Relaxed phylogenetics and dating with confidence drummond
Essentially, such models are only useful in cases in which there is a strong prior hypothesis that the rate of specific taxa will differ from the rest of the tree [ 6].Bayesian relaxed-clock methods, including those published by Thorne et al.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.Such problems with the molecular clock hypothesis have resulted in it being abandoned almost entirely for phylogenetic inference in favor of a model that assumes that every branch has an independent rate of molecular evolution.Under such an assumption, it is possible to infer phylogenies (e.g., [ 9, 10]), but not to estimate molecular rates or divergence times, because the individual contributions of rate and time to molecular evolution cannot be separated.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.
If the rate and time along each branch can only be estimated as their product, then the position of the root of the tree cannot be estimated without additional assumptions such as an outgroup or a non-reversible substitution process.
This unrooted alternative to the molecular clock was first suggested by Felsenstein [ 10] and has formed the basis of all modern phylogenetic inference and is implemented in all major phylogenetic packages (e.g., PHYLIP [ 11], PAUP* [ 12], and Mr Bayes [ 9]).
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.In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum.