Phylogenetics and molecular clocks

[gkw@amnet.net.au]

For those interested in phylogenetics and molecular clocks, the following 
may be of interest.

PLoS Biology, Vol 4, Issue 5, 2006.
Relaxed Phylogenetics and Dating with Confidence

Alexei J. Drummond1¤, Simon Y. W. Ho1, Matthew J. Phillips1, Andrew Rambaut1*

1 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. 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. 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. We describe how it can be used to estimate 
phylogenies and divergence times in the face of uncertainty in evolutionary 
rates and calibration times. Our approach also provides a means for 
measuring the clocklikeness of datasets and comparing this measure between 
different genes and phylogenies. 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. 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.

Graeme Worth