Evolution of Viral Proteins Originated De Novo by Overprinting

Sabath, Niv; Wagner, Andreas; Karlin, David

To understand the evolutionary dynamics of de novo genes, one needs to estimate their age of origin and to compare this age among different clades. This estimation is made difficult by differences in mutation rate, population dynamics, and selection pressures among different viral genomes and genes (Duffy et al. 2008) . To alleviate these difficulties, we calibrated our estimates with a reference molecule, the RdRP protein domain, which is common to all clades in the study (Bruenn 2003) . The RdRP domain has a common origin and similar tertiary structure in the clades we study (Bruenn 2003) , and thus we assume that as a first approximation it is subject to similar functional and structural constraints. In each genome listed in table 1, we identified the RdRP domain by using HHpred (Soding et al. 2005) against the PFAM database (Finn et al. 2008) with an E-value cutoff of 10 À10 . We identified the orthologous RdRP domains within the other genomes of each clade using PSI-BLAST, aligned them, and constructed their phylogenetic trees. Supplementary figure S6, Supplementary Material online, presents these "RdRP trees."