Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)

doi:10.1111/cla.12191

	Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)
	Lu, Limin ; Cox, Cymon J.; Mathews, Sarah 2; Wang, Wei ; Wen, Jun 3; Chen, Zhiduan
	2018
发表期刊	CLADISTICS
ISSN	0748-3007
卷号	34 期号:1 页码:57-77
摘要	Evolutionary rate heterogeneity and rapid radiations are common phenomena in organismal evolution and represent major challenges for reconstructing deep-level phylogenies. Here we detected substantial conflicts in and among data sets as well as uncertainty concerning relationships among lineages of Vitaceae from individual gene trees, supernetworks and tree certainty values. Congruent deep-level relationships of Vitaceae were retrieved by comprehensive comparisons of results from optimal partitioning analyses, multispecies coalescent approaches and the Bayesian concordance method. We found that partitioning schemes selected by PartitionFinder were preferred over those by gene or by codon position, and the unpartitioned model usually performed the worst. For a data set with conflicting signals, however, the unpartitioned model outperformed models that included more partitions, demonstrating some limitations to the effectiveness of concatenation for these data. For a transcriptome data set, fast coalescent methods (STAR and MP-EST) and a Bayesian concordance approach yielded congruent topologies with trees from the concatenated analyses and previous studies. Our results highlight that well-resolved gene trees are critical for the effectiveness of coalescent-based methods. Future efforts to improve the accuracy of phylogenomic analyses should emphasize the development of newmethods that can accommodate multiple biological processes and tolerate missing data while remaining computationally tractable. (C) The Willi Hennig Society 2017.
学科领域	Evolutionary Biology ; Zoology
DOI	10.1111/cla.12191
收录类别	SCI
语种	英语
WOS关键词	PLANT PHYLOGENETICS PROGRESS ; ESTIMATING SPECIES TREES ; LONG-BRANCH ATTRACTION ; NUCLEAR GENE DATA ; EARLY LAND PLANTS ; PARTHENOCISSUS VITACEAE ; CHARACTER EVOLUTION ; MOLECULAR PHYLOGENY ; SEQUENCE ALIGNMENT ; MAXIMUM-LIKELIHOOD
WOS记录号	WOS:000419691500003
出版者	WILEY
文献子类	Article
出版地	HOBOKEN
EISSN	1096-0031
资助机构	National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [NNSF 31500179, 31590822, 31270268] ; National Basic Research Program of ChinaNational Basic Research Program of China [2014CB954101] ; National Science FoundationNational Science Foundation (NSF) [DEB0743474] ; Smithsonian Scholarly Studies Grant Program and the Endowment Grant Program ; CAS/SAFEA International Partnership Program for Creative Research TeamsChinese Academy of Sciences ; Laboratory of Analytical Biology of the National Museum of Natural History, Smithsonian InstitutionSmithsonian InstitutionSmithsonian National Museum of Natural History ; Science and Technology Basic Work [2013FY112100]
作者邮箱	wenj@si.edu ; zhiduan@ibcas.ac.cn
作品OA属性	Green Submitted, Bronze
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/2S10CLM1/20489
专题	系统与进化植物学国家重点实验室
作者单位	1.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 2.Cox, Cymon J.] Univ Algarve, Ctr Ciencias Mar, P-8005319 Faro, Portugal 3.Australian Natl Herbarium, CSIRO Natl Res Collect, Canberra, ACT 2601, Australia 4.Smithsonian Inst, Natl Museum Nat Hist, Dept Bot, MRC166, Washington, DC 20013 USA
推荐引用方式 GB/T 7714	Lu, Limin,Cox, Cymon J.,Mathews, Sarah,et al. Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)[J]. CLADISTICS,2018,34(1):57-77.
APA	Lu, Limin,Cox, Cymon J.,Mathews, Sarah,Wang, Wei,Wen, Jun,&Chen, Zhiduan.(2018).Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae).CLADISTICS,34(1),57-77.
MLA	Lu, Limin,et al."Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)".CLADISTICS 34.1(2018):57-77.

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