A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

(iii) Evidence from trees of proteomes (ToP). To describe the evolutionary relationships between the proteomes of cells and the proteomes of viruses (taxa), we reconstructed ToP from the abundance and occurrence of 442 ABEV FSFs (phylogenetic characters). The ABEV group was selected because it includes many FSFs of ancient origin (median nd~0.4; Fig. 5A ), the entire abe core (Fig. 3B and table S5 ), and ancient FSFs in Ariadne's threads (Figs. 4B and 6A). Because biases in taxon sampling could influence tree reconstruction, we randomly sampled a set of 368 proteomes (taxa) from cells and viruses, including up to 5 viral species from each viral order or family and 34 proteomes corresponding to only free-living organisms in Archaea, Bacteria, and Eukarya. The rooted phylogeny dissected proteomes into four supergroups (Fig. 7A ). Viruses formed a distinct paraphyletic group at the base of ToP that was distinguishable from cells by 76% bootstrap (BS) support. In turn, archaeal organisms were clustered paraphyletically in the more basal branches (black circles), whereas Bacteria and Eukarya formed monophyletic groups (blue and green circles) supported by 66% and 100% BS, respectively (Fig. 7A) . This topology supported an ancient origin of both viruses and Archaea and a sister relationship between Bacteria and Eukarya, which goes against some gene sequence-based phylogenies (58-60) but is congruent with a number of structure-and functionbased studies [discussed elsewhere (18, (61) (62) (63) (64) (65) ].