Figure 3

Phylogenetic trees of the reconstructed HIV-1 genes extracted from genome haplotypes. The phylogenetic trees generated from the nucleotide sequences of the (A) nef, (B) vif, (C) env, (D) pol, and (E) gag genes, that are targeted by one or more CTLs [11] exhibit a strong to intermediate signal for temporal selection. The vpu (F), rev (G), tat (H), and vpr (I) genes exhibit weak or no signal for temporal selection in their phylogenetic trees. The maximum likelihood (ML) phylogenetic trees were reconstructed with PHYML using the GTR nucleotide substitution model, gamma distributed rate variation across sites and 6 substitution rate categories (see Methods for details). 100 bootstrap replicates were performed and support values of > = 90 are shown on the corresponding branch. Colors denote different temporal haplotypes: day 0 (grey), day 3 (red), day 59 (blue), day 165 (green), day 476 (purple) and day 1543 (teal). The dominant haplotype for each sample is highlighted by a colored box.