A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

The seven-set Venn diagram is analogous to a maze or logic puzzle that can be solved using Ariadne's thread logic (Fig. 4B) . Metaphorically, threads keep track of evolutionary paths while traversing a maze sculpted by reductive loss. We define our Ariadne's threads as Venn subgroups of FSFs shared by two to six of the seven viral replicon types (there were no FSFs shared by all seven viral groups). These threads revealed that only 19 of the 120 possible Venn subgroups of shared FSFs existed (total Venn − internal groups: 2 7 − 1 = 127), where 14 were shared by two to three viral groups. They make explicit how sparsely shared FSFs are in viral groups and uncover deep evolutionary patterns likely left by reductive evolution. Only 8 of 21 and only 6 of 35 possible subgroups shared by two and three viral groups, respectively, were pres- Fig. 4B ), all including RNA viruses. As mentioned previously, these five groups represent polymerases, metabolic enzymes, ribonuclease, and capsid-associated FSFs. Because RNA viruses define most threads and their proteomes are the most reduced, they are most informative in explaining FSF distribution in the viral supergroup. This leads to the speculation that perhaps RNA viruses predated DNA viruses in evolution, which we confirm with phylogenetic methods below. Finally, a large number of FSFs were shared between DNA and RNA viruses (Fig. 4C) , suggesting that the virosphere may not be as disjoint as previously thought. In fact, recombination between RNA and DNA viruses can sometimes generate "hybrid" viruses with DNA genomes but capsids typical of RNA viruses [for example, (55) ].