The Asymptotic Behavior of Bootstrap Support Values in Molecular Phylogenetics

doi:10.1093/sysbio/syaa100

CSpace > 应用数学研究所

	The Asymptotic Behavior of Bootstrap Support Values in Molecular Phylogenetics
	Huang, Jun 1,2; Liu, Yuting 1; Zhu, Tianqi3 ; Yang, Ziheng 2
	2021-07-01
发表期刊	SYSTEMATIC BIOLOGY
ISSN	1063-5157
卷号	70 期号:4 页码:774-785
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.
关键词	Bootstrap model selection star-tree paradox support value
DOI	10.1093/sysbio/syaa100
收录类别	SCI
语种	英语
WOS研究方向	Evolutionary Biology
WOS类目	Evolutionary Biology
WOS记录号	WOS:000671573900010
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/58918
专题	应用数学研究所
通讯作者	Liu, Yuting; Zhu, Tianqi; Yang, Ziheng
作者单位	1.Beijing Jiaotong Univ, Dept Math, Beijing 100044, Peoples R China 2.UCL, Dept Genet Evolut & Environm, Gower St, London WC1E 6BT, England 3.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Key Lab Random Complex Struct,Data Sci, Beijing 100000, 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.