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Published on: June 16, 2011
Distinguishing Genetic Drift from Selection in Papillomavirus Evolution.
Robert D Burk1, Lisa Mirabello2, Robert DeSalle3
1Departments of Pediatrics, Microbiology & Immunology, Epidemiology & Population Health, Obstetrics, Gynecology and Woman's Health, and Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
Genetic drift, not just selection, shapes human papillomavirus (HPV) genomes. Different evolutionary forces influenced HPV genome structure across time, impacting even recent variants.
Area of Science:
- * Virology
- * Evolutionary Biology
- * Genomics
Background:
- * Purifying selection impacts papillomavirus non-synonymous substitutions.
- * The role of non-coding DNA motif evolution in HPV diversification is unclear.
Purpose of the Study:
- * To investigate the influence of genetic drift and selection on non-coding DNA motifs in *Alphapapillomavirus* genomes.
- * To understand the evolutionary history and diversification of HPV genomes.
Main Methods:
- * Phylogenetic analysis of over a thousand complete *Alphapapillomavirus* genomes.
- * Examination of nucleotide composition, codon usage, trimer usage, and 13 non-coding DNA motifs.
- * Application of Principal Components Analyses, Ancestral State Reconstructions, and Phylogenetic Independent Contrasts.
Main Results:
- * Nucleotide composition, codon usage, and non-coding motifs revealed phylogenetic clustering indicative of genetic drift in ancient *Alphapapillomavirus* types.
- * CpG and APOBEC3 motifs showed significant ancient genome alterations.
- * Evolutionary analyses indicated distinct structuring of HPV genomes by genetic drift and varying drivers across epochs.
Conclusions:
- * Genetic drift plays a significant role in structuring *Alphapapillomavirus* genomes.
- * Different evolutionary drivers have shaped HPV genomes differently over time.
- * These evolutionary patterns extend to recently emerged variant lineages.
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Mutation, Gene Flow, and Genetic Drift
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Gene Flow
Hardy-Weinberg Principle
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