Comparison of the Accuracies of Several Phylogenetic Methods Using Protein and DNA Sequences

Author: Hall, Barry G.

Source: Molecular Biology and Evolution, Volume 22, Number 3, March 2005 , pp. 792-802(11)

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Abstract:

A biologically realistic method was used to simulate evolutionary trees. The method uses a real DNA coding sequence as the starting point, simulates mutation according to the mutational spectrum of Escherichia coli—including base substitutions, insertions, and deletions—and separates the processes of mutation and selection. Trees of 8, 16, 32, and 64 taxa were simulated with average branch lengths of 50, 100, 150, 200, and 250 changes per branch. The resulting sequences were aligned with ClustalX, and trees were estimated by Neighbor Joining, Parsimony, Maximum Likelihood, and Bayesian methods from both DNA sequences and the corresponding protein sequences. The estimated trees were compared with the true trees, and both topological and branch length accuracies were scored. Over the variety of conditions tested, Bayesian trees estimated from DNA sequences that had been aligned according to the alignment of the corresponding protein sequences were the most accurate, followed by Maximum Likelihood trees estimated from DNA sequences and Parsimony trees estimated from protein sequences.

Keywords: simulation; alignment; method comparison; indels; branch lengths; topology

Document Type: Research article

DOI: http://dx.doi.org/10.1093/molbev/msi066

Publication date: 2005-03-01

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Molecular Biology and Evolution publishes research at the interface between molecular and evolutionary biology. The journal publishes investigations of molecular evolutionary patterns and processes, tests of evolutionary hypotheses that use molecular data, and studies that use molecular evolutionary information to address questions about biological function at all levels of organization.