Figure 3.

Maximum likelihood reconstruction of the MP2-MP3 joint HIV-1 env phylogeny. MP1 (yellow) did not infect either MP2 or MP3 (Figure S1), and is used to root the MP2 (red) and MP3 (blue) HIV-1 tree. Clades with aLTR support (>0.90) are indicated with a “s.” The topology of this tree suggested that at least seven lineages were transmitted between MP2 and MP3. Because the branch lengths were zero or near zero in the bottom clade, we added a small distance for readability purpose to show the four possible transmitted lineages that the topology suggested in this clade. Partially to avoid depending on this single (best) tree, we evaluated a large collection of posterior trees in the main analyses of this case.