Display Settings:

Format

Send to:

Choose Destination
We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
    Mol Biol Evol. 2011 Feb;28(2):873-7. doi: 10.1093/molbev/msq212. Epub 2010 Aug 12.

    Random Tree-Puzzle leads to the Yule-Harding distribution.

    Abstract

    Approaches to reconstruct phylogenies abound and are widely used in the study of molecular evolution. Partially through extensive simulations, we are beginning to understand the potential pitfalls as well as the advantages of different methods. However, little work has been done on possible biases introduced by the methods if the input data are random and do not carry any phylogenetic signal. Although Tree-Puzzle (Strimmer K, von Haeseler A. 1996. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol Biol Evol. 13:964-969; Schmidt HA, Strimmer K, Vingron M, von Haeseler A. 2002. Tree-Puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504) has become common in phylogenetics, the resulting distribution of labeled unrooted bifurcating trees when data do not carry any phylogenetic signal has not been investigated. Our note shows that the distribution converges to the well-known Yule-Harding distribution. However, the bias of the Yule-Harding distribution will be diminished by a tiny amount of phylogenetic information. maximum likelihood, phylogenetic reconstruction, Tree-Puzzle, tree distribution, Yule-Harding distribution.

    PMID:
    20705907
    [PubMed - indexed for MEDLINE]
    Free full text

      Supplemental Content

      Icon for HighWire

      Save items

      Recent activity

      Your browsing activity is empty.

      Activity recording is turned off.

      Turn recording back on

      See more...
      Write to the Help Desk