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Should genes with missing data be excluded from phylogenetic analyses?
Jiang, Wei1,2,3; Chen, Si-Yun2; Wang, Hong1,2,3; Li, De-Zhu1,2,3; Wiens, John J.4; 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; chensiyun@mail.kib.ac.cn; wanghong@mail.kib.ac.cn; dzl@mail.kib.ac.cn; wiensj@email.arizona.edu
2014-11-01
发表期刊MOLECULAR PHYLOGENETICS AND EVOLUTION
ISSN1055-7903 ; 1055-7903
卷号80期号:18B页码:308-318
产权排序第一 ; 第一
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.
关键词Accuracy Maximum Likelihood Missing Data Phylogeny
资助信息National Natural Science Foundation of China [31360081]; National Natural Science Foundation of China [31360081]; 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]; Major Science and Technology Program [110201101003-TS-03, 2011YN02, 2011YN03]; Major Science and Technology Program [110201101003-TS-03, 2011YN02, 2011YN03]
学科领域Biochemistry & Molecular Biology ; Biochemistry & Molecular Biology ; Evolutionary Biology ; Evolutionary Biology ; Genetics & Heredity ; Genetics & Heredity
DOI10.1016/j.ympev.2014.08.006
收录类别SCI
语种英语
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:000343742200027
引用统计
被引频次:49[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.kib.ac.cn/handle/151853/18514
专题中国西南野生生物种质资源库
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.; jiangwei@mail.kib.ac.cn; chensiyun@mail.kib.ac.cn; wanghong@mail.kib.ac.cn; dzl@mail.kib.ac.cn; wiensj@email.arizona.edu
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
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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..,...&wiensj@email.arizona.edu.(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.
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