A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

We discovered that viruses infecting species in each of the three superkingdoms shared a total of 68 FSFs (Fig. 3B , abe group). A closer inspection revealed that these FSFs performed crucial metabolic functions (table S5) and were widespread in cellular proteomes ( f > 0.75) (Fig. 3C ). These FSFs originated very early in evolution ( fig. S2 , abe group) and were detected in a large number of viruses from each replicon type (Fig. 3C ). In fact, 19 abe FSFs (28%) were shared by two or more viral subgroups. It is often argued that, because viruses infect all species, they must have originated before modern cells. Here, we show that viruses infecting the three superkingdoms have a very large and conserved structural core that is particularly enriched in crucial metabolic functions believed to be very ancient. This is a strong indication of both the ancient origin of viruses and their coexistence with ancient cells. An alternative explanation could be the transfer of these FSFs from modern cells to viruses through HGT. However, viruses do not infect hosts separated by large evolutionary distances [ Fig. 3A ; see also (44) ]. Still these FSFs were detected in seemingly unrelated viruses. Moreover, roughly similar patterns were also observed for the ab, ae, and be FSFs (Fig. 3C and table S5 ). This greatly reduces confidence in cell-to-virus HGT because the probability of a large number of similar HGT events occurring in very different environments (that is, different hosts and viruses) is very unlikely.