An Extended Clade Framework for Annotated Trees in the Context of Phylogeography and Transmission Tree Inference

Bayesian phylogenetic inference produces large samples from a posterior distribution over phylogenetic trees that represents uncertainty in both tree topology and associated variables. Such a collection of trees is hard to interpret and it is common practice to summarize such samples into a single representative tree. Methods for constructing representative trees have largely been restricted to plain tree topologies, encoding only relationships among taxa. Inference with more sophisticated models produce annotated tree objects. These have additional information representing nodes locations in the case of phylogeography, host information when inferring transmission trees, or sampled ancestor status when incorporating fossil information. Nevertheless, these annotated representations are reduced to a single representative tree, typically using methods developed for plain tree topologies and without accounting for the resulting methodological mismatch. Here, we introduce the concept of an extended clade and investigate an extension of the conditional clade distribution (CCD) model. Through motivating examples and case studies in discrete trait phylogeography and transmission tree reconstruction, we demonstrate limitations of standard summary tree approaches and show how these can be addressed using an extended CCD framework that explicitly incorporates the annotated tree structure.