A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

(iv) Evidence from distance-based networks. Typically, viral proteomes encode far less proteins and in lower abundance relative to the proteomes of cellular organisms (except for some giant viruses). To account for such differences and to test whether the phylogeny in Fig. 7A was not influenced either by HGT or by technical artifacts associated with our choice of phylogenetic model, we used FSF occurrence in distance-based networks reconstruction (Fig. 7B) . The resulting topology still favored a "tree-like" structure ( Fig. 7B) , suggesting that the phylogeny of Fig. 7A was not influenced by processes that could artificially increase genomic abundance. Moreover, none of the viral proteomes clustered with their hosts (for example, plant RNA viruses did not group with plants), indicating that the predicted cellular nature of viruses was not attributable to HGT from their hosts but was likely a result of ancient coexistence. The phylogenomic network retained most evolutionary relationships defined earlier by ToP but also recovered a closer grouping of herpesviruses with Podoviridae (Caudovirales) that was not so clear in ToP derived from genomic abundance, supporting the proposal that the two viral groups are closely related (47, 72) .