Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis
Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis
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DOI：
10.1080/10635150701883881
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发表时间：
2008-01-01
影响因子：
6.5
通讯作者：
Smith, Stephen A.
中科院分区：
文献类型：
--
作者：
Ree, Richard H.;Smith, Stephen A.
在历史生物地理学中，基于模型的推理方法用于重建系统发育树上地理范围的进化，相对于可用于推断特征进化的相似方法的多样性而言，发展较差。我们试图通过构建一个地理范围进化的扩散-灭绝-分支发生(DEC)模型来纠正这一缺陷，该模型指定了沿系统发育分支的离散状态(范围)之间的瞬时转移率，并将其应用于在分支发生事件中估计祖先状态(范围继承场景)的可能性。与这种方法的早期版本不同，本模型允许作为时间函数的射程转换概率的解析解，使得模型中的自由参数、扩散速率和局部灭绝能够通过最大似然法估计。模拟结果表明，在实际应用中可能很难获得准确的参数估计，但也表明，如果范围进化的速度相对于分支发生的速度较低，则祖先范围遗传场景仍然可以正确地恢复，并且成功率很高。我们将DEC模型应用于先前发表的涉及木兰科(茜草科)夏威夷特有被子植物的岛屿生物地理学的示范案例研究，展示了DEC模型如何通过检查范围进化的推断来迭代地改进，以及如何对似然函数施加涉及岛屿起源时间的地质约束。DEC模型与角色模型非常相似，它可以作为一个门户，通过它可以将许多现有的角色比较方法引入历史生物地理学领域；此外，它还可能启发角色模型的概念扩展，将进化变化作为原因或结果与分支发生事件直接重合。因此，DEC模型是一个渐进的进步，突显了基于模型的历史生物地理推断这一新兴领域的巨大潜力。
In historical biogeography, model-based inference methods for reconstructing the evolution of geographic ranges on phylogenetic trees are poorly developed relative to the diversity of analogous methods available for inferring character evolution. We attempt to rectify this deficiency by constructing a dispersal-extinction-cladogenesis (DEC) model for geographic range evolution that specifies instantaneous transition rates between discrete states (ranges) along phylogenetic branches and apply it to estimating likelihoods of ancestral states (range inheritance scenarios) at cladogenesis events. Unlike an earlier version of this approach, the present model allows for an analytical solution to probabilities of range transitions as a function of time, enabling free parameters in the model, rates of dispersal, and local extinction to be estimated by maximum likelihood. Simulation results indicate that accurate parameter estimates may be difficult to obtain in practice but also show that ancestral range inheritance scenarios nevertheless can be correctly recovered with high success if rates of range evolution are low relative to the rate of cladogenesis. We apply the DEC model to a previously published, exemplary case study of island biogeography involving Hawaiian endemic angiosperms in Psychotria (Rubiaceae), showing how the DEC model can be iteratively refined from inspecting inferences of range evolution and also how geological constraints involving times of island origin may be imposed on the likelihood function. The DEC model is sufficiently similar to character models that it might serve as a gateway through which many existing comparative methods for characters could be imported into the realm of historical biogeography; moreover, it might also inspire the conceptual expansion of character models toward inclusion of evolutionary change as directly coincident, either as cause or consequence, with cladogenesis events. The DEC model is thus an incremental advance that highlights considerable potential in the nascent field of model-based historical biogeographic inference.