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Multiple evolutionary mechanisms drive papillomavirus diversification.

Marc Gottschling1, Alexandros Stamatakis, Ingo Nindl

  • 1Skin Cancer Center Charité, University Hospital of Berlin, Berlin, Germany.

Molecular Biology and Evolution
|March 9, 2007
PubMed
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Papillomavirus (PV) evolution is complex, driven by multiple factors beyond host coevolution. Analyzing PV genomes reveals host-linked evolution and cross-species infections, challenging simple evolutionary models.

Area of Science:

  • Virology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Papillomaviruses (PVs) possess a circular, double-stranded DNA genome encoding key genes (E1, E2, L2, L1).
  • Over 150 PV genomes have been sequenced, providing a rich dataset for evolutionary analysis.

Purpose of the Study:

  • To investigate the evolutionary history and phylogenetic relationships of papillomaviruses.
  • To assess the impact of different genes and analytical methods on PV phylogeny reconstruction.

Main Methods:

  • Analysis of 53 PV genomes using maximum likelihood, Bayesian inference, maximum parsimony, and distance-based methods.
  • Separate and combined analyses of nucleotide and amino acid alignments for E1, E2, L2, and L1 genes.

Main Results:

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  • Amino acid-based phylogenies showed less incongruence than nucleotide-based trees, particularly when excluding the L2 gene.
  • Combined analysis of E1-E2-L1 genes yielded a well-supported phylogeny, identifying distinct PV supertaxa infecting various mammalian orders.
  • Host-linked evolution was evident at shallower taxonomic levels, with evidence of adaptive radiation, recombination, and cross-species infections.

Conclusions:

  • PV evolution is a complex interplay of host-linked adaptation, adaptive radiation, recombination, and cross-species transmission.
  • Phylogenetic incongruence can arise from gene-specific evolutionary dynamics and computational biases.
  • The study supports a multifaceted evolutionary scenario for PVs, not solely driven by coevolution with hosts.