Phylogenetic uncertainty and transmission network inference: Lessons from phylogenetic reconciliation

The inference of transmission networks from genetic sequence data is an important problem in epidemiology. One approach for building transmission networks is to first reconstruct a phylogenetic tree on the sampled sequences and to then infer transmissions based on this tree. This approach depends crucially on the accuracy of the reconstructed phylogeny and of the transmission inference procedure. However, there is often considerable uncertainty and error in reconstructed phylogenies and significant ambiguity in transmission inference. In this talk, we will introduce a new phylogenetic approach to inferring transmission networks, discuss some of the challenges to the successful implementation of such an approach, and consider some ideas for overcoming these challenges inspired by the literature on phylogenetic reconciliation.