A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

(v) ToP derived directly from the age of protein domains. We also developed a multidimensional scaling approach to study the evolution of cells and viruses: the evolutionary principal coordinate (evoPCO) analysis (Fig. 8A) . The evoPCO method combines the power of cladistic and phenetic approaches by calculating principal coordinates directly from temporal evolutionary distances between the proteomes of species (see Materials and Methods). The distance between proteomes reflects phylogenetic dissimilarity in the age of FSF domain repertoires (that is, nd values) and can be displayed in 3D temporal space, assuming that the age of an FSF is the age of the first instance of that FSF appearing in evolution. Because proteomes are biological systems that are made up of component parts (that is, FSFs in this case) but describe cellular organisms and viruses, each component (regardless of its abundance) contributes an age to the overall age of the cellular or viral system. This factor, when taken into account, results in a powerful projection of a multidimensional space of proteomes onto a 3D temporal space that allows visualization of evolutionary relationships. (57) was added as an additional sample to infer the direction of evolutionary splits. a Ignicoccus hospitalis, b Lactobacillus delbrueckii, c Caenorhabditis elegans. (B) A distancebased NJ tree reconstructed from the occurrence of 442 ABEV FSFs in randomly sampled 368 proteomes. Each taxon was given a unique tree ID (tables S1 and S2). Taxa were colored for quick visualization.