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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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Copyright Statement
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 |
| UTAS Author: | Holland, BR (Professor Barbara Holland) |
| ID Code: | 62972 |
| Year Published: | 2007 |
| Web of Science® Times Cited: | 58 |
| Deposited By: | Mathematics |
| Deposited On: | 2010-03-31 |
| Last Modified: | 2010-04-30 |
| Downloads: | 0 |
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