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MBE Advance Access published online on August 23, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm178
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© The Author 2007. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

The Problem of Rooting Rapid Radiations

Liat Shavit1,*, David Penny1, Michael D. Hendy1 and Barbara R. Holland1

1 The Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand

* Corresponding author, Liat Shavit, The Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11 222, Palmerston North, New Zealand. Email: l.shavit{at}massey.ac.nz, Phone: 0064 (0)6 3569099 xtn 2569

Accepted for publication August 10, 2007.

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 towards 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.

Key Words: Maximum-Parsimony • Maximum-Likelihood • Misleading-Zones • Neighbor-Joining • Outgroup-Rooting • Topological-Bias


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