To model distribution ranges, the most popular methods of phylogenetic biogeography divide Earth into a handful of predefined areas. Other methods use explicit geographic ranges, but unfortunately, these methods assume a static Earth, ignoring the effects of plate tectonics and the changes in the landscape. To address this limitation, I propose a method that uses explicit geographic ranges and incorporates a plate motion model and a paleolandscape model directly derived from the models used by geologists in their tectonic and paleogeographic reconstructions. The underlying geographic model is a high-resolution pixelation of a spherical Earth. Biogeographic inference is based on diffusion, approximates the effects of the landscape, uses a time-stratified model to take into account the geographic changes, and directly integrates over all probable histories. By using a simplified stochastic mapping algorithm, it is possible to infer the ancestral locations as well as the distance traveled by the ancestral lineages. For illustration, I applied the method to an empirical phylogeny of the Sapindaceae plants. This example shows that methods based on explicit geographic data, coupled with high-resolution paleogeographic models, can provide detailed reconstructions of the ancestral areas but also include inferences about the probable dispersal paths and diffusion speed across the taxon history. The method is implemented in the program PhyGeo.

中文翻译：

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使用动态古地理模型和显式地理范围的系统发育生物地理学推理


为了对分布范围进行建模，最流行的系统发育生物地理学方法将地球划分为几个预定义的区域。其他方法使用明确的地理范围，但不幸的是，这些方法假设地球是静止的，而忽略了板块构造的影响和景观的变化。为了解决这一限制，我提出了一种方法，该方法使用明确的地理范围，并结合了板块运动模型和古景观模型，该模型直接源自地质学家在构造和古地理重建中使用的模型。基础地理模型是球形地球的高分辨率像素化。生物地理学推理基于扩散，近似景观的影响，使用时间分层模型来考虑地理变化，并直接整合所有可能的历史。通过使用简化的随机映射算法，可以推断祖先的位置以及祖先谱系行进的距离。为了说明，我将该方法应用于无患子科植物的经验系统发育。此示例表明，基于显式地理数据的方法与高分辨率古地理模型相结合，可以提供祖先区域的详细重建，但也包括有关整个分类群历史中可能的扩散路径和扩散速度的推断。该方法在 PhyGeo 程序中实现。