Combined transmission and phylogenetic tree for the first simulation study. The tips of the tree are samples taken from infected hosts. The tree topology provides the dated phylogenetic tree, including the date of the most recent common ancestor for any set of samples. The transmission tree is added to the phylogenetic tree through coloring. Asterisks show transmission events, separating different hosts. With a relaxed bottleneck, multiple synchronous asterisks may represent a single transmission event involving multiple lineages. Hosts are colored according to their deme. Some hosts are unsampled, contributing no tips to the phylogenetic tree. The tree contains 302 infected hosts, of which 250 are sampled.