Phylogenomics and molecular evolution of polyomaviruses

Keith A. Crandall, Marcos Prérez-Losada, Ryan G. Christensen, David A. McClellan, Raphael P Viscidi

Research output: Contribution to journalArticle

Abstract

We provide in this chapter an overview of the basic steps to reconstruct evolutionary relationships through standard phylogeny estimation approaches as well as network approaches for sequences more closely related. We discuss the importance of sequence alignment, selecting models of evolution, and confidence assessment in phylogenetic inference. We also introduce the reader to a variety of software packages used for such studies. Finally, we demonstrate these approaches throughout using a data set of 33 whole genomes of polyomaviruses. A robust phylogeny of these genomes is estimated and phylogenetic relationships among the polyomaviruses determined using Bayesian and maximum likelihood approaches. Furthermore, population samples of SV40 are used to demonstrate the utility of network approaches for closely related sequences. The phylogenetic analysis suggested a close relationship among the BK viruses, JC viruses, and SV40 with a more distant association with mouse polyomavirus, monkey polymavirus (LPV) and then avian polyomavirus (BFDV).

Original languageEnglish (US)
Pages (from-to)46-59
Number of pages14
JournalAdvances in Experimental Medicine and Biology
Volume577
DOIs
StatePublished - 2006

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Polyomavirus
Molecular Evolution
Viruses
Genes
Phylogeny
Software packages
Maximum likelihood
Genome
BK Virus
JC Virus
Sequence Alignment
Haplorhini
Software
Population

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Phylogenomics and molecular evolution of polyomaviruses. / Crandall, Keith A.; Prérez-Losada, Marcos; Christensen, Ryan G.; McClellan, David A.; Viscidi, Raphael P.

In: Advances in Experimental Medicine and Biology, Vol. 577, 2006, p. 46-59.

Research output: Contribution to journalArticle

Crandall, Keith A. ; Prérez-Losada, Marcos ; Christensen, Ryan G. ; McClellan, David A. ; Viscidi, Raphael P. / Phylogenomics and molecular evolution of polyomaviruses. In: Advances in Experimental Medicine and Biology. 2006 ; Vol. 577. pp. 46-59.
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