Assessment of the reliability of a given phylogenetic hypothesis is an important 
step in phylogenetic analysis. Historically, the nonparametric bootstrap 
procedure has been the most frequently used method for assessing the support for 
specific phylogenetic relationships. The recent employment of Bayesian methods 
for phylogenetic inference problems has resulted in clade support being 
expressed in terms of posterior probabilities. We used simulated data and the 
four-taxon case to explore the relationship between nonparametric bootstrap 
values (as inferred by maximum likelihood) and posterior probabilities (as 
inferred by Bayesian analysis). The results suggest a complex association 
between the two measures. Three general regions of tree space can be identified: 
(1) the neutral zone, where differences between mean bootstrap and mean 
posterior probability values are not significant, (2) near the two-branch 
corner, and (3) deep in the two-branch corner. In the last two regions, 
significant differences occur between mean bootstrap and mean posterior 
probability values. Whether bootstrap or posterior probability values are higher 
depends on the data in support of alternative topologies. Examination of star 
topologies revealed that both bootstrap and posterior probability values differ 
significantly from theoretical expectations; in particular, there are more 
posterior probability values in the range 0.85-1 than expected by theory. 
Therefore, our results corroborate the findings of others that posterior 
probability values are excessively high. Our results also suggest that 
extrapolations from single topology branch-length studies are unlikely to 
provide any general conclusions regarding the relationship between bootstrap and 
posterior probability values.