Evolution of Viral Proteins Originated De Novo by Overprinting

Sabath, Niv; Wagner, Andreas; Karlin, David

We defined the focal clade of the RdRP tree as the smallest clade that contains all the taxa found within the focal clade of the phylogenetic tree of the overlapping genes. The LCA for the RdRP tree was defined as earlier. We compared the focal clades in the RdRP tree and the tree of overlapping genes and found that in 9 of 12 cases the focal clades were identical, whereas in three cases (2, 5, and 12, within the genera Cardiovirus, Tymovirus, and Betanodavirus, respectively), we found minor differences (supplementary fig. S6 , Supplementary Material online). Overall, this comparison suggested that the RdRP genes and the overlapping gene pairs have similar evolutionary histories. On the basis of the RdRP tree, we thus estimated as a proxy for the age of a de novo gene the sequence divergence of the RdRP domain in each focal clade since the origin of the de novo gene, i.e., its accumulated genetic distance D along the tree branches since the LCA. To estimate D, we generated 100 bootstrap RdRP trees. For each tree i (1 i 100), we calculated D i , the average length of the phylogenetic tree branches between the LCA and each extant genome that contains the de novo gene. For the example in figure 1b, D i would calculate as [d(LCA, T1) + d(LCA, T2) + d(LCA, T3)]/3, where d(LCA, T1) = b1 + b2, d(LCA, T2) = b3 + b2, and d(LCA, T3) = b4, and b1, b2, b3, and b4 are the branch lengths shown in the figure. Finally, we estimate D as the average over all the bootstrap trees, D ¼ ð1=100Þ P 100 i¼1 D i . We estimated all branch lengths by the BIONG method (Gascuel 1997) . In supplementary figure S7, Supplementary Material online, we present D and the standard deviation within each group. For convenience, we ordered the clades in table 1 according to increasing D.