Advertisement

Journal of Molecular Evolution

, Volume 44, Supplement 1, pp S65–S75 | Cite as

Networks and viral evolution

  • Walter M. Fitch
Viral evolution

Abstract

In studying population data, it is common to have many equally possible parsimonious trees. This has caused representational problems, all of which have been addressed by using various kinds of consensus trees. Recognizing that the incubus may in fact be the constraint of having to have a tree representation, several authors have investigated networks as a better form. In this paper, a beginning to a new procedure for making most parsimonious networks is developed. The algorithm, as developed so far, is presented. Its applicability to several viral evolutionary problems is illustrated and the nature of the problems needing yet to be addressed are discussed.

Key words

Phylogeny Parsimony Networks Viruses 
This is a preview of subscription content, log in to check access.

References

  1. Ahmad N, Baroudy BM, Baker RC, Chappey C (1995) Genetic analysis of human immunodeficiency virus type 1 envelope V3 region isolates from mothers and infants after perinatal transmission. J Virol 69:1001–1012PubMedGoogle Scholar
  2. Bandelt H-J, Dress AWM (1992) Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol Phylogenet Evol 1:242–252PubMedCrossRefGoogle Scholar
  3. Bandelt H-J, Forster P, Sykes BC, Richards MB (1995) Mitochondrial portraits of human populations using median networks. Genetics 141:743–753Google Scholar
  4. Cornelissen M et al. (1995) Syncytium-inducing (SI) phenotype suppression at seroconversion after intramuscular inoculation of a nonsyncytium inducing/(SI) phenotypically mixed human immunodeficiency virus population. Virology 69:1810–1818Google Scholar
  5. Eigen M, Winkler-Oswatitsch R, Dress A (1988) Statistical geometry in sequence space: a method of quantitative sequence analysis. PNAS 85:5913–5917PubMedCrossRefGoogle Scholar
  6. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  7. Holmes EC, Zhang LQ, Simmonds P, Ludlam CA, Leigh-Brown AJ (1992) Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient. PNAS 89:4835–4839PubMedCrossRefGoogle Scholar
  8. Naas T, Blot M, Fitch WM, Arber W (1995) Dynamics of IS-related genetic rearrangements in resting Escherichia coli K-12. Mol Biol Evol 12:198–207PubMedGoogle Scholar
  9. Swofford DL (1993) PAUP (phylogenetic analysis using parsimony). Illinois Natural History Survey, Champaign, ILGoogle Scholar
  10. Templeton AR, Crandall KA, Sing CF (1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132:619–633PubMedGoogle Scholar

Copyright information

© Springer-Verlag 1997

Authors and Affiliations

  • Walter M. Fitch
    • 1
  1. 1.Department of Ecology and Evolutionary BiologyUniversity of CaliforniaIrvineUSA

Personalised recommendations

Cite article

Buy options