MBE Advance Access published online on March 6, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm039
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Research Article |
Multiple evolutionary mechanisms drive papillomavirus diversification
1 Department of Dermatology, Charité, Skin Cancer Center Charité, University Hospital of Berlin, Berlin, Germany
2 École Polytechnique Fédérale de Lausanne, School of Computer & Communication Sciences, Laboratory for Computational Biology and Bioinformatics, Lausanne, Switzerland
3 Deutsches Krebsforschungszentrum, Infection and Cancer, Heidelberg, Germany
4 Corresponding author. Deutsches Krebsforschungszentrum / German Cancer Research Centre, Infection and Cancer (F020), Im Neuenheimer Feld 280, D 69120 Heidelberg, Germany. Phone: ++49-(0)6221-424 935, Fax: ++49-(0)6221-424 932, e-mail: i.bravo{at}dkfz.de
Received for publication November 11, 2006. Revision received January 17, 2007. Revision received February 19, 2007. Accepted for publication February 28, 2007.
The circular, double-stranded 8 kb DNA genome of papillomaviruses (PVes) consists mainly of four large genes, E1, E2, L2, and L1. Approximately 150 PV genomes have been sequenced to date. We analyzed a representative sample of 53 PVes genomes using Maximum Likelihood, Bayesian inference, Maximum Parsimony, and distance-based methods both on nucleotide and on amino acid alignments. When the four genes were analyzed separately, amino acid-inferred phylogenies contradicted each other less than nucleotide-inferred trees (judged by partition homogeneity tests). In particular, gene combinations including the L2 gene generated significant incongruence (p < 0.001). Combined analyses of the remaining genes E1-E2-L1 produced a well-supported phylogeny including supertaxon ß+
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-PVes (infecting Artiodactyla, Carnivora, Primates, and Rodentia) and supertaxon 
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-PVes (infecting Carnivora, Lagomorpha, Primates, and Rodentia). Based on the tree topology, host-linked evolution appears plausible at shallow, rather than deeper, taxonomic levels. Diversification within PVes may also involve adaptive radiation establishing different niches (within a single host species) and recombination events (within single host cells). Heterogeneous groups of closely related PVes infecting, for example, humans and domestic animals such as hamster, dog, and cattle suggest multiple infections across species borders. Additional evolutionary phenomena such as strong codon usage preferences, and computational biases including reconstruction artifacts and insufficient taxon sampling, may contribute to the incomplete resolution of deep phylogenetic nodes. The molecular data globally supports a complex evolutionary scenario for PVes, which is driven by multiple mechanisms but not exclusively by co-evolution with corresponding hosts.
Key Words: adaptive radiation • co-evolution • high performance computing • host • interspecies transmission • recombination • virology • zoonosis
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