A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

A tree of viruses (ToV) reconstructed from abe core FSFs ( fig. S4 ) further confirmed an early origin in RNA viruses. Although the distribution patterns of replicon types were not entirely clear-cut, there was clear enrichment of RNA viral proteomes at the base of ToP, specifically minus-ssRNA and dsRNA viruses. This tree was poorly resolved partly as a result of the limited number of phylogenetic characters that were used to distinguish proteomes and largely as a result of the patchy distribution of abe FSFs in viral proteomes (a consequence of reductive evolution in viruses). Finally, grouping viruses by host type (that is, archaeoviruses, bacterioviruses, and eukaryoviruses) did not yield three independent groups, suggesting that viruses, regardless of host type, could be structurally (and evolutionarily) more related to each other ( fig. S5 ). It also suggests that viruses can jump hosts [for example, severe acute res-piratory syndrome (SARS) and Ebola viruses, loss of RNA viruses in prokaryotes (44) ], and thus, evolutionary relationships based on virus-host preferences should be considered with caution [sensu (43) ]. All characters were parsimony informative. Differently colored branches represent BS support values. Major groups are identified. Viral genera names are given inside parentheses. The viral order "Megavirales" is awaiting approval by the ICTV and hence written inside quotes. Viral families that form largely unified or monophyletic groups are labeled with an asterisk. Virion morphotypes were mapped to ToP and illustrated with images from the ViralZone Web resource (131) . No picture was available for Turriviridae. a Actinobacteria, Bacteroidetes/Chlorobi, Chloroflexi, Cyanobacteria, Fibrobacter, Firmicutes, Planctomycetes, and Thermotogae. (B) A distancebased phylogenomic network reconstructed from the occurrence of 442 ABEV FSFs in randomly sampled 368 proteomes (uncorrected P distance; equal angle; least-squares fit = 99.46). Numbers on branches indicate BS support values. Taxa were colored for easy visualization. Important groups are labeled. b Actinobacteria, Bacteroidetes/Chlorobi, Chloroflexi, Cyanobacteria, Deinococcus-Thermus, Fibrobacter, Firmicutes, and Planctomycetes. c Amoebozoa Chromalveolata.