尤尔-合并模型（Generalized Mixed Yule Coalescent，GMYC），检验物种级以上进化显著单元（evolutionarily significant units, ESUs，即高阶ESUs）的存在性。该方法聚焦于支系（clade）识别与速率估算，我们将其称为支系依赖型（clade-dependent）方法。然而，GMYC检测高阶ESUs的系统发育信号的能力尚未得到充分探究，且该方法也未与其他支系独立型（clade-independent）方法进行对比分析。 2. 本研究基于9棵实证系统发育树的参数估计值与更通用的参数取值，在两种支系独立型模型——恒定速率生灭模型（constant-rate birth-death, CRBD）与可变速率生灭模型（variable-rate birth-death, VRBD）——下模拟了超过32000棵系统发育树。我们利用这些模拟得到的系统发育树，评估GMYC可能错误检测到高阶ESUs存在的场景。 3. 在CRBD模型模拟得到的系统发育树中，GMYC零模型（null model）被高频率地拒绝，这会导致高阶ESUs的虚假推断（spurious inference）。不过，在大多数实证支系中，GMYC模型得到的支持度显著高于CRBD过程下的预期值。因此，基于实证参数的模拟可用于排除CRBD作为多样性分化格局的解释模型。相较而言，仅基于GMYC方法的话，无法排除VRBD过程作为实证支系中高阶ESUs表观信号的替代解释。不过，系统发育树形态结构的其他度量指标在实证树与VRBD模拟树之间存在显著差异。未来可借助这些度量指标区分支系依赖型与支系独立型模型。 4. 综上，只要通过模拟对替代模型进行评估，基于GMYC的高阶ESUs检测方法对部分支系独立型模型具有鲁棒性，但对另一部分模型则不具备鲁棒性。支系依赖型与支系独立型演化过程之间的差异具有生物学研究价值，但当前多数模型仅聚焦于后者。我们呼吁针对大尺度多样性格局开展更多支系依赖型模型的相关研究。