Pattern and Temporal Dynamics of Protein Sequence Evolution in Envelope

<p>V1V2 amino acid sequence for SI, SM1, and RM1 at days 10 and 578. The consensus of all sequences is indicated at the top with amino acid positions labeled above. Glycosylation consensus motifs (NXT/S) are highlighted in yellow.</p

Phylogenetic Tree of V1V2 Variants

<p>An NJ tree of all day 14 and SI V1V2 variants, constructed using a GTR model of evolution. Bootstrap support values greater than 50% are shown in italics at nodes and the number of multiple clones from the same animal at the ends of branches is indicated beside the symbol.</p

Phylogenetic Analysis of SIVsmm <i>gag</i> Variants in Natural and Nonnatural Hosts

<p>An NJ unrooted phylogenetic tree of all day-10 <i>gag</i> variants was constructed in PAUP* [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.0010003#ppat-0010003-b43" target="_blank">43</a>] using the GTR model with a gamma rate distribution of shape α = 1.0. The SI variants are represented by triangles and identified by the legend. Bootstrap values greater than 50% are shown at nodes, and the number of multiple clones from the same animal at the ends of branches is indicated within the symbol.</p

Temporal Changes in Nucleotide Sequence Evolution in SMs and RMs

<p>Mean pairwise nucleotide diversity of the V1V2 sequences for each animal at each time point, calculated using the Tamura-Nei model of nucleotide substitution in MEGA 2.1 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.0010003#ppat-0010003-b52" target="_blank">52</a>]. The diversity of the SI is indicated on the y-axis. Trend lines are drawn for RMs (red) and SMs (blue).</p

Evidence for Greater Positive Selection in SIV <i>env</i> at Later Times Postinfection

<div><p>(A–E) Calculations for dN and dS were performed along the 124 amino acids of the V1V2 region using SNAP (<a href="http://hiv-web.lanl.gov/" target="_blank">http://hiv-web.lanl.gov/</a>). The average dN and dS at each codon is shown for SMs at day 14 (A) and day 578 (B), as well as for RMs at day 14 (C) and day 578 (D), and for the SI (E). Yellow boxes indicate predicted N-gly sites, and asterisks indicate N-gly sites not present at early time points in RMs.</p><p>(F) Cumulative dN and dS are shown across all sites for each animal at day 14 and day 578. Raw values of cumulative dN and cumulative dS are indicated below the graph.</p></div

Reemergence of Donor-Related Variants in Late Infection of Nonnatural Hosts

<p>ML tree of sequences from the SI and RM1 at days 10 and 100. Bootstrap values greater than 50% are shown at nodes. The SI variants are identified by the legend.</p