Data from: Uncovering higher-taxon diversification dynamics from clade age and species-richness data

The relationship between clade age and species richness has been increasingly used in macroevolutionary studies as evidence for ecologically versus time-dependent diversification processes. However, theory suggests that phylogenetic structure, age type (crown or stem age) and taxonomic delimitation can affect estimates of the age-richness correlation (ARC) considerably. We currently lack an integrative understanding of how these different factors affect ARCs, which in turn, obscures further interpretations. To assess its informative breadth, we characterise ARC behaviour with simulated and empirical phylogenies, considering phylogenetic structure and both crown and stem ages. First, we develop a two-state birth-death model to simulate phylogenies including the origin of higher taxa and a hierarchical taxonomy to determine ARC expectations under ecologically and time-dependent diversification processes. Then, we estimate ARCs across various taxonomic ranks of extant amphibians, squamate reptiles, mammals, birds and flowering plants. We find that our model reproduces the general ARC trends of a wide range of biological systems despite the particularities of taxonomic practice within each, suggesting that the model is adequate to establish a framework of ARC null expectations for different diversification processes when taxa are defined with a hierarchical taxonomy. ARCs estimated with crown ages were positive in all the scenarios we studied, including ecologically dependent processes. Negative ARCs were only found at less inclusive taxonomic ranks, when considering stem age, and when rates varied among clades. This was the case both in ecologically and time-dependent processes. Together, our results warn against direct interpretations of single ARC estimates and advocate for a more integrative use of ARCs across age types and taxonomic ranks in diversification studies.

支系年龄与物种丰富度之间的关系，在大进化研究中已被愈发广泛地用作区分生态依赖与时间依赖分化过程的证据。然而，理论研究表明，系统发育结构、年龄类型（冠群年龄或茎群年龄）以及分类界定，均会显著影响年龄-丰富度相关性（age-richness correlation, ARC）的估算结果。目前学界尚缺乏对这些不同因素如何影响ARC的整合性认知，这进一步阻碍了相关研究的深入解读。为评估ARC的信息应用广度，我们结合模拟与经验系统发育数据对ARC的行为特征进行表征，同时考量系统发育结构、冠群年龄与茎群年龄。首先，我们构建两态生灭模型以模拟系统发育过程，其中包含高级分类单元的起源，并通过层级分类法确定生态依赖与时间依赖分化过程下ARC的预期结果。随后，我们针对现生两栖动物、有鳞爬行动物、哺乳动物、鸟类以及被子植物的不同分类等级估算ARC。研究发现，尽管各生物类群的分类实践存在各自的特殊性，但我们的模型能够复现多种生物系统中普遍存在的ARC总体趋势，这表明当通过层级分类法界定类群时，该模型足以构建不同分化过程下ARC的零期望框架。在所有研究场景中，基于冠群年龄估算的ARC均为正值，即便在生态依赖型分化过程中亦是如此。而负向ARC仅在以下三种情况中出现：使用茎群年龄时、分类等级的包容性较低时，以及类群间分化速率存在差异时——这一规律在生态依赖与时间依赖的分化过程中均成立。综上，我们的研究结果警示研究者不应直接解读单一的ARC估算结果，并呼吁在分化研究中更整合地结合不同年龄类型与分类等级的ARC数据开展分析。