The Asymptotic Behavior of Bootstrap Support Values in Molecular Phylogenetics

doi:10.1093/sysbio/syaa100

	The Asymptotic Behavior of Bootstrap Support Values in Molecular Phylogenetics
	Huang, Jun 2,3; Liu, Yuting 3; Zhu, Tianqi 1; Yang, Ziheng 2
刊名	SYSTEMATIC BIOLOGY
	2021-07-01
卷号	70 期号:4 页码:774-785
关键词	Bootstrap model selection star-tree paradox support value
ISSN号	1063-5157
DOI	10.1093/sysbio/syaa100
英文摘要	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 data sets 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 data sets 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 data sets, with no convergence to a point value, when the compared models are equally right or equally wrong. Thus, in large data sets 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.
WOS研究方向	Evolutionary Biology
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000671573900010
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/58917]
专题	中国科学院数学与系统科学研究院
通讯作者	Liu, Yuting; Zhu, Tianqi; Yang, Ziheng
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Key Lab Random Complex Struct,Data Sci, Beijing 100000, Peoples R China 2.UCL, Dept Genet Evolut & Environm, Gower St, London WC1E 6BT, England 3.Beijing Jiaotong Univ, Dept Math, Beijing 100044, Peoples R China
推荐引用方式 GB/T 7714	Huang, Jun,Liu, Yuting,Zhu, Tianqi,et al. The Asymptotic Behavior of Bootstrap Support Values in Molecular Phylogenetics[J]. SYSTEMATIC BIOLOGY,2021,70(4):774-785.
APA	Huang, Jun,Liu, Yuting,Zhu, Tianqi,&Yang, Ziheng.(2021).The Asymptotic Behavior of Bootstrap Support Values in Molecular Phylogenetics.SYSTEMATIC BIOLOGY,70(4),774-785.
MLA	Huang, Jun,et al."The Asymptotic Behavior of Bootstrap Support Values in Molecular Phylogenetics".SYSTEMATIC BIOLOGY 70.4(2021):774-785.