Applying the Bootstrap in Phylogeny Reconstruction

With the increasing emphasis in biology on reconstruction of phylogenetic trees, questions have arisen as to how confident one should be in a given phylogenetic tree and how support for phylogenetic trees should be measured. Felsenstein suggested that bootstrapping be applied across characters of a taxon-by-character data matrix to produce replicate "bootstrap data sets," each of which is then analyzed phylogenetically, with a consensus tree constructed to summarize the results of all replicates. The proportion of trees/replicates in which a grouping is recovered is presented as a measure of support for that group. Bootstrapping has become a common feature of phylogenetic analysis. However, the interpretation of bootstrap values remains open to discussion, and phylogeneticists have used these values in multiple ways. The usefulness of phylogenetic bootstrapping is potentially limited by a number of features, such as the size of the data matrix and the underlying assu! mptions of the phylogeny reconstruction program. Recent studies have explored the application of bootstrapping to large data sets and the relative performance of bootstrapping and jackknifing.