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. 学界再度兴起通过系统发育（phylogeny）建模多样化速率以推断演化历史的研究热潮。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。此前我们提出了一种分析宏观多样性模式的新方法：利用广义混合尤尔-合并模型（Generalized Mixed Yule Coalescent, GMYC）检测物种以上级别进化显著单元（evolutionarily significant units, ESUs，即higher ESUs）的存在。该方法兼具支系（clade）识别与速率估算功能，我们将其命名为支系依赖型方法。然而，GMYC检测高等ESUs系统发育信号的能力尚未得到充分探究，且该方法尚未与其他支系独立型方法开展对标分析。
2. 我们基于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——恒定速率出生-死亡模型（constant-rate birth-death, CRBD）与可变速率出生-死亡模型（variable-rate birth-death, VRBD）——下模拟生成了超过32000棵系统发育树。这些模拟树被用于评估GMYC可能错误检测到高等ESUs存在的场景。
3. 在CRBD模型模拟生成的系统发育树中，GMYC零假设被大量拒绝，这将导致高等ESUs的虚假推断。但在多数实证支系中，GMYC模型的支持度显著高于CRBD过程下的预期值，因此基于实证参数值开展的模拟可用于排除CRBD作为多样化模式的解释机制。与之相对，仅基于GMYC方法，无法排除VRBD过程作为实证支系中高等ESUs表观信号的替代解释。不过，实证系统发育树与VRBD模拟树的其他树形态指标存在显著差异，未来可利用这些指标区分支系依赖型与支系独立型模型。
4. 综上，只要通过模拟评估这些替代模型，基于GMYC的高等ESUs检测对部分支系独立型模型具备鲁棒性，但对另一部分则不然。支系依赖型与支系独立型演化过程之间的差异具有重要生物学意义，但当前多数模型均聚焦于后者。我们呼吁针对宏观多样性模式开展更多支系依赖型模型相关研究。