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2008), have made the Bayesian MCMC approach increasingly popular in phylogenetic studies.
To date, the suitability of Bayesian relaxed clock analyses of divergence times in shallow phylogenies has not been rigorously assessed. Most previous investigations of relaxed clock Bayesian dating have used longer more divergent sequences in which the likelihood has a greater influence on the posterior.
Bayesian methods are increasingly being used to estimate divergence times without the restrictive assumption of a global clock.
Little is known about their reliability for shallow phylogenies where DNA sequence divergence is low.
This is implemented in the program MCMCTREE (Rannala and Yang 2007; Yang and Rannala 2006; Yang 2007).