Burk, R.D.; Mirabello, L.; DeSalle, R. Genetic Drift and Alphapapillomavirus Evolution. Preprints2023, 2023060020. https://doi.org/10.20944/preprints202306.0020.v1
APA Style
Burk, R.D., Mirabello, L., & DeSalle, R. (2023). Genetic Drift and <em>Alphapapillomavirus</em> Evolution. Preprints. https://doi.org/10.20944/preprints202306.0020.v1
Chicago/Turabian Style
Burk, R.D., Lisa Mirabello and Robert DeSalle. 2023 "Genetic Drift and <em>Alphapapillomavirus</em> Evolution" Preprints. https://doi.org/10.20944/preprints202306.0020.v1
Abstract
Pervasive purifying selection on non-synonymous substitutions is a hallmark of papillomavirus genome history. Whereas the role of selection on, and drift of, non-coding DNA elements on HPV diversification is poorly understood. More than a thousand complete genomes representing Alphapapillomavirus types, lineages and SNP variants were examined phylogenetically and interrogated for the number and position of non-coding DNA sequence motifs using Principal Components Analyses, Ancestral State Reconstructions and Phylogenetic Independent Contrasts. For anciently diverged Alphapapillomavirus types, composition of the 4 nucleotides (A,C,G,T), codon usage, trimer usage and 13 established non-coding DNA sequence motifs revealed phylogenetic clusters consistent with genetic drift. Ancestral state reconstruction and Phylogenetic Independent Contrasts revealed ancient genome alterations, particularly for CpG and APOBEC3 motifs. Each evolutionary analytical method we performed supports the unanticipated conclusion that genetic drift and different evolutionary drivers have structured Alphapapillomavirus genomes in distinct ways during successive epochs, even extending to differences in more recently formed variant lineages
Keywords
molecular evolution; genetic drift; human papillomavirus (HPV)
Subject
Medicine and Pharmacology, Epidemiology and Infectious Diseases
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
