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The asymptotic behavior of bootstrap support values in molecular phylogenetics

Huang, J; Liu, Y; Zhu, T; Yang, Z; (2021) The asymptotic behavior of bootstrap support values in molecular phylogenetics. Systematic Biology , 70 (4) pp. 774-785. 10.1093/sysbio/syaa100. Green open access

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Abstract

The phylogenetic bootstrap is the most commonly used method for assessing statistical confidence in estimated phylogenies by non-Bayesian methods such as maximum parsimony and maximum likelihood (ML). It is observed that bootstrap support tends to be high in large genomic datasets whether or not the inferred trees and clades are correct. Here we study the asymptotic behavior of bootstrap support for the ML tree in large datasets when the competing phylogenetic trees are equally right or equally wrong. We consider phylogenetic reconstruction as a problem of statistical model selection when the compared models are nonnested and misspecified. The bootstrap is found to have qualitatively different dynamics from Bayesian inference, and does not exhibit the polarized behavior of posterior model probabilities, consistent with the empirical observation that the bootstrap is more conservative than Bayesian probabilities. Nevertheless bootstrap support similarly shows fluctuations among large datasets, with no convergence to a point value, when the compared models are equally right or equally wrong. Thus in large datasets strong support for wrong trees or models is likely to occur. Our analysis provides a partial explanation for the high bootstrap support values for incorrect clades observed in empirical data analysis.

Type: Article
Title: The asymptotic behavior of bootstrap support values in molecular phylogenetics
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/sysbio/syaa100
Publisher version: https://doi.org/10.1093/sysbio/syaa100
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
Keywords: Bootstrap, model selection, star-tree paradox, support value
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/10118309
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