FIG. 1.

Evolutionary relationships among primate lentivirus Nef sequences. Nef alleles newly analyzed in the present study are highlighted with yellow boxes, and those of vpu-containing viruses are underlined. Nef alleles that downmodulate CD3 are shown in green, those that are selectively defective in CD3 downmodulation in red, and those that are generally poorly functional in blue. The tree was midpoint routed and inferred by the Bayesian method (23) implemented in MrBayes v3.2.1 as described in Methods. Numbers on branches are percent estimated posterior probabilities. Only those 95% and above are shown.