Evolution of Viral Proteins Originated De Novo by Overprinting

Sabath, Niv; Wagner, Andreas; Karlin, David

A prerequisite to identify a de novo gene is that it must have a monophyletic distribution in one clade-the "focal" clade ( fig. 1a , taxa T1, T2, and T3)-while being absent from organisms outside this clade ( fig. 1a , taxa T4 and T5). We note that this prerequisite is necessary but not sufficient. Genes fulfilling it may have an ancient origin, older than the focal clade, but they might have diverged beyond recognition outside this clade (Elhaik et al. 2006 ). Alternatively, they may have entered the focal clade through horizontal gene transfer. These confounding factors can be easily excluded for genes that arose by overprinting ( fig. 1b , blue arrows) within a pre-existing "ancestral" reading frame (red arrows). Specifically, if the ancestral gene is present outside the focal clade (e.g., taxa T4 and T5 in fig. 1b ), one can exclude divergence beyond recognition and horizontal gene transfer, because in either case, the ancestral gene would not be present outside the focal clade.