Fig. S3.

First principle time trends of reconstruction of paraphyletic relationships of donor and recipient populations. In these examples subject A infected subject B, with a single phylogenetic lineage (A) or with multiple phylogenetic lineages (B). In each case the phylogeny grows from left to right (trees s1…4 and m1…5) by some amount of time (Δt), all while branches grow, divide, or die. Labels indicate in which subject the tip was sampled (letters) and an arbitrary clone identifier (numbers). Note that these examples are not exhaustive, but rather show the principle phylogenies that can occur.