RT Journal Article
SR Electronic
T1 Boosting Felsenstein’s Phylogenetic Bootstrap
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 154542
DO 10.1101/154542
A1 F. Lemoine
A1 J.-B. Domelevo Entfellner
A1 E. Wilkinson
A1 T. De Oliveira
A1 O. Gascuel
YR 2017
UL http://biorxiv.org/content/early/2017/06/23/154542.abstract
AB Felsenstein’s 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, Felsenstein’s 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 Felsenstein’s bootstrap fails to do so.