Evolutionary conservation at disome sites. (A) Association of highly conserved codons with the P- and A-sites of disome sites revealed by position-specific enrichment analysis. Along coding regions, phyloP conservation scores were grouped into categories: neutral - blue, [−3, 3), conserved - orange, [3, 5), and highly conserved [5,). Normalized ratios of observed-to-expected occurrences (y-axis, log-scaled) of conservation categories were plotted relative to the estimated A-site (0 at x-axis) of the leading ribosome (disomes, left), or of the individual ribosome (monosomes, middle). See Figure 3A for other elements. (B) Box-and-whiskers illustrating the estimated percentages of ribosomes that were in disomes for groups of transcripts with different overall evolutionary conservation. Groups included all detectable genes (all, gray, N = 7375), which were stratified into four groups (N = 2270 or 2271 for each; color code at the top) based on the quartiles of average phyloP scores with the following right-closed boundaries: −0.585, 2.327, 3.356, 4.239, 6.437. x-axis and other features are as in Figure 2P. (C) Odds ratio estimates of dipeptides and disome sites for increased phyloP scores. Odds ratios (OR) for having a high phyloP score at P-A dicodons were estimated for dipeptides encoded by the dicodon (orange dots, 399 levels relative to dipeptide VH, which had moderate phyloP scores in both models) and presence of a disome peak (green dots, A-position disome density > mean transcript density) using a logistic regression model. Confidence levels of estimates were represented by transparency levels that corresponded to deciles of the logarithm of absolute values of their z-scores (legend). Two separate regression models were fitted using phyloP scores from the 60-way vertebrate data set (left) and the Euarchontoglire subset (right). For disomes, OR is larger than 1 (dashed line) indicating that it is more likely to observe a high phyloP score when disome peaks are present than when they are absent.