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Phylogenomics and Molecular Evolution of Polyomaviruses

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Polyomaviruses and Human Diseases

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 577))

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).

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Author information

Authors and Affiliations

  1. Brigham Young University, Provo, Utah, USA

    Keith A. Crandall Ph.D., Marcos Prérez-Losada Ph.D. & Ryan G. Christensen

  2. Integrative Biology, Brigham Young University, Provo, Utah, USA

    David A. McClellan Ph.D.

  3. Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Raphael P. Viscidi M.D.

Authors
  1. Keith A. Crandall Ph.D.
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  2. Marcos Prérez-Losada Ph.D.
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  3. Ryan G. Christensen
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  4. David A. McClellan Ph.D.
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  5. Raphael P. Viscidi M.D.
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Editor information

Editors and Affiliations

  1. Mayo Clinic Transplant Center, Mayo Clinic - College of Medicine, Jacksonville, Florida, USA

    Nasimul Ahsan M.D., FACP

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Crandall, K.A., Prérez-Losada, M., Christensen, R.G., McClellan, D.A., Viscidi, R.P. (2006). Phylogenomics and Molecular Evolution of Polyomaviruses. In: Ahsan, N. (eds) Polyomaviruses and Human Diseases. Advances in Experimental Medicine and Biology, vol 577. Springer, New York, NY. https://doi.org/10.1007/0-387-32957-9_3

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