Data from: Model inadequacy and mistaken inferences of trait-dependent speciation

Species richness varies widely across the tree of life, and there is great interest in identifying ecological, geographic, and other factors that affect rates of species proliferation. Recent methods for explicitly modeling the relationships among character states, speciation rates, and extinction rates on phylogenetic trees- BiSSE, QuaSSE, GeoSSE, and related models - have been widely used to test hypotheses about character state-dependent diversification rates. Here, we document the disconcerting ease with which neutral traits are inferred to have statistically significant associations with speciation rate. We first demonstrate this unfortunate effect for a known model assumption violation: shifts in speciation rate associated with a character not included in the model. We further show that for many empirical phylogenies, characters simulated in the absence of state-dependent diversification exhibit an even higher Type I error rate, indicating that the method is susceptible to additional, unknown model inadequacies. For traits that evolve slowly, the root cause appears to be a statistical framework that does not require replicated shifts in character state and diversification. However, spurious associations between character state and speciation rate arise even for traits that lack phylogenetic signal, suggesting that phylogenetic pseudoreplication alone cannot fully explain the problem. The surprising severity of this phenomenon suggests that many trait-diversification relationships reported in the literature may not be real. More generally, we highlight the need for diagnosing and understanding the consequences of model inadequacy in phylogenetic comparative methods.

生命之树（tree of life）各分支的物种丰富度（species richness）差异悬殊，学界始终致力于探明影响物种增殖速率的生态、地理及其他相关因素。近年来，针对系统发育树（phylogenetic tree）上的性状状态（character state）、物种形成速率（speciation rate）与灭绝速率（extinction rate）之间的关系开展显式建模的一系列方法——包括BiSSE、QuaSSE、GeoSSE及相关模型——已被广泛用于检验依赖性状状态的物种分化速率相关假说。
本研究揭示了一个令人不安的现象：中性性状（neutral trait）极易被推断出与物种形成速率存在统计学意义上的显著关联。我们首先通过已知的模型假设违背场景验证了这一不良效应：当未纳入模型的性状对应的物种形成速率发生偏移时，便会出现该虚假关联。进一步研究发现，针对众多经验系统发育树，在不存在状态依赖性分化的条件下模拟生成的性状，其一型错误率（Type I error rate）反而更高，这表明该方法易受其他未知的模型缺陷影响。
对于演化速率较慢的性状而言，其根源似乎在于现有统计框架未要求性状状态与物种分化发生重复偏移。但即便对于不具备系统发育信号（phylogenetic signal）的性状，性状状态与物种形成速率之间也会出现虚假关联，这表明仅用系统发育伪重复（phylogenetic pseudoreplication）无法完全解释这一问题。这一现象的惊人严重性表明，文献中报道的诸多性状-分化关联可能并非真实存在。
更广泛而言，本研究强调了在系统发育比较方法（phylogenetic comparative method）中，诊断并明确模型缺陷所带来的后果的必要性。