Data from: Investigating the timing of origin and evolutionary processes shaping regional species diversity: insights from simulated data and Neotropical butterfly diversification rates

Different diversification scenarios have been proposed to explain the origin of extant biodiversity. However, most existing meta-analyses of time-calibrated phylogenies rely on approaches that do not quantitatively test alternative diversification processes. Here, I highlight the shortcomings of using species divergence ranks, which is a method widely used in meta-analyses. Divergence ranks consist of categorizing cladogenetic events to certain periods of time, typically to either Pleistocene or to pre-Pleistocene ages. This approach has been claimed to shed light on the origin of most extant species and the timing and dynamics of diversification in any biogeographical region. However, interpretations drawn from such method often confound two fundamental questions in macroevolutionary studies, tempo (timing of evolutionary rate shifts) and mode (“how” and “why” of speciation). By using simulated phylogenies under four diversification scenarios, constant-rate, diversity-dependence, high extinction, and high speciation rates in the Pleistocene, I showed that interpretations based on species divergence ranks might have been seriously misleading. Future meta-analyses of dated phylogenies need to be aware of the impacts of incomplete taxonomic sampling, tree topology, and divergence time uncertainties, as well as they might be benefited by including quantitative tests of alternative diversification models that acknowledge extinction and diversity dependence.已有多种多样化情景被提出，用以解释现存生物多样性的起源。然而，当前绝大多数针对时间校准系统发育树（time-calibrated phylogenies）的元分析（meta-analyses），所采用的分析方法均无法对不同的多样化过程开展定量检验。本文着重指出了元分析中广泛使用的物种分化等级法（species divergence ranks）的缺陷。该方法将分支演化事件（cladogenetic events）归类至特定地质时段，通常分为更新世（Pleistocene）与更新世前两个时期，曾被认为能够阐明绝大多数现存物种的起源，以及任意生物地理区域内多样化的时间进程与动态模式。然而，基于该方法得出的解读往往混淆了宏观演化研究（macroevolutionary studies）中的两个核心问题：即速率（演化速率转变的时间节点）与模式（物种形成的方式与动因）。本文通过在四种多样化情景下生成模拟系统发育树——涵盖恒定速率、多样性依赖、高灭绝速率以及更新世时期高物种形成速率四类情景——证明，基于物种分化等级法得出的解读可能存在严重误导性。未来针对定年系统发育树（dated phylogenies）的元分析，需要充分考量不完整分类采样、树拓扑结构以及分化时间不确定性所带来的影响；同时，纳入考虑灭绝与多样性依赖的不同多样化模型的定量检验方法，或将为相关研究提供助力。