FIG 5.

The selection results are consistent with the hypothesis that PLVA is not adapted to the mountain lion and is therefore under strong pressure to evolve in this host. All nonrecombinant regions of PLVA and PLVB genomes were analyzed by branch-site REL without a priori designation of isolates as originating from a bobcat or a mountain lion. Diversifying selection was detected in 3 of 6 PLVA isolates from mountain lions, 0 of 20 bobcat PLVA isolates, and 1 of 33 PLVB isolates from mountain lions. The table at the top lists the isolates evolving under diversifying selection, the corresponding genomic regions under selection, and the proportion of sites (codons) diversifying in each region (L, leader; SU, surface; TM, transmembrane). P values shown were derived via ANOVA and corrected for multiple tests by using the Holm-Bonferroni method. The bottom panel depicts the locations of the PLVA regions identified as evolving under episodic diversifying selection. All segments under selection were at the 3′ end of the genome and included multiple loci within env and vif. Previously characterized recombination breakpoints are indicated by arrows. The full PLVA genome is outlined below for reference.