TY - CHAP
T1 - Phylogenomics and molecular evolution of polyomaviruses
AU - Crandall, Keith A.
AU - Prérez-Losada, Marcos
AU - Christensen, Ryan G.
AU - McClellan, David A.
AU - Viscidi, Raphael P.
N1 - Copyright:
Copyright 2009 Elsevier B.V., All rights reserved.
PY - 2006
Y1 - 2006
N2 - 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).
AB - 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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U2 - 10.1007/0-387-32957-9_3
DO - 10.1007/0-387-32957-9_3
M3 - Chapter
C2 - 16626026
AN - SCOPUS:33745625417
SN - 9780387292335
T3 - Advances in Experimental Medicine and Biology
SP - 46
EP - 59
BT - Polyomaviruses and Human Diseases
ER -