FIG 3.

Population dynamic analysis of blood and genital tract virus populations derived from macaques H1 and H2. (A) Maximum likelihood phylogenetic tree generated from all macaque sequences (blood, semen, and male genital organs) together with viral stock demonstrating the absence of cross-contamination (H1, red; H2, dark blue; M1, green; M2, light blue; M3, orange; viral stock, black). (B) GMRF skyride plots generated from all sequences of macaques H1 (top) and H2 (bottom). (C and D) Bayesian maximum clade credibility tree generated from all sequences of macaques H1 (C) and H2 (D).