FIG. 7.
Representative phylogenetic reconstructions for subjects (Subj) 8 (A), 7 (B), and 1 (C). Colors of tip symbols indicate the years after seroconversion each sample was obtained. Colors of nodes and branches reflect PSSM scores of the reconstructed ancestors or the sample (tip) V3 sequences; cooler colors represent lower values and warmer colors represent higher values, as indicated by the scale. Various extreme scores among subjects were seen, so the color scales differ among the trees. For each tree, however, light green represents a value of −5, approximately intermediate between the R5 and X4 cutoff values. Branches are colored according to the score of the sequence of the branch's right-hand node. For subject 8 (A), filled triangle symbols on the tree represent sequences obtained from biological clones derived from the given time point. Phenotypes of these clones are indicated by the callouts. Scale bars indicate genetic distances along branches.