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.
journal_name
Naturejournal_title
Natureauthors
Lemoine F,Domelevo Entfellner JB,Wilkinson E,Correia D,Dávila Felipe M,De Oliveira T,Gascuel Odoi
10.1038/s41586-018-0043-0subject
Has Abstractpub_date
2018-04-01 00:00:00pages
452-456issue
7702eissn
0028-0836issn
1476-4687pii
10.1038/s41586-018-0043-0journal_volume
556pub_type
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