Journal ArticleDOI
Phylogenetic analysis of the grape family (Vitaceae) based on the noncoding plastid trnC-petN, trnH-psbA, and trnL-F sequences
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This article is published in Taxon.The article was published on 2011-06-01. It has received 63 citations till now.read more
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Journal ArticleDOI
Natural stilbenoids: distribution in the plant kingdom and chemotaxonomic interest in Vitaceae
TL;DR: This review focuses on the distribution of stilbenes and 2-arylbenzofuran derivatives in the plant kingdom, the chemical structure of stILbenes in the Vitaceae family and their taxonomic implication.
Journal ArticleDOI
Using nuclear gene data for plant phylogenetics: progress and prospects.
Elizabeth A. Zimmer,Jun Wen +1 more
TL;DR: The paper reviews the current state of low and single copy nuclear markers that have been applied successfully in plant phylogenetics to date, and discusses case studies highlighting the potential of massively parallel high throughput or next-generation sequencing approaches for molecular phylogenetic and evolutionary investigations.
Journal ArticleDOI
Massive Mitochondrial Gene Transfer in a Parasitic Flowering Plant Clade
Zhenxiang Xi,Yuguo Wang,Robert K. Bradley,M. Sugumaran,Christopher J. Marx,Joshua S. Rest,Charles C. Davis +6 more
TL;DR: This study is the first to comprehensively assess the magnitude of HGT in plants involving a genome and a species interaction where it has been hypothesized to be potentially rampant, and indicates that HGT involving mitochondrial genes is substantially higher than previously thought.
Journal ArticleDOI
Transcriptome sequences resolve deep relationships of the grape family.
Jun Wen,Zhiqiang Xiong,Ze-Long Nie,Likai Mao,Yabing Zhu,Xianzhao Kan,Stefanie M. Ickert-Bond,Jean M. Gerrath,Elizabeth A. Zimmer,Xiao Dong Fang +9 more
TL;DR: The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous, and the pros and cons of transcriptomic data for phylogenetic inference in plants.
Journal ArticleDOI
Congruent Deep Relationships in the Grape Family (Vitaceae) Based on Sequences of Chloroplast Genomes and Mitochondrial Genes via Genome Skimming.
TL;DR: The topology based on either plastome data or mitochondrial genes is congruent with the one using hundreds of nuclear genes, indicating that the grape family did not exhibit significant reticulation at the deep level.
References
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Journal ArticleDOI
Confidence limits on phylogenies: an approach using the bootstrap.
TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
Journal ArticleDOI
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
TL;DR: ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results.
Journal ArticleDOI
MrBayes 3: Bayesian phylogenetic inference under mixed models
TL;DR: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models to analyze heterogeneous data sets and explore a wide variety of structured models mixing partition-unique and shared parameters.
Journal ArticleDOI
MODELTEST: testing the model of DNA substitution.
David Posada,Keith A. Crandall +1 more
TL;DR: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.
Journal ArticleDOI
Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology
TL;DR: A method is presented that is asserted to provide all hypothetical ancestral character states that are consistent with describing the descent of the present-day character states in a minimum number of changes of state using a predetermined phylogenetic relationship among the taxa represented.
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