Given the low levels of genetic diversity expected during the early stages of disease outbreaks, isolates with identical haplotypes but different collection dates and Figure 1 Illustration of possible reconstructions of genealogical relations. Panel a represents a hypothetical genealogy of six isolates from which three were sampled (highlighted by a blue glow and numbered from 1 to 3). Panels b and c illustrate phylogenetic reconstructions where the red dots represent inferred nodes; panel b corresponds to a classical phylogenetic reconstruction and c to a tree that accounts for heterochronous sampling (e.g., BEAST software; Drummond and Rambaut, 2007) . Panel d illustrates the direct ancestry reconstruction method implemented in SeqTrack.