Figure 4.

Examples of intra-host population dynamics, and the phylogenetic relationship between different individuals. For individual subjects, the tree is restricted to represent up to 25 most common haplotypes per time point (see text), whereas the joint env tree uses up to 10 most common haplotypes. Branch coloring and thickness conventions are the same in Fig. 2, except that black crosses mark the most recent common ancestors for CSF-only clades. For an alternative rendering of the trees as cladograms, refer to Supplementary materials.