Wurff, Andre vander <Andre.vanderWurff at wur.nl> wrote:
> we have used MrBayes software on about 400 full length 18S rDNA (1700
> bp)with the TGR model of evolution. With MrBayes, the bootstrap support
> for deeper (and basically all) phylogenetic nodes is strikingly high
> (about 100%). Does anybody have the same experience with MrBayes ? Does
> anybody know some relevant literature on this ? (Our NJ trees with PAUP
> have remarkably low support at deeper nodes).
The differences between nonparametric bootstrap values and posterior
probabilities are discussed in
Huelsenbeck JP, Larget B, Miller RE, Ronquist F (2002). Potential
applications and pitfalls of Bayesian inference in phylogeny. Systematic
Biology 51: 673-688.
In my analyses, I also encountered high posterior probabilites at internal
branches with moderate to no bootstrap support (for distance as well as for
maximum parsimony and maximum likelihood bootstraps; I can do the latter
because my data sets are smaller), but the consensus tree of the Bayesian
analysis usually is in congruence with the maximum likelihood tree. It
seemingly is not yet clear whether the nonparametric bootstrap is more
biased than the posterior probabilities or vice versa. But there have been
some papers addressing a possible bias in nonparametric bootstrapping and
according to the discussion in the Huelsenbeck et al. publication above,
there are also some publications around introducing corrected bootstrapping
procedures (which I haven't read yet).
BTW, issue 51 of Systematic Biology comes with a whole bunch of articles
addressing different aspects of Bayesian analysis.
Dr. Kerstin Hoef-Emden=09=09=09Gyrhofstr. 15
Universit=E4t zu K=F6ln=09=09=0950931 K=F6ln