Boosting Felsenstein Phylogenetic Bootstrap

Abstract

Felsensteins article describing the application of the bootstrap to evolutionary trees, is one of the most cited papers of all time. That statistical method, based on resampling and replications, is used extensively to assess the robustness of phylogenetic inferences. However, increasing numbers of sequences are now available for a wide variety of species, and phylogenies with hundreds or thousands of taxa are becoming routine. In that framework, Felsensteins bootstrap tends to yield very low supports, especially on deep branches. We propose a revised version, in which the presence of inferred branches in replications is measured using a gradual \"transfer\" distance, as opposed to the original version using a binary presence/absence index. The resulting supports are higher, while not inducing falsely supported branches. Our method is applied to large simulation, mammal and HIV datasets, for which it reveals the phylogenetic signal, while Felsensteins bootstrap fails to do so.