BOOTSTRAPPING PHYLOGENIES - LARGE DEVIATIONS AND DISPERSION EFFECTS

A large deviation result is established for the bootstrap empirical di stribution in a finite sample space, thereby validating both nonparame tric and parametric bootstrapping in certain phylogenetic inference pr oblems. The bias previously observed in the bootstrap distribution of the estimated tree topology is shown to stem from dispersion effects i n the joint distribution of sample and bootstrap empirical distributio ns. Both results are examined for maximum likelihood estimation in a t hree-taxon model having particularly simple geometry. They are also ap plicable to discrete parameter problems outside of phylogenetic infere nce.