Matthew Hall

Methods for the reconstruction of time-calibrated phylogenies can be extended to simultaneously reconstruct epidemic transmission trees under quite complex epidemic models if each internal node is annotated with a host in the epidemic. Such assignments cannot, however, be made freely if the characteristics of a plausible epidemic are to be retained. In this talk, I will describe the rules for node augmentation for three categories of transmission model. The most simple are those which assume no within-host diversity and thus that lineages split only at transmission. I then move on to those which allow for within-host genetic diversity under the assumption of a complete transmission bottleneck. Finally, I outline how methods for species tree reconstruction can be adapted to relax the bottleneck assumption, which also enables transmission tree reconstruction in a multilocus phylogenetic framework. I describe how a Markov Chain Monte Carlo procedure for phylogenetic reconstruction can be adapted to sample from the space of trees whose nodes are augmented according to these rules, giving a posterior sample of both phylogenies and transmission trees. These approaches are implemented in the BEAST 2 package BEASTLIER, which is now publicly available.