Evolution of Viral Proteins Originated De Novo by Overprinting

Sabath, Niv; Wagner, Andreas; Karlin, David

We asked how these properties depend on the time since a de novo gene originated. To this end, we estimated this time by using the sequence divergence of the RNA-dependent RNA polymerase domain of each genome (see Materials and Methods). We then plotted the three properties against this estimated age in figures 3 and 4. The horizontal axis of figures 3 and 4 corresponds to the origination time of de novo genes (labeled by viral genus), with the most recently originated de novo genes shown to the left. The vertical axis shows the relative divergence ( fig. 3a ), selective constraint ( fig. 3b ), and CSI ( fig. 4 ). Note that the relative divergence and the selective constraints are calculated for pairs of homologous genes, whereas the CSI is calculated for single genes (see Materials and Methods). Thus, dots in figure 3a and b correspond to values obtained for pairs, whereas dots in figure 4 correspond to values for single genes. Regression lines for ancestral genes (red) and de novo genes (blue) indicate general trends. We used analysis of covariance (ANCOVA) to test whether the slopes of the two regression lines in each panel were different.