Renewing Felsenstein’s Phylogenetic Bootstrap in the Era of Big Data

By Frédéric Lemoine, Jean-Baka Domelevo Entfellner, Eduan Wilkinson, Damien Correia, Miraine Dávila Felipe, Tulio de Oliveira, Olivier Gascuel. Nature, 2018

636 citations recorded by the source corpus.

Felsenstein’s application of the bootstrap method to evolutionary trees is one of the most cited scientific papers of all time. The bootstrap method, which is 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 based on hundreds or thousands of taxa are becoming routine. With phylogenies of this size Felsenstein’s bootstrap tends to yield very low supports, especially on deep branches. Here we propose a new version of the phylogenetic bootstrap in which the presence of inferred branches in replications is measured using a gradual ‘transfer’ distance rather than the binary presence or absence index used in Felsenstein’s original version. The resulting supports are higher and do not induce falsely supported branches. The application of our method to large mammal, HIV and simulated datasets reveals their phylogenetic signals, whereas Felsenstein’s bootstrap fails to do so. A new version of the phylogenetic bootstrap method enables assessment of the robustness of phylogenies that are based on large datasets of hundreds or thousands of taxa.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/00b0ae9246fb444b4862c4e4a40126d776974f7e

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Citations in the corpus

raxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML (2020, methodology): “Among the novel methods implemented in RAxML-NG, and available through raxmlGUI, is the Transfer Bootstrap Expectation algorithm to quantify topological support for a tree (Lemoine et al., 2018).”
Petabase-scale sequence alignment catalyses viral discovery (2020, methodology): “The pipeline also automatically produces versions of the best maximum likelihood tree annotated with Felsenstein’s Bootstrap ([103]) support values, and Transfer Bootstrap Expectation ([104]) values.”
NGPhylogeny.fr: new generation phylogenetic services for non-specialists (2019, methodology): “It is worth noticing that we integrated Felsenstein Bootstrap Proportions (FBP) and Transfer Bootstrap Expectation (TBE) (5) for branch support computation to several tree inference tools, which can be configured at this step and was not available in Phylogeny.”