Figure 5. Measures of selective pressure on blood and gut nef quasispecies.

A.) The global non-synonymous to synonymous substitution rate ratio (dN/dS) with 95% confidence intervals (CI) was calculated for all 234 sequences in the dataset, all gut-derived sequences, all plasma-derived sequences, and for all individual pairs of gut and plasma sequences. The range of the 95% CI for the dN/dS estimate for all sequences is highlighted in grey so that those estimates with a 95% CI entirely outside this range (542 gut, 648 gut and plasma, 650 gut) can be easily identified. B.) The diversity among all sequences from plasma and gut as well as among blood and gut isolates from each subject was calculated with a s.e.m. from 500 bootstrap replicates. The difference in diversity between plasma and gut sequences was evaluated with a two-tailed t test and pairs with significant differences are marked with a bar with the p-value indicated above it.