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    Polytomies and Bayesian Phylogenetic Inference

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    Issue Date
    2005
    Author
    Lewis, Paul O.
    Holder, Mark T.
    Holsinger, Kent E.
    Publisher
    Oxford University Press
    Type
    Article
    Article Version
    Scholarly/refereed, publisher version
    Metadata
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    Abstract
    Bayesian phylogenetic analyses are now very popular in systematics and molecular evolution because they allow the use of much more realistic models than currently possible with maximum likelihood methods. There are, however, a growing number of examples in which large Bayesian posterior clade probabilities are associated with very short branch lengths and low values for non-Bayesian measures of support such as nonparametric bootstrapping. For the four-taxon case when the true tree is the star phylogeny, Bayesian analyses become increasingly unpredictable in their preference for one of the three possible resolved tree topologies as data set size increases. This leads to the prediction that hard (or near-hard) polytomies in nature will cause unpredictable behavior in Bayesian analyses, with arbitrary resolutions of the polytomy receiving very high posterior probabilities in some cases. We present a simple solution to this problem involving a reversible-jump Markov chain Monte Carlo (MCMC) algorithm that allows exploration of all of tree space, including unresolved tree topologies with one or more polytomies. The reversible-jump MCMC approach allows prior distributions to place some weight on less-resolved tree topologies, which eliminates misleadingly high posteriors associated with arbitrary resolutions of hard polytomies. Fortunately, assigning some prior probability to polytomous tree topologies does not appear to come with a significant cost in terms of the ability to assess the level of support for edges that do exist in the true tree. Methods are discussed for applying arbitrary prior distributions to tree topologies of varying resolution, and an empirical example showing evidence of polytomies is analyzed and discussed.
    Description
    This is an electronic version of an article published in Systematic Biology [Lewis, Paul O., Mark T. Holder, and Kent E. Holsinger. Polytomies and Bayesian phylogenetic inference. Systematic Biology, 54:241{253, 2005.] Systematic Biology is available online at informaworld http://dx.doi.org/10.1080/10635150590924208
    URI
    http://hdl.handle.net/1808/9206
    DOI
    https://doi.org/10.1080/10635150490522584
    Collections
    • Ecology & Evolutionary Biology Scholarly Works [1516]
    Citation
    Lewis, Paul O., Mark T. Holder, and Kent E. Holsinger. Polytomies and Bayesian phylogenetic inference. Systematic Biology, 54:241{253, 2005. http://dx.doi.org/10.1080/10635150490522584

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    785-864-8983
    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    785-864-8983

    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
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    Contact KU ScholarWorks
    785-864-8983
    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    785-864-8983

    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    Image Credits
     

     

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