A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

The evoPCO method revealed four clouds of proteomes in temporal space that correspond to viruses and to the three cellular superkingdoms (Fig. 8A ). The first three coordinates explained~85% of the total variability. Using the previously reconstructed proteome of the last common ancestor of modern cells as reference point (57), we inferred viruses as the most ancient supergroup, followed by Archaea, Bacteria, and Eukarya, in that order (Fig. 8A) . This topology supports earlier results from comparative genomic and phylogenomic analyses, adding a fifth line of evidence in support of the early origin of viruses. Remarkably, Lassa virus, which belongs to Arenaviridae and harbors segmented RNA genomes, appeared at the most basal position of the evoPCO plot, supporting the early origin of segmented RNA viruses in ToP (Fig. 7A) . Some giant viruses appeared more derived, supporting their ancient coexistence with cells (19, 73) . The topology and ordering of proteomes in evoPCO analysis were further supported by a distancebased neighbor-joining (NJ) tree (Fig. 8B) reconstructed directly from the temporal distance matrix, which retained the cohesive and ancient nature of the viral supergroup. The NJ tree made explicit the early origins of RNA viral families and was largely congruent with ToP recovered earlier (Fig. 7A) , validating the power of the evoPCO strategy.