Current state-of-the-art genetic methods for the reconstruction of pathogen genealogies rely on the phylogenetic paradigm (Grenfell et al., 2004; Templeton, 1998; Drummond and Rambaut, 2007; Cottam et al., 2008a; Lemey et al., 2009a) based on the reconstruction of ancestries between hypothetical common ancestors (most recent common ancestor) and sampled isolates. Unfortunately, such approaches may be inappropriate when ancestors and their descendents are both present in the sample analyzed, as is likely during the early stages of an outbreak. Phylogenetic methods consider that sampled strains are all tips of an unknown genealogy, making it impossible for a sampled strain to be (directly or indirectly) ancestral to another sampled strain. By definition, these methods are thus unable to uncover ancestries between sampled isolates, and can fail to reconstruct the transmission tree of an emerging pathogen (Figures 1a-c) .