FIG 4.

Recombination and positive selection contribute to the molecular evolution of PLVA and PLVB. The locations of recombination breakpoints and residues under selection are depicted for PLVA and PLVB genomes (see Table SA3 in the supplemental material). PLV14 and PLV1695 were used as the reference genomes for PLVA and PLVB, respectively (11, 15). Each genome is annotated with the four viral open reading frames studied (gag, pol, vif, and env) (top) as well as the protease cleavage products for the polyproteins (bottom). The scale below each genome represents base pairs starting at base 1 in the 5′ long terminal repeat (LTR).