Deep phylogenetic incongruence in the angiosperm clade Rosidae

scientific article

Deep phylogenetic incongruence in the angiosperm clade Rosidae is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1016/J.YMPEV.2014.11.003
P698PubMed publication ID25463749
P5875ResearchGate publication ID269175439

P50authorDouglas E. SoltisQ2373320
Pamela S. SoltisQ2876410
J. Gordon BurleighQ118164310
Zhi Duan ChenQ26712556
P2093author name stringMiao Sun
Xinyu Zhu
P2860cites workAn update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IIIQ13683362
Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiospermsQ21093401
A functional phylogenomic view of the seed plantsQ21144934
Mitochondrial matR sequences help to resolve deep phylogenetic relationships in rosidsQ21283923
Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicotsQ22066285
Paternal inheritance of chloroplast DNA in interspecific hybrids in the genus Larrea (Zygophyllaceae)Q73085810
A model for chloroplast captureQ79076936
Paternal inheritance of plastids in Medicago sativaQ86719006
High transmission of paternal plastid DNA in alfalfa plants demonstrated by restriction fragment polymorphic analysisQ86719187
Gene Trees and Species Trees: Molecular Systematics as One-Character TaxonomyQ95465824
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patternsQ22066341
The genome of woodland strawberry (Fragaria vesca)Q22122058
Broad phylogenomic sampling improves resolution of the animal tree of lifeQ22337246
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groupsQ24538674
MAFFT version 5: improvement in accuracy of multiple sequence alignmentQ24556683
Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolutionQ24561429
Rosid radiation and the rapid rise of angiosperm-dominated forestsQ24651414
A rapid bootstrap algorithm for the RAxML Web serversQ27860864
A survey of tricolpate (eudicot) phylogenetic relationshipsQ28239874
Phylogenomics and the reconstruction of the tree of lifeQ28247594
Genome-scale phylogeny and the detection of systematic biasesQ28256558
Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence timesQ28654622
From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomesQ28658690
Advances in the floral structural characterization of the major subclades of Malpighiales, one of the largest orders of flowering plantsQ28708907
Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysisQ28730813
Sources of signal in 62 protein-coding nuclear genes for higher-level phylogenetics of arthropodsQ28741772
Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene treesQ28742821
Reconstructing patterns of reticulate evolution in plantsQ28764677
Towards a phylogenetic nomenclature of TracheophytaQ28960391
Gene tree discordance, phylogenetic inference and the multispecies coalescentQ29614318
Inferring phylogeny despite incomplete lineage sortingQ29614322
Angiosperm phylogeny inferred from multiple genes as a tool for comparative biologyQ29618182
The age and diversification of the angiosperms re-revisitedQ29619385
Insect phylogenomics: exploring the source of incongruence using new transcriptomic dataQ30578291
Nonuniform concerted evolution and chloroplast capture: heterogeneity of observed introgression patterns in three molecular data partition phylogenies of Asian Mitella (saxifragaceae).Q30969983
Discordance of species trees with their most likely gene trees.Q33245076
Deciphering ancient rapid radiationsQ33273805
Using supernetworks to distinguish hybridization from lineage-sortingQ33351540
The role of hybridization in plant speciationQ33477947
Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levelsQ33534007
The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shellQ33578905
A maximum pseudo-likelihood approach for estimating species trees under the coalescent modelQ33714988
Automated removal of noisy data in phylogenomic analyses.Q33728795
The inheritance of genes in mitochondria and chloroplasts: laws, mechanisms, and modelsQ34100918
Angiosperm phylogeny: 17 genes, 640 taxaQ34187312
Resolving the evolutionary relationships of molluscs with phylogenomic toolsQ34227800
Coalescent versus concatenation methods and the placement of Amborella as sister to water liliesQ34431575
Phylogenetic signal variation in the genomes of Medicago (Fabaceae).Q34589326
Genealogical trees, coalescent theory and the analysis of genetic polymorphismsQ34623776
Rapid radiation and dispersal out of the Qinghai-Tibetan Plateau of an alpine plant lineage Rhodiola (Crassulaceae).Q35159569
Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent modelQ36236100
The inheritance of organelle genes and genomes: patterns and mechanismsQ36359914
An unusual ribosomal DNA sequence from Gossypium gossypioides reveals ancient, cryptic, intergenomic introgression.Q39586853
Microevolutionary processes generate phylogenomic discordance at ancient divergencesQ42008222
Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiospermsQ42509430
The root of the mammalian tree inferred from whole mitochondrial genomesQ44524056
Testing hybridization hypotheses based on incongruent gene treesQ44905121
Angiosperm phylogeny based on matK sequence informationQ44966552
A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methodsQ45106204
A method of alignment masking for refining the phylogenetic signal of multiple sequence alignmentsQ45393337
Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes.Q45735013
Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale).Q47207011
Four new avian mitochondrial genomes help get to basic evolutionary questions in the late cretaceousQ47247937
Molecular phylogenetic dating of asterid flowering plants shows early Cretaceous diversificationQ47305789
The phylogeny of the Asteridae sensu lato based on chloroplast ndhF gene sequencesQ47848393
Trees within trees: phylogeny and historical associationsQ49095393
Multigene phylogeny of the green lineage reveals the origin and diversification of land plants.Q50531796
Estimating species phylogenies using coalescence times among sequences.Q51612381
A statistical approach for distinguishing hybridization and incomplete lineage sorting.Q51658545
Paternally biased cpDNA inheritance in Turnera ulmifolia (Turneraceae).Q53085631
A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap ValuesQ54153226
Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1Q54542738
Phylogenetics of Seed Plants: An Analysis of Nucleotide Sequences from the Plastid Gene rbcLQ55867267
The Hows and Whys of Cytoplasmic Inheritance in Seed PlantsQ55888993
A 567‐Taxon Data Set for Angiosperms: The Challenges Posed by Bayesian Analyses of Large Data SetsQ56040041
Angiosperm phylogeny inferred from sequences of four mitochondrial genesQ56093000
Evidence of chloroplast capture in South American Nothofagus (subgenus Nothofagus, Nothofagaceae)Q56949123
PhylogenomicsQ57027972
Phylogenetic relationships in the monocot order Commelinales, with a focus on PhilydraceaeThis paper is one of a selection of papers published in the Special Issue on Systematics ResearchQ57233373
Difficulties in Detecting HybridizationQ57822789
Interspecific Pollen Competition as a Reproductive Barrier Between Sympatric Species of Helianthus (Asteraceae)Q57973719
Gene Trees in Species TreesQ59699645
Inference of phylogenetic relationships among the subfamilies of grasses (Poaceae: Poales) using meso-scale exemplar-based sampling of the plastid genomeQ60434218
Robust Inference of Monocot Deep Phylogeny Using an Expanded Multigene Plastid Data SetQ60434222
Maternal inheritance of chloroplast genome and paternal inheritance of mitochondrial genome in bananas (Musa acuminata)Q72710908
P407language of work or nameEnglishQ1860
P921main subjectphylogeneticsQ171184
RosidaeQ3442619
AngiospermaeQ14832431
P1104number of pages11
P304page(s)156-166
P577publication date2014-11-18
P1433published inMolecular Phylogenetics and EvolutionQ4248868
P1476titleDeep phylogenetic incongruence in the angiosperm clade Rosidae
P478volume83

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cites work (P2860)
Q89559484-Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae)
Q64979133A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering.
Q36188057A molecular phylogeny of Caraganeae (Leguminosae, Papilionoideae) reveals insights into new generic and infrageneric delimitations.
Q111629843A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily
Q23803501An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV
Q57126945Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex
Q111629751Animal‐mediated long‐distance dispersals and migrations shaping the intercontinental disjunctions of Celastrus (Celastraceae) among five continents
Q36006466Another look at the phylogenetic position of the grape order Vitales: Chloroplast phylogenomics with an expanded sampling of key lineages
Q39831653Biases of tree-independent-character-subsampling methods
Q111629869Capturing single‐copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
Q97551416Complex evolutionary history of coffees revealed by full plastid genomes and 28,800 nuclear SNP analyses, with particular emphasis on Coffea canephora (Robusta coffee)
Q38883637Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium).
Q36341062Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae).
Q34551008Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics
Q28603066Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data
Q38998859Homology-Aware Phylogenomics at Gigabase Scales
Q126726128How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example
Q126726154Incomplete lineage sorting and reticulate evolution mask species relationships in Brunelliaceae, an Andean family with rapid, recent diversification
Q92406386Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes
Q33776364Ixora (Rubiaceae) on the Philippines - crossroad or cradle?
Q91757248Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts
Q90874803Multilocus data reveal deep phylogenetic relationships and intercontinental biogeography of the Eurasian-North American genus Corylus (Betulaceae)
Q90970859Nuclear genomes of two magnoliids
Q111629583Phylogenetic relationships of Cyrtandromoea and Wightia revisited: A new tribe in Phrymaceae and a new family in Lamiales
Q36066323Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids
Q111630370Phylogenomic analysis of Picramnia , Alvaradoa, and Leitneria supports the independent Picramniales
Q91892459Phylogenomic conflict resulting from ancient introgression following species diversification in Stewartia s.l. (Theaceae)
Q111629813Phylogenomics of Fargesia and Yushania reveals a history of reticulate evolution
Q90685590Phylogeny and divergence time estimation of the walnut family (Juglandaceae) based on nuclear RAD-Seq and chloroplast genome data
Q55870632Phylogeny of theRosidae: A dense taxon sampling analysis
Q60932599Phylogeography of western Mediterranean Cymbalaria (Plantaginaceae) reveals two independent long-distance dispersals and entails new taxonomic circumscriptions
Q91727997Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)
Q89866795Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution
Q38810987Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants
Q28607516Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials
Q92009004Target sequence capture in the Brazil nut family (Lecythidaceae): Marker selection and in silico capture from genome skimming data
Q37692362The Chloroplast Genome of Passiflora edulis (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales
Q91554902The Litsea genome and the evolution of the laurel family
Q28584511The emergence of core eudicots: new floral evidence from the earliest Late Cretaceous
Q39509335The rubber tree genome reveals new insights into rubber production and species adaptation.

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