Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks

Finding the Minimum Number of Recombination Events
  • Yun S. Song
  • Jotun Hein
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2812)


Under the infinite-sites model of mutation, we consider the problem of finding the minimum number of recombination events which must have occurred in the evolutionary history of sampled DNA sequences. Our approach is deterministic and is based on the combinatorics of leaf-labelled rooted trees. In contrast to previously known approaches, which only yield estimated lower bounds, our approach always gives the exact minimum number of recombination events. Furthermore, our method can be used to reconstruct explicitly evolutionary histories with the minimum number of recombination events. As an additional application, we discuss how our work can be used to define haplotype blocks.


Recombination Event Rooted Tree Sequence Evolution Haplotype Block Minimal Path 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Daly, M.J., et al.: High-Resolution Haplotype Structure in the Human Genome. Nat. Genet. 29, 229–232 (2001)CrossRefGoogle Scholar
  2. 2.
    Fearnhead, P., Donnelly, P.: Estimating Recombination Rates from Population Genetic Data. Genetics 159, 1299–1318 (2001)Google Scholar
  3. 3.
    Gabriel, S.B., et al.: The Structure of Haplotype Blocks in the Human Genome. Science 296, 2225–2229 (2002)CrossRefGoogle Scholar
  4. 4.
    Hein, J.: Reconstructing Evolution of Sequences Subject to Recombination Using Parsimony. Math. Biosci. 98, 185–200 (1990)zbMATHCrossRefMathSciNetGoogle Scholar
  5. 5.
    Hein, J.: A Heuristic Method to Reconstruct the History of Sequences Subject to Recombination. J. Mol. Evol. 36, 396–405 (1993)CrossRefGoogle Scholar
  6. 6.
    Hudson, R.R., Kaplan, N.L.: Statistical Properties of the Number of Recombination Events in the History of a Sample of DNA Sequences. Genetics 11, 147–164 (1985)Google Scholar
  7. 7.
    Johnson, G.C., et al.: Haplotype Tagging for the Identification of common Disease Genes. Nat. Genet. 29, 233–237 (2001)CrossRefGoogle Scholar
  8. 8.
    Kreitman, M.: Nucleotide Polymorphism at the Alcohol Dehydrogenase Locus of Drosophila Melanogaster. Nature 304, 412–417 (1983)CrossRefGoogle Scholar
  9. 9.
    Myers, S.R., Griffiths, R.C.: Bounds on the Minimum Number of Recombination Events in a Sample History. Genetics 163, 375–394 (2003)Google Scholar
  10. 10.
    Schröder, E.: Vier Combinatorische Probleme. Zeit. für. Math. Phys 15, 361–376 (1870)Google Scholar
  11. 11.
    Song, Y.S.: Notes on the Combinatorics of Rooted Binary Phylogenetic Trees, submitted to Annals of Combinatorics for publicationGoogle Scholar
  12. 12.
    Song, Y.S., Hein, J.: On the Minimum Number of Recombination Events in the Evolutionary History of DNA Sequences. J. Math. Biol. (to appear)Google Scholar
  13. 13.
    Wang, L., Zhang, K., Zhang, L.: Perfect Phylogenetic Networks with Recombination. J. Comp. Biol 8, 69–78 (2001)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Yun S. Song
    • 1
  • Jotun Hein
    • 1
  1. 1.Department of StatisticsUniversity of OxfordOxfordUK

Personalised recommendations