A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

Normalization and rescaling ensure compatibility with PAUP* and protect against the effects of unequal proteome sizes and variances. Maximum parsimony (MP) was used to reconstruct ToD and ToP. ToD described the evolution of FSF domains (taxa) using proteomes as characters. In turn, ToP resembled conventional phylogenies that described the evolution of proteomes (taxa) using FSF domain characters. Trees were rooted by the method of Lundberg (122) , which does not require specification of any outgroup taxon. Instead, first, an unrooted network is calculated, which is rooted a posteriori by the branch yielding a minimum increase in tree length. For this purpose, ancestral character states were specified using the ANCSTATES command in PAUP*. ToD were polarized by the maximum character state, assuming that the more abundant and widespread FSFs should be more ancient relative to those with lower abundance and limited spread. In contrast, ToP were rooted by the minimum character state, assuming that modern proteomes evolved from a relatively simpler urancestral organism that harbored only few FSFs (57) (see text S1 for a discussion of phylogenetic assumptions and models). MP approximates maximum likelihood when phylogenetic characters evolve at different rates (123) and is appropriate for global proteome studies. BS analysis with 1000 replicates was performed to assess the reliability of deep evolutionary relationships. Trees were visualized with Dendroscope (version 3.2.8) (124) .