Phylogeny of Viruses

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Abstract

Biological species, including viruses, change through generations and over time in the process known as evolution. Viruses may evolve at high, uneven, and fluctuating rates among genome sites. The accumulated changes, through either mutation or recombination with other species, are first fixed in the genome of successful individuals that give rise to genetic lineages. The relationship between biological lineages related by common descent is called ‘phylogeny’. For inferring phylogeny, the differences between aligned sequences of genomes and proteins are quantified and depicted in the form of a tree, in which contemporary species and their intermediate and common ancestors occupy, respectively, the terminal nodes, internal nodes, and the root. The tree is characterized by a topology, length of branches, shape, and the root position. A complex mathematical apparatus has been developed for phylogeny inference that can evaluate inter-species differences, facilitate tree building and comparison of trees, and assess the fit between data and tree through, typically, computationally intensive calculations. A reconstructed tree is an approximation of the true phylogeny that practically remains unknown. The phylogenetic analysis is used in applied and fundamental virus research, including epidemiology, diagnostics, forensic studies, phylogeography, evolutionary studies, and virus taxonomy. It can provide an evolutionary perspective on variation of any trait that can be measured for a group of viruses.

Keywords

Bayesian reasoning
Character-based inference
Distance-based inference
Epidemiology
Evolution
Evolutionary rate
Maximum likelihood reasoning
Molecular clock
Mutation
Phylogenetic tree
Phylogenomics
Phylogeography
Recombination
Taxonomy
Tree of Life

Further Reading

  1. Dolja and Koonin, 2006
    VV Dolja, EV Koonin (Eds.), Comparative genomics and evolution of complex viruses, Virus Research, 117 (2006), pp. 1-184
  1. Domingo, 2007
    E. Domingo
    Virus evolution
    D.M. Knipe, P.M. Howley, D.E. Griffin, et al. (Eds.), Fields virology (5th edn.), Wolters Kluwer, Lippincott Williams and Wilkins, Philadelphia, PA (2007), pp. 389-421
  1. Domingo et al., 1999
    E Domingo, RG Webster, JJ Holland (Eds.), Origin and evolution of viruses, Academic Press, San Diego (1999)
  1. Drummond et al., 2012
    A.J. Drummond, M.A. Suchard, D. Xie, A. Rambaut
    Bayesian phylogenetics with BEAUti and the BEAST 1.7
    Molecular Biology and Evolution, 29 (2012), pp. 1969-1973
  1. Felsenstein, 2004
    J. Felsenstein
    Inferring phylogenies
    Sinauer Associates, Inc, Sunderland, MA (2004)
  1. Gibbs et al., 1995
    A.J. Gibbs, C.H. Calisher, F. Garcia-Arenal
    Molecular basis of virus evolution
    Cambridge University Press, Cambridge (1995)
  1. King et al., 2012
    A.M.Q. King, M.J. Adams, E.B. Carstens, E.J. Lefkowitz (Eds.), Virus taxonomy: the 9th report of the international committee on taxonomy of viruses, Elsevier, Academic Press, San Diego, CA (2012)
  1. Lauber et al., 2013
    C. Lauber, J. Goeman, M.D.C. Parquet, P.T. Nga, E.J. Snijder, K. Morita, A.E. Gorbalenya
    The footprint of genome architecture in the largest genome expansion in RNA viruses
    PLoS Pathogens, 9 (7) (2013), p. e1003500
  1. Moya et al., 2004
    A. Moya, E.C. Holmes, F. Gonzalez-Candelas
    The population genetics and evolutionary epidemiology of RNA viruses
    Nature Reviews Microbiology, 2 (2004), pp. 279-288
  1. Page and Holmes, 1998
    R.D. Page, E.C. Holmes
    Molecular evolution. A phylogenetic approach
    Blackwell Publishing, Boston (1998)
  1. Salemi and Vandamme, 2003
    M Salemi, AM Vandamme (Eds.), The phylogenetic handbook. A practical approach to DNA and protein phylogeny, Cambridge University Press, Cambridge (2003)
  1. Stamatakis, 2014
    A. Stamatakis
    RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
    Bioinformatics, 30 (2014), pp. 1312-1313
  1. Villarreal, 2005
    L.P. Villarreal
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  1. Weaver et al., 2016
    S.C. Weaver, M. Denison, M. Roosinck, M. Vignuzzi (Eds.), Virus Evolution, Current Research and Future Directions, Academic Press, Caister (2016)

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Change History: December 2016. AE Gorbalenya and C Lauber updated sections Introduction, Tree Definitions, Phylogenetic Analysis and Applications of Phylogeny in Virology, the reference section. Introduced Figures 1-4.

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