Distinguishing Genetic Drift from Selection in Papillomavirus Evolution

Pervasive purifying selection on non-synonymous substitutions is a hallmark of papillomavirus genome history, but the role and drift non-coding DNA motifs HPV diversification poorly understood. In this study, more than thousand complete genomes representing Alphapapillomavirus types, lineages, SNP variants were examined phylogenetically interrogated for number position sequence using Principal Components Analyses, Ancestral State Reconstructions, Phylogenetic Independent Contrasts. For anciently diverged composition four nucleotides (A, C, G, T), codon usage, trimer 13 established revealed phylogenetic clusters consistent with genetic drift. state reconstruction Contrasts ancient alterations, particularly CpG APOBEC3 motifs. Each evolutionary analytical method we performed supports unanticipated conclusion that different drivers have structured in distinct ways during successive epochs, even extending to differences recently formed variant lineages.