Evolution of Viral Proteins Originated De Novo by Overprinting

Sabath, Niv; Wagner, Andreas; Karlin, David

Selective Constraint Figure 3b presents the selective constraint (dN/dS) for the ancestral and de novo genes in each group of viruses we studied. The ancestral and de novo genes are subject to very different constraints, as attested by the significant difference (P < 4.9 Â 10 À13 ) between the slopes of their respective regression lines, and the fact that the ancestral regression line has a positive slope, whereas the de novo regression line has FIG. 3 . Evolutionary dynamics of ancestral (red) and de novo genes (blue). The vertical axes show (a) relative divergence and (b) selective constraint (dN/dS) for the 12 taxa. The horizontal axis represents the evolutionary distance from the origin of each de novo gene (i.e., the estimated age of genes within the clade). Regression lines are plotted for visualization of general trends. Low dN/dS values represent strong selective constraints (see text). Note that dN/dS in (b) could only be calculated for gene pairs that have less than 50% amino acid divergence at the amino acid level (see Materials and Methods) . No selective constraint data could be calculated for cases 6 and 8 (bottom panel) as the sequence pairs in these clades have all diverged beyond 50%. Where neighboring groups had similar ages, we shifted their position slightly for visual clarity (groups 5 and 6). a negative slope. The low values of dN/dS < 1 below for most genes indicate that they are under strong selective constraints (purifying selection), i.e., mutations that change the protein sequence are likely to be selected against. In several viruses, the values of dN/dS for the ancestral genes are particularly low, suggesting an extreme functional or structural constraint. For example, the ratio dN/dS of the ancestral gene in viruses 1, 4, and 5 is below 0.05. In contrast, in some cases, either the de novo gene (the influenzavirus A PB1-F2, the betacoronavirus protein I, and the tymovirus movement protein, respectively, from groups 1, 3, and 5) or the ancestral gene (the ilavirus polymerase and the betanodavirus protein A, from groups 7 and 12, respectively) exhibits dN/dS ! 1, which indicates neutral evolution or positive selection. As explained at the beginning of the Results section, the test we employ cannot distinguish between them. For all groups, the trends in relative divergence ( fig. 3a ) and selective constraints ( fig. 3b ) were consistent with one another. For example, the de novo proteins of cardioviruses are more highly diverged than the ancestral proteins and they also show a lower selective constraint.