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The Problem of Rooting Rapid Radiations

Citation

Shavit, L and Penny, D and Hendy, MD and Holland, BR, The Problem of Rooting Rapid Radiations, Molecular Biology and Evolution, 24, (11) pp. 2400-2411. ISSN 0737-4038 (2007) [Refereed Article]


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The definitive publisher-authenticated version is available online at: www.oxfordjournals.org

DOI: doi:10.1093/molbev/msm178

Abstract

There are many examples of groups (such as birds, bees, mammals, multicellular animals, and flowering plants) that have undergone a rapid radiation. In such cases, where there is a combination of short internal and long external branches, correctly estimating and rooting phylogenetic trees is known to be a difficult problem. In this simulation study, we tested the performances of different phylogenetic methods at estimating a tree that models a rapid radiation. We found that maximum likelihood, corrected and uncorrected neighbor-joining, and corrected and uncorrected parsimony, all suffer from biases toward specific tree topologies. In addition, we found that using a single-taxon outgroup to root a tree frequently disrupts an otherwise correct ingroup phylogeny. Moreover, for uncorrected parsimony, we found cases where several individual trees (in which the outgroup was placed incorrectly) were selected more frequently than the correct tree. Even for parameter settings where the correct tree was selected most frequently when using extremely long sequences, for sequences of up to 60,000 nucleotides the incorrectly rooted trees were each selected more frequently than the correct tree. For all the cases tested here, tree estimation using a two taxon outgroup was more accurate than when using a single-taxon outgroup. However, the ingroup was most accurately recovered when no outgroup was used.

Item Details

Item Type:Refereed Article
Keywords:maximum parsimony • maximum likelihood • misleading zones • neighbor-joining • outgroup rooting • topological bias
Research Division:Mathematical Sciences
Research Group:Applied Mathematics
Research Field:Biological Mathematics
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Biological Sciences
Author:Holland, BR (Associate Professor Barbara Holland)
ID Code:62972
Year Published:2007
Web of Science® Times Cited:49
Deposited By:Mathematics
Deposited On:2010-03-31
Last Modified:2010-04-30
Downloads:0

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