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

文献类型：期刊论文

作者Lu, Limin; Cox, Cymon J.; Mathews, Sarah2; Wang, Wei; Wen, Jun4; Chen, Zhiduan
刊名CLADISTICS
出版日期2018
卷号34期号:1页码:57-77
ISSN号0748-3007
DOI10.1111/cla.12191
文献子类Article
英文摘要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.
学科主题Evolutionary Biology ; Zoology
出版地HOBOKEN
电子版国际标准刊号1096-0031
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
语种英语
WOS记录号WOS:000419691500003
出版者WILEY
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]
源URL[http://ir.ibcas.ac.cn/handle/2S10CLM1/20489]  
专题植物研究所_系统与进化植物学研究中心_系统与进化植物学研究中心_学位论文
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.Smithsonian Inst, Natl Museum Nat Hist, Dept Bot, MRC166, Washington, DC 20013 USA
4.Australian Natl Herbarium, CSIRO Natl Res Collect, Canberra, ACT 2601, Australia
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.

入库方式： OAI收割

来源：植物研究所

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