© 2008 Society of Systematic Biologists
Consistent Estimation of Divergence Times in Phylogenetic Trees with Local Molecular Clocks
Edited by Tim Collins
Department of Mathematics, Uppsala University Box 480, SE-751 06 Uppsala, Sweden; E-mail: bodil.svennblad@ucr.uu.se
Received December 9, 2007; Revised February 28, 2008; Accepted July 9, 2008
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Estimating divergence times in a phylogenetic tree without assuming a global molecular clock is a nontrivial task. In phylogenetic inference, branch lengths are a product of rates and times and therefore estimated divergence times cannot be extracted without additional assumptions or information about rates. If a global molecular clock is assumed and at least one time calibration node is known, then the rate can be estimated and hence also the divergence times of the internal nodes.
If the global molecular clock assumption is violated, a method of divergence times estimation assuming a molecular clock gives misleading results. No method can consistently estimate divergence times without assumptions about rate variation over the tree (Britton, 2005). There are methods that implement relaxed clocks, such as nonparametric rate smoothing (e.g., R8s; Sanderson, 2003) or local molecular clocks (e.g., BASEML; Yang, 1997; and QDATE; Rambaut and Bromham, 1998). For a
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Algorithm of PATHd8 |
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Adjusted MPL |
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Simulation Study |
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Conclusions |
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Appendix. Algorithm for Adjusted Mean Path Length |
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