Relaxed phylogenies and dating with confidence
Recently, it has been realized that less drastic alternatives to the unrooted model of phylogeny may exist.Instead of dispensing with the molecular clock entirely, attempts have been made to relax the molecular clock assumption by allowing the rate to vary across the tree .Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments.From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution. If you do not see its contents the file may be temporarily unavailable at the journal website or you do not have a PDF plug-in installed and enabled in your browser. Phillips 0 1 2 Andrew Rambaut[ 0 1 2 0 Current address: Department of Computer Science, University of Auckland , Auckland , New Zealand 1 Academic Editor: David Penny, Massey University , New Zealand 2 Department of Zoology, University of Oxford , Oxford , United Kingdom In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum.Alternatively, you can download the file locally and open with any standalone PDF reader: Object.action? Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes.uri=info:doi/10.1371/0040088&representation=PDF Citation: Drummond AJ, Ho SYW, Phillips MJ, Rambaut A ( Relaxed Phylogenetics and Dating with Confidence Alexei J. Fortunately, intermediate models employing relaxed molecular clocks have been described.We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data.In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme.
Relaxed-clock models present a potentially useful method for removing the assumption of a strict molecular clock, but a major shortcoming of the methods that have been proposed thus far is that they require the user to specify the tree topology.
 and Aris-Brosou and Yang , present an enticing alternative to local clock models.
These model the molecular rate among lineages as varying in an autocorrelated manner, with the rate in each branch being drawn (a priori) from a parametric distribution whose mean is a function of the rate on the parent branch.
Fortunately, intermediate models employing relaxed molecular clocks have been described.
These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis.