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Counting coalescent histories.

Noah A Rosenberg1

  • 1Department of Human Genetics, Bioinformatics Program, and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109-2218, USA. rnoah@umich.edu

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|June 15, 2007
PubMed
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This study introduces a new method to count valid coalescent histories for species and gene trees. This finding aids in calculating gene tree probabilities on species trees.

Area of Science:

  • Computational Biology
  • Phylogenetics
  • Evolutionary Genetics

Background:

  • Understanding gene tree-species tree discordance is crucial in evolutionary studies.
  • Coalescent theory models the evolutionary history of gene lineages within a species tree.
  • Calculating probabilities of gene tree topologies requires enumerating valid coalescent histories.

Purpose of the Study:

  • To develop a novel recursion for counting valid coalescent histories for any given gene tree and species tree pair.
  • To provide a more efficient method for evaluating probabilities of gene tree topologies.

Main Methods:

  • Defined and utilized the concept of m-extended coalescent histories.
  • Developed a recursive formula for enumerating and counting these histories.

Related Experiment Videos

  • Applied the method to the specific case of m = 1 for one gene lineage per species.

    • Main Results:

    • A general recursion for the number of valid coalescent histories has been established.
    • The method simplifies the enumeration of histories for arbitrary gene tree/species tree pairs.
    • The derived recursion can significantly reduce computational effort in probability calculations.

    Conclusions:

    • The developed recursion offers an efficient way to count valid coalescent histories.
    • This work provides a valuable tool for phylogenetic analyses and evolutionary modeling.
    • The findings facilitate the assessment of gene tree probabilities on species trees.