Detecting hidden diversification shifts in models of trait-dependent speciation and extinction
Detecting hidden diversification shifts in models of trait-dependent speciation and extinction
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DOI：
10.1101/016386
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发表时间：
2015-03
期刊：
影响因子：
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通讯作者：
Jeremy M Beaulieu;B. O’Meara
中科院分区：
文献类型：
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作者：
Jeremy M Beaulieu;B. O’Meara
多样性的分布在不同的进化枝上有很大的不同。了解这些模式的尝试通常采用依赖状态的物种形成和灭绝模型来确定特定新特征的进化是否增加了物种形成率和/或降低了物种灭绝率。然而，目前尚不清楚这些模型是否揭示了多样化的重要驱动因素，或者它们是否只是指向了涉及许多未测量和共分布因素的更复杂的模式。在这里，我们描述了对流行的状态依赖物种形成和灭绝模型的扩展，该模型特别考虑了可能影响任何观察到的性状状态估计的多样化率的未测量因素的存在，解决了至少一个对BiSSE方法的主要批评。具体来说，我们的模型，我们称之为HiSSE（隐藏状态物种形成和灭绝），假设与模型中的每个观察状态相关的是“隐藏”状态，这些状态表现出潜在的不同多样化动态和过渡率，而不是孤立的观察状态。我们还演示了如何将我们的模型用作字符独立多样化（CID）模型，该模型允许独立于字符进化的复杂多样化过程。在严格的模拟测试和应用于经验数据时，我们发现HiSSE表现相当好，至少可以检测到观察状态和隐藏状态之间的净多样化率差异，以及多样化率差异与观察状态不相关的情况。我们讨论了与状态依赖的物种形成和灭绝模型的剩余问题，以及HiSSE提供对性状依赖多样化更细致理解的重要方式。
The distribution of diversity can vary considerably from clade to clade. Attempts to understand these patterns often employ state-dependent speciation and extinction models to determine whether the evolution of a particular novel trait has increased speciation rates and/or decreased their extinction rates. It is still unclear, however, whether these models are uncovering important drivers of diversification, or whether they are simply pointing to more complex patterns involving many unmeasured and co-distributed factors. Here we describe an extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait, addressing at least one major criticism of BiSSE methods. Specifically, our model, which we refer to as HiSSE (Hidden-State Speciation and Extinction), assumes that related to each observed state in the model are “hidden” states that exhibit potentially distinct diversification dynamics and transition rates than the observed states in isolation. We also demonstrate how our model can be used as character-independent diversification (CID) models that allow for a complex diversification process that is independent of the evolution of a character. Under rigorous simulation tests and when applied to empirical data, we find that HiSSE performs reasonably well, and can at least detect net diversification rate differences between observed and hidden states and detect when diversification rate differences do not correlate with the observed states. We discuss the remaining issues with state-dependent speciation and extinction models in general, and the important ways in which HiSSE provides a more nuanced understanding of trait-dependent diversification.