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

2018-02Journal article Open access
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dc.contributor.authorLu, Limin
dc.contributor.authorCox, C. J.
dc.contributor.authorMathews, Sarah
dc.contributor.authorWang, Wei
dc.contributor.authorWen, Jun
dc.contributor.authorChen, Zhiduan
dc.date.accessioned2018-12-07T14:52:55Z
dc.date.available2018-12-07T14:52:55Z
dc.date.issued2018-02
dc.description.abstractEvolutionary 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.
dc.description.sponsorshipNational Natural Science Foundation of China [NNSF 31500179, 31590822, 31270268]; National Basic Research Program of China [2014CB954101]; National Science Foundation [DEB0743474]; Smithsonian Scholarly Studies Grant Program and the Endowment Grant Program; CAS/SAFEA International Partnership Program for Creative Research Teams; Laboratory of Analytical Biology of the National Museum of Natural History, Smithsonian Institution; Science and Technology Basic Work [2013FY112100]
dc.description.versioninfo:eu-repo/semantics/publishedVersion
dc.identifier.doi10.1111/cla.12191
dc.identifier.issn0748-3007
dc.identifier.issn1096-0031
dc.identifier.urihttp://hdl.handle.net/10400.1/11267
dc.language.isoeng
dc.peerreviewedyes
dc.publisherWiley
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectLong-branch attraction
dc.subjectMolecular phylogenetic analysis
dc.subjectEstimating species trees
dc.subjectNuclear gene data
dc.subjectEarly land plants
dc.subjectSeed plants
dc.subjectCompositional heterogeneity
dc.subjectChloroplast phylogenomics
dc.subjectParthenocissus vitaceae
dc.subjectCharacter evolution
dc.titleOptimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)
dc.typejournal article
dspace.entity.typePublication
oaire.citation.endPage77
oaire.citation.issue1
oaire.citation.startPage57
oaire.citation.titleCladistics
oaire.citation.volume34
person.familyNameCox
person.givenNameCymon
person.identifier.ciencia-id6B15-9771-1D04
person.identifier.orcid0000-0002-4927-979X
person.identifier.ridD-1303-2012
person.identifier.scopus-author-id7402112716
rcaap.rightsopenAccess
rcaap.typearticle
relation.isAuthorOfPublication82c3689c-60b6-440d-9d7b-49e6dbd6861b
relation.isAuthorOfPublication.latestForDiscovery82c3689c-60b6-440d-9d7b-49e6dbd6861b

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