A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

We also stress that we focused on protein domain structure and not on protein sequence. We therefore avoided the time-erasing effect of mutations and the confounding convergent effects of historical patchworks present in multidomain protein sequences, which represent a substantial fraction of every proteome that has been sequenced (16) . A global analysis involving both viral and cellular proteomes is perhaps only possible by focusing on domain structure and molecular functioncharacters that are relatively more conserved in evolution than gene sequence (16) . Thus, our analysis provides an evolutionarily deep "structural" view that, as expected, is not always in line with the shallow "sequence" view of viral evolution. This fact should be taken into consideration when interpreting our results.