Should genes with missing data be excluded from phylogenetic analyses?

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	Should genes with missing data be excluded from phylogenetic analyses?
	Jiang, Wei 1,2,3; Chen, Si-Yun 2; Wang, Hong1,2,3 ; Li, De-Zhu1,2,3 ; Wiens, John J.4
刊名	MOLECULAR PHYLOGENETICS AND EVOLUTION
	2014-11-01
卷号	80 期号:18B 页码:308-318
关键词	Accuracy Maximum likelihood Missing data Phylogeny
ISSN号	1055-7903 ; 1055-7903
通讯作者	Li,DZ (reprint author),Chinese Acad Sci,Kunming Inst Bot,Key Lab Plant Divers & Biogeog East Asia,Kunming 650201,Yunnan,Peoples R China. ; Li,DZ (reprint author),Chinese Acad Sci,Kunming Inst Bot,Key Lab Plant Divers & Biogeog East Asia,Kunming 650201,Yunnan,Peoples R China. ; jiangwei@mail.kib.ac.cn ; jiangwei@mail.kib.ac.cn ; chensiyun@mail.kib.ac.cn ; chensiyun@mail.kib.ac.cn ; wanghong@mail.kib.ac.cn ; wanghong@mail.kib.ac.cn ; dzl@mail.kib.ac.cn ; dzl@mail.kib.ac.cn ; wiensj@email.arizona.edu ; wiensj@email.arizona.edu
产权排序	第一 ; 第一
英文摘要	Phylogeneticists often design their studies to maximize the number of genes included but minimize the overall amount of missing data. However, few studies have addressed the costs and benefits of adding characters with missing data, especially for likelihood analyses of multiple loci. In this paper, we address this topic using two empirical data sets (in yeast and plants) with well-resolved phylogenies. We introduce varying amounts of missing data into varying numbers of genes and test whether the benefits of excluding genes with missing data outweigh the costs of excluding the non-missing data that are associated with them. We also test if there is a proportion of missing data in the incomplete genes at which they cease to be beneficial or harmful, and whether missing data consistently bias branch length estimates. Our results indicate that adding incomplete genes generally increases the accuracy of phylogenetic analyses relative to excluding them, especially when there is a high proportion of incomplete genes in the overall dataset (and thus few complete genes). Detailed analyses suggest that adding incomplete genes is especially helpful for resolving poorly supported nodes. Given that we find that excluding genes with missing data often decreases accuracy relative to including these genes (and that decreases are generally of greater magnitude than increases), there is little basis for assuming that excluding these genes is necessarily the safer or more conservative approach. We also find no evidence that missing data consistently bias branch length estimates. (C) 2014 Elsevier Inc. All rights reserved.
学科主题	Biochemistry & Molecular Biology;Evolutionary Biology;Genetics & Heredity ; Biochemistry & Molecular Biology;Evolutionary Biology;Genetics & Heredity
类目[WOS]	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
研究领域[WOS]	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
关键词[WOS]	DATA SETS ; INCOMPLETE TAXA ; SPECIES TREES ; MAXIMUM-LIKELIHOOD ; BAYESIAN-INFERENCE ; ACCURACY ; PHYLOGENOMICS ; LEPIDOPTERA ; CHARACTERS ; SELECTION
收录类别	SCI
资助信息	National Natural Science Foundation of China [31360081]; Major Science and Technology Program [110201101003-TS-03, 2011YN02, 2011YN03]; National Natural Science Foundation of China [31360081]; Major Science and Technology Program [110201101003-TS-03, 2011YN02, 2011YN03]
语种	英语
WOS记录号	WOS:000343742200027
公开日期	2015-01-20 ; 2015-01-20
内容类型	期刊论文
源URL	[http://ir.kib.ac.cn/handle/151853/18514]
专题	昆明植物研究所_中国西南野生生物种质资源库
作者单位	1.Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China 2.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Plant Germplasm & Genom Ctr, Kunming 650201, Yunnan, Peoples R China 3.Univ Chinese Acad Sci, Kunming Coll Life Sci, Kunming 650201, Yunnan, Peoples R China 4.Univ Arizona, Dept Ecol & Evolutionary Biol, Tucson, AZ 85721 USA
推荐引用方式 GB/T 7714	Jiang, Wei,Chen, Si-Yun,Wang, Hong,et al. Should genes with missing data be excluded from phylogenetic analyses?[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2014,80(18B):308-318.
APA	Jiang, Wei,Chen, Si-Yun,Wang, Hong,Li, De-Zhu,&Wiens, John J..(2014).Should genes with missing data be excluded from phylogenetic analyses?.MOLECULAR PHYLOGENETICS AND EVOLUTION,80(18B),308-318.
MLA	Jiang, Wei,et al."Should genes with missing data be excluded from phylogenetic analyses?".MOLECULAR PHYLOGENETICS AND EVOLUTION 80.18B(2014):308-318.