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Improving Divergence Time Estimation in Phylogenetics: More Taxa vs. Longer Sequences

Svennblad Bodil and Britton Tom
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Svennblad Bodil: Uppsala University
Britton Tom: Stockholm University

Statistical Applications in Genetics and Molecular Biology, 2007, vol. 6, issue 1, 1-26

Abstract: Maximum Likelihood (ML) is used as a standard method for estimating divergence times in phylogenetic trees. The method is consistent and hence the precision can be improved by analyzing longer sequences. In this paper we show that the precision can be improved also by including more taxa to the existing tree. It is a theoretical study, complemented with simulations, showing that the gain in precision is faster with increasing sequence length than with increasing number of taxa.We further compare the results of estimating divergence times using Maximum Likelihood with the much faster and less complex estimation method of Mean Path Length (MPL), which works with the evolution model of Jukes-Cantor (1969). It is shown that MPL is as good as ML in estimating divergence times of nodes that are located near the root in the tree, but ML is better in estimating the divergence times of nodes lower down.

Date: 2007
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DOI: 10.2202/1544-6115.1313

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