Resolving the systematic positions of enigmatic taxa: Manipulating the chloroplast genome data of Saxifragales

doi:10.1016/j.ympev.2018.04.033

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	Resolving the systematic positions of enigmatic taxa: Manipulating the chloroplast genome data of Saxifragales
	Dong, Wenpan 3; Xu, Chao 2; Wu, Ping 2; Cheng, Tao ; Yu, Jing ; Zhou, Shiliang 2; Hong, De-Yuan
刊名	MOLECULAR PHYLOGENETICS AND EVOLUTION
	2018
卷号	126 页码:321-330
关键词	Analytical methodology Paeoniaceae Phylogenomics Saxifragales Systematics error
ISSN号	1055-7903
DOI	10.1016/j.ympev.2018.04.033
文献子类	Article
英文摘要	Accurately resolving the phylogeny of enigmatic taxa is always a challenge in phylogenetic inference. Such uncertainties could be due to systematic errors or model violations. Here, we provide an example demonstrating how these factors affect the positioning of Paeoniaceae within Saxifragales based on chloroplast genome data. We newly assembled 14 chloroplast genomes from Saxifragales, and by combining these genomes with those of 63 other angiosperms, three datasets were assembled to test different hypotheses proposed by recent studies. These datasets were subjected to maximum parsimony, maximum likelihood and Bayesian analyses with site-homogeneous/heterogeneous models, different data partitioning strategies, and the inclusion/exclusion of weak phylogenetic signals. Three datasets exhibited remarkable heterogeneity among sites and among taxa of Saxifragales. Phylogenetic analyses under homogeneous models or maximum parsimony showed a closer relationship of Paeoniaceae with herbaceous families in the order. Data partitioning strategies did not change the general tree topology. However, PhyloBayes analysis under the CAT + GTR model resulted in a relationship closer to woody families. We conclude that although genomic data significantly increase the phylogenetic resolution of enigmatic taxa with high support, the phylogenetic results inferred from such data might be analysis or signal dependent. The analytical pipeline outlined here combines phylogenomic inference methods with evaluation of lineage-specific rates of substitution, model selection, and assessment of systematic error. These methods would be applicable to resolve similar difficult questions in the tree of life.
学科主题	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
电子版国际标准刊号	1095-9513
出版地	SAN DIEGO
WOS关键词	EARLY LAND PLANTS ; PHYLOGENETIC-RELATIONSHIPS ; HETEROGENEOUS MODELS ; OUTGROUP SELECTION ; SCALE DATA ; PHYLOGENOMICS ; ANGIOSPERMS ; EVOLUTION ; PERFORMANCE ; ANCIENT
语种	英语
出版者	ACADEMIC PRESS INC ELSEVIER SCIENCE
WOS记录号	WOS:000437663900029
资助机构	NSFCNational Natural Science Foundation of China (NSFC) [30930010, 31270239]
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/20566]
专题	系统与进化植物学国家重点实验室
作者单位	1.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 2.Peking Univ, Acad Adv Interdisciplinary Studies, Peking Tsinghua Ctr Life Sci, Beijing 100871, Peoples R China 3.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, 20 Nanxincun, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Dong, Wenpan,Xu, Chao,Wu, Ping,et al. Resolving the systematic positions of enigmatic taxa: Manipulating the chloroplast genome data of Saxifragales[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2018,126:321-330.
APA	Dong, Wenpan.,Xu, Chao.,Wu, Ping.,Cheng, Tao.,Yu, Jing.,...&Hong, De-Yuan.(2018).Resolving the systematic positions of enigmatic taxa: Manipulating the chloroplast genome data of Saxifragales.MOLECULAR PHYLOGENETICS AND EVOLUTION,126,321-330.
MLA	Dong, Wenpan,et al."Resolving the systematic positions of enigmatic taxa: Manipulating the chloroplast genome data of Saxifragales".MOLECULAR PHYLOGENETICS AND EVOLUTION 126(2018):321-330.