Assessing significance [JF 20]

With the exception of Bayesian analysis, phylogenetic inference procedures typically identify a best estimate of phylogenetic relationships, a so called point estimate of the phylogeny. However, the point estimate is often relatively uninteresting in itself unless we have some measure of its reliability. This lecture will be about techniques for examining the robustness or significance of the results of phylogenetic analysis. The techniques can be divided into non-parametric and parametric approaches. The non-parametric methods are quite general in that they can be combined with any approach to phylogenetic inference; the parametric approaches, however, rely on stochastic models. Five different methods will be discussed here, three of which are non-parametric (permutation tests, jackknifing and bootstrapping) and two of which are parametric (parametric bootstrapping and posterior predictive distributions).