Relaxed phylogenetics and dating
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.This development has been characterized by increases, both in the complexity of the models used to describe molecular sequence evolution, and in the sophistication of the methods for analyzing these new models.Nevertheless, a well-known problem that has persistently troubled phylogenetic inference is that of substitution rate variation among lineages.
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.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. 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.For example, local molecular clock models estimate a separate molecular rate for each user-circumscribed group of branches in the tree [6,13,16].