Advertisement

Journal of Molecular Evolution

, Volume 36, Issue 4, pp 396–405 | Cite as

A heuristic method to reconstruct the history of sequences subject to recombination

  • Jotun Hein
Article

Summary

Sequences subject to recombination and gene conversion defy phylogenetic analysis by traditional methods since their evolutionary history cannot be adequately summarized by a tree. This study investigates ways to describe their evolutionary history and proposes a method giving a partial reconstruction of this history. Multigene families, viruses, and alleles from within populations experience recombinations/gene conversions, so the questions studied here are relevant for a large body of data and the suggested solutions should be very practical. The method employed was implemented in a program, RecPars, written in C and was used to analyze nine retroviruses.

Key words

Phylogenetic analysis Multigene families Recombination Parsimony 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Felsenstein J (1988) Phylogenies from molecular sequence: inference and reliability. Ann Rev Genet 22:521–565Google Scholar
  2. Fitch WM (1971) Towards defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416Google Scholar
  3. Hartigan JA (1973) Minimum mutation fits to a given tree. Biometrics 29:53–65Google Scholar
  4. Hein J (1990) Reconstructing evolution of sequences subject to recombination using parsimony. Math Biosc 98:185–200Google Scholar
  5. Hein J (1990) A unified approach to alignments and phylogeny reconstruction. R. Doolittle (ed.) Meth Enz 183:626–645Google Scholar
  6. Hudson R (1983) Properties of a neutral allele model with intragenic recombination. Theor Pop Biol 23:183–201Google Scholar
  7. Hudson RR, Kaplan N (1985) Statistical properties of the numbers of recombination events in the history of a sample of DNA sequences. Genetics 111:147–164PubMedGoogle Scholar
  8. Kaplan N, Hudson R (1985) The use of sample genealogies for studying selectively neutral M-loci model with recombination. Theor Pop Biol 28:382–396Google Scholar
  9. Le Quesne WJ (1969) A method for selection of characters in numerical taxonomy. Syst Zool 18:201–205Google Scholar
  10. Sankoff D (1975) Minimal mutation trees of sequences. SIAM J Appl Math 78:35–42Google Scholar
  11. Sawyer S (1989) Statistical tests to detecting gene conversion. Mol Biol Evol 6:526–539Google Scholar
  12. Sneath PHA, Sackin MJ, Ambler RP (1975) Detecting evolutionary incompatibilities from protein sequences. Syst Zool 24:311–332Google Scholar
  13. Stephens JC (1985) Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion. Mol Biol Evol 2(6):539–556Google Scholar

Copyright information

© Springer-Verlag 1993

Authors and Affiliations

  • Jotun Hein
    • 1
  1. 1.National Institute of GeneticsMishima, Shizuoka KenJapan

Personalised recommendations