Statistical tests of molecular phylogenies
Résumé
This chapter provides a summary of methods for testing the significance of inferred phylogenies. In terms of parsimony a nucleotide site is informative (useful) for choosing among the three trees only if it is in the same state in two of the four species and in another state in the other two species. Under the assumption of rate constancy, an informative site has a higher probability of supporting the true tree and a lower probability of supporting each of the two other trees. Instead of testing the significance of an inferred phylogeny, it is simpler to test the significance of estimated intemodal distances. Like the jackknife, the bootstrap is a method of resampling the data under study to infer the variability of the estimate. This method was introduced into phylogenetic studies by Felsenstein. It is not a tree-making method but a statistical method that can be used to evaluate the confidence level of a phylogenetic estimate obtained from a data set by a tree-making method.