Fig 1. Examples of transmission complexities.

Reconstruction of transmission can be hindered by several complexities causing disagreement between the actual transmission history and the phylogeny of the sampled pathogen. Here we show four examples of these complexities: A) Within-host evolution (similar to incomplete lineage sorting, can happen even with strong transmission bottlenecks), B) Incomplete transmission bottlenecks (or large transmission inocula) and within-host evolution, C) Non-sampled hosts (such as unknown or asymptomatic hosts), D) Multiple infections of the same host (or mixed infections). Different hosts (named H1, H2, and H3) are represented as black rectangles, and the rectangle with a dashed border represents a non-sampled host (a host for which no pathogen sample has been collected and sequenced, and for which there is no exposure time information). The top and bottom edge of each rectangle indicate the introduction and removal times, that is, the beginning and the end of the time interval within which a host is either infective or can be infected (e.g., arrival and departure time from the contaminated ward). Red dots represent pathogen sequence samples (respectively S1, S2, and S3), and red lines are lineages of the pathogen phylogeny. Blue tubes represent transmission/bottleneck events, where the contained lineages are transferred between hosts. Below each “nested” tree plot (representing phylogeny and transmission tree simultaneously, see Fig A in S1 Text), the corresponding transmission history is represented with black “beanbags”, and, in red, the phylogenetic tree of the sequences.