MBE Advance Access originally published online on August 23, 2007
Molecular Biology and Evolution 2007 24(11):2400-2411; doi:10.1093/molbev/msm178
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Research Articles |
The Problem of Rooting Rapid Radiations
The Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
E-mail: l.shavit{at}massey.ac.nz.
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 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.
Key Words: maximum parsimony • maximum likelihood • misleading zones • neighbor-joining • outgroup rooting • topological bias
Arndt Von Haeseler, Associate Editor