A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

The reconstruction of phylogenomic trees of domains (ToD), which describe the evolution of the 1995 FSF domains (taxa) that were surveyed in the 5080 sampled proteomes (characters) (see Materials and Methods for the tree reconstruction protocol), showed that most viral FSFs originated very early in evolution (see the legend bar on top of ToD in Fig. 5A ). Because of its highly unbalanced nature, ToD enabled the calculation of a "proxy" for the relative age of each FSF domain, which was defined as the node distance (nd) value. This value was derived simply by counting the number of nodes from a terminal taxon to the root node of the tree and by expressing the phylogenetic distance on a relative scale from 0 (most ancient) to 1 (most recent) [methodology discussed elsewhere (18) ]. We have previously shown that nd is a reliable proxy for the evolutionary age of FSFs and describes a clock-like behavior of FSF evolution that is remarkably consistent with geological records (56) . To uncover likely evolutionary scenarios, we plotted FSFs in each of the 15 Venn groups in Fig. 1A against their FSF ages (that is, nd values) (boxplots in Fig. 5A) .