Data from: Historical biogeography using species geographical ranges

Spatial variation in biodiversity is the result of complex interactions between evolutionary history and ecological factors. Methods in historical biogeography combine phylogenetic information with current species locations to infer the evolutionary history of a clade through space and time. A major limitation of most methods for historical biogeographic inference is the requirement of single locations for terminal lineages, reducing contemporary species geographical ranges to a point in two-dimensional space. In reality, geographic ranges usually show complex geographic patterns, irregular shapes, or discontinuities. In this paper, we describe a method for phylogeographic analysis using polygonal species geographic ranges of arbitrary complexity. By integrating the geographic diversification process across species ranges, we provide a method to infer the geographic location of ancestors in a Bayesian framework. By modeling migration conditioned on a phylogenetic tree, this approach permits reconstructing the geographic location of ancestors through time. We apply this new method to the diversification of two neotropical bird genera, Trumpeters (Psophia) and Cinclodes ovenbirds. We demonstrate the usefulness of our method (called rase) in phylogeographic reconstruction of species ancestral locations and contrast our results with previous methods that compel researchers to reduce the distribution of species to one point in space. We discuss model extensions to enable a more general, spatially explicit framework for historical biogeographic analysis.

生物多样性的空间变异是演化历史与生态因子间复杂相互作用的产物。历史生物地理学（historical biogeography）方法将系统发育信息与当前物种分布位点相结合，用以推断某一演化支（clade）在时空维度上的演化历史。当前多数历史生物地理学推断方法存在核心局限：要求终端谱系仅对应单个分布位点，将现生物种的地理分布范围简化为二维空间中的单点。但现实中，物种的地理分布往往呈现复杂的空间格局、不规则形态或间断分布的特征。

本文提出一种基于任意复杂度多边形物种地理分布范围的系统地理学（phylogeography）分析方法。通过整合物种分布范围内的地理分化过程，我们构建了一套可在贝叶斯框架（Bayesian framework）下推断祖先地理位点的分析方法。该方法以系统发育树为条件构建迁移模型，能够逐时间维度重建祖先的地理分布位点。

我们将该新方法应用于两个新热带鸟类类群的演化分化研究：喇叭鸟（Trumpeters，学名*Psophia*）与Cinclodes灶鸟（*Cinclodes* ovenbirds）。我们验证了该方法（命名为rase）在物种祖先分布位点系统地理学重建中的有效性，并将其结果与此前要求研究者将物种分布简化为空间单点的传统方法进行了对比。最后我们讨论了该模型的扩展方向，以期为历史生物地理学分析构建更为通用的空间显式框架。