Therefore, it may be advantageous to exclude them from the diagnostic.Mr Bayes allows the user to set a cutoff frequency (default value 0.10); all splits or clades occurring minimally at that frequency in at least one of the runs will be incorporated in the ASDSF.
The addition of new fossil pollen calibrations led to older crown ages than have previously been found for tribes such as Eucalypteae and Myrteae.
Estimates of rate variation among lineages were affected by the choice of calibrations, suggesting that the use of multiple calibrations can improve estimates of rate heterogeneity among lineages.
Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method.
The new version provides more output options than previously, including samples of ancestral states, site rates, site Bayesian Markov chain Monte Carlo (MCMC) methods quickly gained in popularity after they were introduced in statistical phylogenetics in the late 1990's (Mau and Newton 1997, Yang and Rannala 1997, Larget and Simon 1999, Mau et al. This was due to the inherent advantages of the approach but also to the availability of easy-to-use software packages, such as Mr Bayes (Huelsenbeck and Ronquist 2001).
ASDSF is calculated by comparing split or clade frequencies across multiple independent MCMC runs that ideally should be started from different randomly chosen starting trees (Lakner et al. ASDSF should approach 0.0 as runs converge to the same distribution.
The frequencies of rare splits or clades are difficult to estimate accurately and these groupings are usually of marginal interest.
With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003.
The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly.
These fossils were used to inform age constraints in a Bayesian phylogenetic analysis of a sequence alignment comprising two sequences from the chloroplast genome (mat K and ndh F) and one nuclear locus (ITS), sampled from 106 taxa representing 80 genera.