Analysis of plastid and nuclear DNA data in plant phylogenetics-evaluation and improvement

doi:10.1007/s11427-014-4620-7

	Analysis of plastid and nuclear DNA data in plant phylogenetics-evaluation and improvement
	Wang Wei; Li HongLei; Chen ZhiDuan
	2014
发表期刊	SCIENCE CHINA-LIFE SCIENCES
ISSN	1674-7305
卷号	57 期号:3 页码:280-286
摘要	Correct combination of plastid (cp) and nuclear (nr) DNA data for plant phylogenetic reconstructions is not a new issue, but with an increasing number of nrDNA loci being used, it is of ever greater practical concern. For accurately reconstructing the phylogeny and evolutionary history of plant groups, correct treatment of phylogenetic incongruence is a vital step in the proper analysis of cpDNA and nrDNA data. We first evaluated the current status of analyzing cpDNA and nrDNA data by searching all articles published in the journal Systematic Botany between 2005 and 2011. Many studies combining cpDNA and nrDNA data did not rigorously assess the combinability of the data sets, or did not address in detail possible reasons for incongruence between the two data sets. By reviewing various methods, we outline a procedure to more accurately analyze and/or combine cpDNA and nrDNA data, which includes four steps: identifying significant incongruence, determining conflicting taxa, providing possible interpretations for incongruence, and reconstructing the phylogeny after treating incongruence. Particular attention is given to explanation of the cause of incongruence. We hope that our procedure will help raise awareness of the importance of rigorous analysis and help identify the cause of incongruence before combining cpDNA and nrDNA data.
关键词	combined analysis plastid DNA incongruence nuclear DNA phylogenetics
学科领域	Biology
DOI	10.1007/s11427-014-4620-7
收录类别	SCI
语种	英语
WOS关键词	SPECIES TREE ; SENECIONEAE ASTERACEAE ; RHUS ANACARDIACEAE ; MOLECULAR EVIDENCE ; GENE-SEQUENCES ; DATA SETS ; HYBRIDIZATION ; CHLOROPLAST ; INCONGRUENCE ; EVOLUTION
WOS研究方向	Life Sciences & Biomedicine - Other Topics
WOS记录号	WOS:000332740100003
出版者	SCIENCE PRESS
文献子类	Review
出版地	BEIJING
EISSN	1869-1889
资助机构	National Natural Science Foundation of China [31270269, 30800059, 30990241] ; Knowledge Innovation Program of the Chinese Academy of Sciences [KSCX2-EW-Z-2]
作者邮箱	wangwei1127@ibcas.ac.cn
作品OA属性	hybrid
引用统计	被引频次：34[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/27158
专题	系统与进化植物学国家重点实验室
作者单位	Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Wang Wei,Li HongLei,Chen ZhiDuan. Analysis of plastid and nuclear DNA data in plant phylogenetics-evaluation and improvement[J]. SCIENCE CHINA-LIFE SCIENCES,2014,57(3):280-286.
APA	Wang Wei,Li HongLei,&Chen ZhiDuan.(2014).Analysis of plastid and nuclear DNA data in plant phylogenetics-evaluation and improvement.SCIENCE CHINA-LIFE SCIENCES,57(3),280-286.
MLA	Wang Wei,et al."Analysis of plastid and nuclear DNA data in plant phylogenetics-evaluation and improvement".SCIENCE CHINA-LIFE SCIENCES 57.3(2014):280-286.

条目包含的文件
文件名称/大小	文献类型	版本类型	开放类型	使用许可
Wang-2014-Analysis o（464KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	浏览请求全文