Fig 4.

Phylogenetic analyses of partial env (gp41) (263 bp [A] and 195 bp [B]) nucleotide sequences of SIVgor strains. The trees were inferred by maximum likelihood phylogeny (PhyML) with previously characterized SIVcpzPtt/SIVgor/HIV-1 strains (in black). Stars represent support values above 800 (A) or 700 (B) for 1,000 maximum likelihood bootstraps. Bar, 0.1 substitution per site. Sample numbers and collection dates (i.e., 11-CP6466 is sample CP6466, collected in 2011), individual identification numbers (IDs), clusters (i.e., 20, 61, and 64 [in gray]), and social groups (A, C, G, E, and F1/2/3 [in color]) are noted and are used in Table 1. The color code for social groups is conserved in Fig. 2 to 4 and in Fig. S1 in the supplemental material. Solid brackets highlight individuals from the same group/cluster that were infected with closely related strains (very short genetic distance), whereas dashed links indicate individuals from the same group/cluster that were infected with divergent strains.