Complexity of the simplest species tree problem

doi:10.1093/molbev/msab009

CSpace > 应用数学研究所

	Complexity of the simplest species tree problem
	Zhu, Tianqi1,2 ; Yang, Ziheng 1,3
	2021-09-01
发表期刊	MOLECULAR BIOLOGY AND EVOLUTION
ISSN	0737-4038
卷号	38 期号:9 页码:3993-4009
摘要	The multispecies coalescent model provides a natural framework for species tree estimation accounting for gene-tree conflicts. Although a number of species tree methods under the multispecies coalescent have been suggested and evaluated using simulation, their statistical properties remain poorly understood. Here, we use mathematical analysis aided by computer simulation to examine the identifiability, consistency, and efficiency of different species tree methods in the case of three species and three sequences under the molecular clock. We consider four major species-tree methods including concatenation, two-step, independent-sites maximum likelihood, and maximum likelihood. We develop approximations that predict that the probit transform of the species tree estimation error decreases linearly with the square root of the number of loci. Even in this simplest case, major differences exist among the methods. Full-likelihood methods are considerably more efficient than summary methods such as concatenation and two-step. They also provide estimates of important parameters such as species divergence times and ancestral population sizes,whereas these parameters are not identifiable by summary methods. Our results highlight the need to improve the statistical efficiency of summary methods and the computational efficiency of full likelihood methods of species tree estimation.
关键词	concatenation efficiency molecular clock MSC multispecies coalescent species tree
DOI	10.1093/molbev/msab009
收录类别	SCI
语种	英语
资助项目	Biotechnology and Biological Sciences Research Council[BB/P006493/1] ; BBSRC equipment grant[BB/R01356X/1] ; Natural Science Foundation[32070685] ; Natural Science Foundation[31671370] ; Youth Innovation Promotion Association of Chinese Academy of Sciences[201901]
WOS研究方向	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS类目	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS记录号	WOS:000693664800036
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/59243
专题	应用数学研究所
通讯作者	Yang, Ziheng
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Inst Appl Math, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Acad Math & Syst Sci, Key Lab Random Complex Struct & Data Sci, Beijing 100190, Peoples R China 3.UCL, Dept Genet, Gower St, London WC1E 6BT, England
推荐引用方式 GB/T 7714	Zhu, Tianqi,Yang, Ziheng. Complexity of the simplest species tree problem[J]. MOLECULAR BIOLOGY AND EVOLUTION,2021,38(9):3993-4009.
APA	Zhu, Tianqi,&Yang, Ziheng.(2021).Complexity of the simplest species tree problem.MOLECULAR BIOLOGY AND EVOLUTION,38(9),3993-4009.
MLA	Zhu, Tianqi,et al."Complexity of the simplest species tree problem".MOLECULAR BIOLOGY AND EVOLUTION 38.9(2021):3993-4009.