Renewing Felsenstein’s phylogenetic Bootstrap in the era of big data
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Date
2018
Journal Title
Journal ISSN
Volume Title
Publisher
Nature Publishing Group
Abstract
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.
Description
Keywords
Felsenstein, Bootstrap method, Phylogenetic inferences
Citation
Lemoine, F. (2018). Renewing Felstein’s phylogenetic Bootstrap in the era of big data. Nature, 556: 452 – 456.