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Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers

https://doi.org/10.1073/pnas.97.8.4086
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Seed plant phylogeny and the origin of angiosperms: An experimental cladistic approach
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Sequence Peculiarity of Gnetalean Legumin-Like Seed Storage Proteins
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Molecular Data from the Chloroplast rpoC1 Gene Suggest a Deep and Distinct Dichotomy of Contemporary Spermatophytes into Two Monophyla: Gymnosperms (Including Gnetales) and Angiosperms
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A rare chloroplast-DNA structural mutation is shared by all conifers
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Multigene analyses identify the three earliest lineages of extant flowering plants
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The origin and early diversification of angiosperms
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MADS-box genes reveal that gnetophytes are more closely related to conifers than to flowering plants
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Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers
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Seed Plant Phylogeny and the Relationships of Gnetales
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Wood, Bark, and Stem Anatomy of Gnetales: A Summary
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fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood
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Noncoding sequences from the slowly evolving chloroplast inverted repeat in addition to rbcL data do not support gnetalean affinities of angiosperms
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Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025702openalex-snapshot
Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences
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The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal?
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Gnetum and the Angiosperms: Molecular Evidence that Their Shared Morphological Characters Are Convergent, Rather than Homologous
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Model selection in the estimation of the number of nucleotide substitutions.
inferredcites →https://doi.org/10.1093/sysbio/41.3.273openalex-snapshot
Evolutionary Relationships Within the Ensatina Eschscholtzii Complex Confirm the Ring Species Interpretation
inferredcites →https://doi.org/10.1126/science.247.4945.951openalex-snapshot
Double Fertilization in Ephedra, a Nonflowering Seed Plant: Its Bearing on the Origin of Angiosperms
inferredcites →https://doi.org/10.1126/science.255.5052.1697openalex-snapshot
Chloroplast DNA Evidence on the Ancient Evolutionary Split in Vascular Land Plants
inferredcites →https://doi.org/10.1126/science.286.5441.947openalex-snapshot
The Root of Angiosperm Phylogeny Inferred from Duplicate Phytochrome Genes
inferredcites →https://doi.org/10.1146/annurev.ecolsys.29.1.567openalex-snapshot
PHYLOGENY OF VASCULAR PLANTS
inferredcites →https://doi.org/10.2307/2399221openalex-snapshot
Phylogenetic Analysis of Seed Plants and the Origin of Angiosperms
inferredcites →https://doi.org/10.2307/2399901openalex-snapshot
A Reevaluation of Seed Plant Phylogeny
inferredcites →https://doi.org/10.2307/2399902openalex-snapshot
Functional Constraints and rbcL Evidence for Land Plant Phylogeny
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Lignophyte Phylogeny and the Evolution of Spermatophytes: A Numerical Cladistic Analysis
inferredcites →https://doi.org/10.2307/2446539openalex-snapshot
Phylogenetic relationships of conifers inferred from Partial 28S rRNA gene sequences
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Cladistics of the Spermatophyta
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An Ordinal Classification for the Families of Flowering Plants
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Flowering plant origin, evolution & phylogeny
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The origin and early diversification of land plants: a cladistic study
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A Cladistic Analysis of Conifers: Preliminary Results

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Plant biodiversity and regulation of photosynthesis in the natural environment
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A novel MADS-box gene subfamily with a sister-group relationship to class B floral homeotic genes
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Maternal inheritance of plastids and mitochondria in Cycas L. (Cycadaceae)
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Association of cone thermogenesis and volatiles with pollinator specificity in Macrozamia cycads
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Asymmetrical development of biovulate cones resulting in uniovulate cones in Ephedra rhytidosperma (Ephedraceae)
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Molecular and morphological phylogeny of Menispermaceae (Ranunculales)
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Pollen wall development in Sciadopitys verticillata (Sciadopityaceae)
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Cladistic analysis of Taxaceae s. l.
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Phylogeny and divergence of basal angiosperms inferred from APETALA3- and PISTILLATA-like MADS-box genes
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Microtubules in early development of the megagametophyte of Ginkgo biloba
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Leaf anatomy and its implications for phylogenetic relationships in Taxaceae s. l.
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Functional characterization of blue-light-induced responses and PHOTOTROPIN 1 gene in Welwitschia mirabilis
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Fossil record of Ephedra in the Lower Cretaceous (Aptian), Argentina
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Comparative Analysis of Expressed Sequence Tags of Conifers and Angiosperms Reveals Sequences Specifically Conserved in Conifers
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Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae)
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Characterization and Transcriptional Profiling of Ginkgo biloba Mevalonate Diphosphate Decarboxylase Gene (GbMVD) Promoter Towards Light and Exogenous Hormone Treatments
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Karyotype evolution in cycads
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Gymnosperms
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Evolutionary History of Lignins
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Prehistory of the Angiosperms
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Evolution and Diversity of Woody and Seed Plants
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When Earth started blooming: insights from the fossil record
inferred← citeshttps://doi.org/10.1016/j.phytochem.2008.07.001openalex-snapshot
Serine proteinase inhibitors in seeds of Cycas siamensis and other gymnosperms
inferred← citeshttps://doi.org/10.1016/j.plaphy.2010.04.009openalex-snapshot
Plastid ndh genes in plant evolution
inferred← citeshttps://doi.org/10.1016/j.plaphy.2010.05.003openalex-snapshot
Lineage-specific group II intron gains and losses of the mitochondrial rps3 gene in gymnosperms
inferred← citeshttps://doi.org/10.1016/j.pld.2022.05.003openalex-snapshot
Recent advances on phylogenomics of gymnosperms and a new classification
inferred← citeshttps://doi.org/10.1016/j.ppees.2017.08.001openalex-snapshot
Protognetaceae: A new gnetoid macrofossil family from the Jurassic of northeastern China
inferred← citeshttps://doi.org/10.1016/j.revpalbo.2008.08.002openalex-snapshot
Pollen of the Triassic cycad Delemaya spinulosa and implications on cycad evolution
inferred← citeshttps://doi.org/10.1016/j.revpalbo.2017.10.003openalex-snapshot
Growth habit indicators from Permian Antarctic glossopterids
inferred← citeshttps://doi.org/10.1016/j.revpalbo.2023.105035openalex-snapshot
Archangelskyoxylon carlquistii gen. et sp. nov. Taxonomy and phylogeny of an unequivocal gnetoid Jurassic fossil wood from Argentina
inferred← citeshttps://doi.org/10.1016/j.revpalbo.2025.105353openalex-snapshot
A new species of Stutzeliastrobus (Cupressaceae) from the Early Cretaceous of the Guyang Basin, northern China, and its paleoenvironmental implications
inferred← citeshttps://doi.org/10.1016/j.sajb.2007.12.002openalex-snapshot
Abnormal morphology of the embryo and seedling of Welwitschia mirabilis, and some observations on seed-associated fungi
inferred← citeshttps://doi.org/10.1016/j.tplants.2012.03.004openalex-snapshot
Biosynthesis of amphetamine analogs in plants
inferred← citeshttps://doi.org/10.1016/j.virusres.2015.03.007openalex-snapshot
Catharanthus mosaic virus: A potyvirus from a gymnosperm, Welwitschia mirabilis
inferred← citeshttps://doi.org/10.1016/j.ympev.2003.08.013openalex-snapshot
The sequence of the largest subunit of RNA polymerase II is a useful marker for inferring seed plant phylogeny
inferred← citeshttps://doi.org/10.1016/j.ympev.2004.12.020openalex-snapshot
Phylogenetic relationships in Ephedra (Ephedraceae) inferred from chloroplast and nuclear DNA sequences
inferred← citeshttps://doi.org/10.1016/j.ympev.2005.01.006openalex-snapshot
A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region
inferred← citeshttps://doi.org/10.1016/j.ympev.2005.04.008openalex-snapshot
Incongruence between primary sequence data and the distribution of a mitochondrial atp1 group II intron among ferns and horsetails
inferred← citeshttps://doi.org/10.1016/j.ympev.2006.03.006openalex-snapshot
Seed plant phylogeny: Gnetophytes are derived conifers and a sister group to Pinaceae
inferred← citeshttps://doi.org/10.1016/j.ympev.2006.06.017openalex-snapshot
Phylogenetic utility of rapidly evolving DNA at high taxonomical levels: Contrasting matK, trnT-F, and rbcL in basal angiosperms
inferred← citeshttps://doi.org/10.1016/j.ympev.2008.05.003openalex-snapshot
Phylogeography of a living fossil: Pleistocene glaciations forced Ginkgo biloba L. (Ginkgoaceae) into two refuge areas in China with limited subsequent postglacial expansion
inferred← citeshttps://doi.org/10.1016/j.ympev.2008.12.026openalex-snapshot
Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: Selection toward a lower-cost strategy
inferred← citeshttps://doi.org/10.1016/j.ympev.2009.09.011openalex-snapshot
Fast evolution of the retroprocessed mitochondrial rps3 gene in Conifer II and further evidence for the phylogeny of gymnosperms
inferred← citeshttps://doi.org/10.1016/j.ympev.2009.11.020openalex-snapshot
High nrDNA ITS polymorphism in the ancient extant seed plant Cycas: Incomplete concerted evolution and the origin of pseudogenes
inferred← citeshttps://doi.org/10.1016/j.ympev.2012.05.004openalex-snapshot
Three genome-based phylogeny of Cupressaceae s.l.: Further evidence for the evolution of gymnosperms and Southern Hemisphere biogeography
inferred← citeshttps://doi.org/10.1016/j.ympev.2012.08.019openalex-snapshot
Using multiple analytical methods to improve phylogenetic hypotheses in Minaria (Apocynaceae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2014.02.005openalex-snapshot
Evolution and biogeography of gymnosperms
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.05.010openalex-snapshot
Multiplexed shotgun sequencing reveals congruent three-genome phylogenetic signals for four botanical sections of the flax genus Linum
inferred← citeshttps://doi.org/10.1016/s0065-2296(06)44002-7openalex-snapshot
Recent Developments Regarding the Evolutionary Origin of Flowers
inferred← citeshttps://doi.org/10.1016/s0092-8674(00)80618-2openalex-snapshot
The ABCs of Floral Evolution
inferred← citeshttps://doi.org/10.1016/s0378-1119(02)00689-3openalex-snapshot
Dealing with saturation at the amino acid level: a case study based on anciently duplicated zebrafish genes
inferred← citeshttps://doi.org/10.1016/s0748-3007(02)00104-4openalex-snapshot
Taxon sampling and seed plant phylogeny
inferred← citeshttps://doi.org/10.1016/s0764-4469(01)01320-8openalex-snapshot
Reproduction et développement des plantes à fleurs
inferred← citeshttps://doi.org/10.1016/s0764-4469(01)01326-9openalex-snapshot
Developmental and evolutionary hypotheses for the origin of double fertilization and endosperm
inferred← citeshttps://doi.org/10.1016/s0960-9822(00)00304-3openalex-snapshot
Seed plant phylogeny: Demise of the anthophyte hypothesis?
inferred← citeshttps://doi.org/10.1016/s0960-9822(00)80119-0openalex-snapshot
Multigene analyses identify the three earliest lineages of extant flowering plants
inferred← citeshttps://doi.org/10.1016/s1055-7903(03)00131-3openalex-snapshot
Inference of higher-order relationships in the cycads from a large chloroplast data set
inferred← citeshttps://doi.org/10.1016/s1055-7903(03)00207-0openalex-snapshot
The major clades of MADS-box genes and their role in the development and evolution of flowering plants
inferred← citeshttps://doi.org/10.1016/s1360-1385(02)02300-2openalex-snapshot
Pleiotropy, redundancy and the evolution of flowers
inferred← citeshttps://doi.org/10.1016/s1360-1385(03)00190-0openalex-snapshot
Cycads: evolutionary innovations and the role of plant-derived neurotoxins
inferred← citeshttps://doi.org/10.1016/s1369-5266(00)00139-4openalex-snapshot
Development of floral organ identity: stories from the MADS house
inferred← citeshttps://doi.org/10.1017/cbo9780511535512.020openalex-snapshot
The macrophyte flora of the Crato Formation
inferred← citeshttps://doi.org/10.1017/pab.2018.23openalex-snapshot
Experimental signal dissection and method sensitivity analyses reaffirm the potential of fossils and morphology in the resolution of the relationship of angiosperms and Gnetales
inferred← citeshttps://doi.org/10.1017/s0960258511000134openalex-snapshot
Deep simple morphophysiological dormancy in seeds of the basal taxad Cephalotaxus
inferred← citeshttps://doi.org/10.1017/s1464793101005735openalex-snapshot
Did dinosaurs invent flowers? Dinosaur—angiosperm coevolution revisited
inferred← citeshttps://doi.org/10.1017/s1477200003001051openalex-snapshot
Genesis of phenotypic and genotypic diversity in land plants: The present as the key to the past
inferred← citeshttps://doi.org/10.1017/ssr2006256openalex-snapshot
Evolutionary considerations of the presence of both morphophysiological and physiological seed dormancy in the highly advanced euasterids II order Dipsacales
inferred← citeshttps://doi.org/10.1038/35054555openalex-snapshot
Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants
inferred← citeshttps://doi.org/10.1038/35056041openalex-snapshot
Function and evolution of the plant MADS-box gene family
inferred← citeshttps://doi.org/10.1038/415522aopenalex-snapshot
Identification of diploid endosperm in an early angiosperm lineage
inferred← citeshttps://doi.org/10.1038/hdy.2016.65openalex-snapshot
Relative strength of fine-scale spatial genetic structure in paternally vs biparentally inherited DNA in a dioecious plant depends on both sex proportions and pollen-to-seed dispersal ratio
inferred← citeshttps://doi.org/10.1038/npre.2007.320openalex-snapshot
Third-codon transversion rate-based Nymphaea basal angiosperm phylogeny—concordance with developmental evidence
inferred← citeshttps://doi.org/10.1038/npre.2007.320.1openalex-snapshot
Third-codon transversion rate-based Nymphaea basal angiosperm phylogeny -- concordance with developmental evidence
inferred← citeshttps://doi.org/10.1038/nrg1114openalex-snapshot
An evolutionary scenario for the origin of flowers
inferred← citeshttps://doi.org/10.1038/nrg929openalex-snapshot
The origin and evolution of model organisms
inferred← citeshttps://doi.org/10.1038/s41559-017-0224-5openalex-snapshot
Molecular signatures of fossil leaves provide unexpected new evidence for extinct plant relationships
inferred← citeshttps://doi.org/10.1038/s41586-019-1693-2openalex-snapshot
One thousand plant transcriptomes and the phylogenomics of green plants
inferred← citeshttps://doi.org/10.1038/srep41005openalex-snapshot
Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae)
inferred← citeshttps://doi.org/10.1046/j.1365-313x.2002.01375.xopenalex-snapshot
On the origin of class B floral homeotic genes: functional substitution and dominant inhibition in Arabidopsis by expression of an orthologue from the gymnosperm Gnetum
inferred← citeshttps://doi.org/10.1046/j.1420-9101.2003.00577.xopenalex-snapshot
Noncoding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms
inferred← citeshttps://doi.org/10.1046/j.1469-8137.2003.00846.xopenalex-snapshot
Some reflections on double fertilization, from its discovery to the present
inferred← citeshttps://doi.org/10.1046/j.1525-142x.2003.03060.xopenalex-snapshot
The DAL10 gene from Norway spruce (Picea abies) belongs to a potentially gymnosperm‐specific subclass of MADS‐box genes and is specifically active in seed cones and pollen cones
inferred← citeshttps://doi.org/10.1046/j.1529-8817.2000.03654.xopenalex-snapshot
MADS‐BOX GENES: DEVELOPMENT AND EVOLUTION OF PLANT BODY PLANS
inferred← citeshttps://doi.org/10.1051/medsci/200218111146openalex-snapshot
Phylogénie et évolution moléculaires
inferred← citeshttps://doi.org/10.1055/s-2003-40791openalex-snapshot
Morphogenesis of Male Sporangiophores of Zamia amblyphyllidia D. W. Stev.
inferred← citeshttps://doi.org/10.1071/bt17048openalex-snapshot
Thermogenesis and developmental progression of Macrozamia macleayi pollen cones
inferred← citeshttps://doi.org/10.1071/sb01002openalex-snapshot
Phylogenetic assessment of the monotypic genera Sundacarpus and Manoao (Coniferales: Podocarpaceae) utilising evidence from 18S rDNA sequences
inferred← citeshttps://doi.org/10.1073/pnas.0305562101openalex-snapshot
Mitochondrial DNA sequences reveal the photosynthetic relatives of Rafflesia , the world's largest flower
inferred← citeshttps://doi.org/10.1073/pnas.0402473101openalex-snapshot
Cretaceous flowers of Nymphaeaceae and implications for complex insect entrapment pollination mechanisms in early Angiosperms
inferred← citeshttps://doi.org/10.1073/pnas.0407588101openalex-snapshot
On the evolutionary history of Ephedra: Cretaceous fossils and extant molecules
inferred← citeshttps://doi.org/10.1073/pnas.0408302101openalex-snapshot
Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants
inferred← citeshttps://doi.org/10.1073/pnas.1110677108openalex-snapshot
Morphological and functional stasis in mycorrhizal root nodules as exhibited by a Triassic conifer
inferred← citeshttps://doi.org/10.1073/pnas.1132171100openalex-snapshot
Apparent homology of expressed genes from wood-forming tissues of loblolly pine ( Pinus taeda L.) with Arabidopsis thaliana
inferred← citeshttps://doi.org/10.1073/pnas.220427497openalex-snapshot
Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny
inferred← citeshttps://doi.org/10.1073/pnas.2506320123openalex-snapshot
Intermediate evolutionary state of motile sperm and pollen tubes in the extant gymnosperm Cycas revoluta
inferred← citeshttps://doi.org/10.1073/pnas.97.8.4092openalex-snapshot
Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers
inferred← citeshttps://doi.org/10.1078/0367-2530-00171openalex-snapshot
Morphogenesis of leaves and cones of male short-shoots of Ginkgo biloba L.
inferred← citeshttps://doi.org/10.1078/1433-8319-00024openalex-snapshot
Is clustering of plastid RNA editing sites a consequence of transitory loss of gene function? – Implications for past environmental and evolutionary events in plants
inferred← citeshttps://doi.org/10.1078/1433-8319-00039openalex-snapshot
Interplate dispersal paths for megathermal angiosperms
inferred← citeshttps://doi.org/10.1080/00173130500424557openalex-snapshot
Early evolution of angiosperm pollen as inferred from molecular and morphological phylogenetic analyses
inferred← citeshttps://doi.org/10.1080/00173130902754437openalex-snapshot
Upatoia barnardiigen. et sp. nov., an araucarian pollen cone within situpollen from the Late Cretaceous (Santonian) of Georgia, USA
inferred← citeshttps://doi.org/10.1080/07352680490433240openalex-snapshot
Gymnosperm Orthologues of Class B Floral Homeotic Genes and Their Impact on Understanding Flower Origin
inferred← citeshttps://doi.org/10.1080/10635150390223613openalex-snapshot
Phylogeny Reconstruction: The Role of Morphology
inferred← citeshttps://doi.org/10.1080/10635150590906000openalex-snapshot
Morphology's Role in Phylogeny Reconstruction: Perspectives from Paleontology
inferred← citeshttps://doi.org/10.1080/10635150600812619openalex-snapshot
Dating Dispersal and Radiation in the Gymnosperm Gnetum (Gnetales)—Clock Calibration When Outgroup Relationships Are Uncertain
inferred← citeshttps://doi.org/10.1080/10635150701324225openalex-snapshot
Distinguishing Terminal Monophyletic Groups from Reticulate Taxa: Performance of Phenetic, Tree-Based, and Network Procedures
inferred← citeshttps://doi.org/10.1080/10635150701499563openalex-snapshot
Experimental Design Criteria in Phylogenetics: Where to Add Taxa
inferred← citeshttps://doi.org/10.1080/11263504.2020.1810813openalex-snapshot
The origin of double fertilization in flowering plants: looking into the history of plant reproduction evolution
inferred← citeshttps://doi.org/10.1080/14772019.2022.2133644openalex-snapshot
Silicified cupulate seed-bearing structures from the Early Cretaceous of eastern Inner Mongolia, China: rethinking the corystosperm concept
inferred← citeshttps://doi.org/10.1086/317575openalex-snapshot
New Perspectives on the Pollination Biology of Basal Angiosperms
inferred← citeshttps://doi.org/10.1086/317578openalex-snapshot
Morphological Phylogenetic Analysis of Basal Angiosperms: Comparison and Combination with Molecular Data
inferred← citeshttps://doi.org/10.1086/317584openalex-snapshot
Phylogeny of Basal Angiosperms: Analyses of Five Genes from Three Genomes
inferred← citeshttps://doi.org/10.1086/319586openalex-snapshot
Phylogenetic Implications of the Multiple Losses of the Mitochondrial coxII.i3 Intron in the Angiosperms
inferred← citeshttps://doi.org/10.1086/320131openalex-snapshot
A New Species ofPityostrobusfrom the Lower Cretaceous of California and Its Bearing on the Evolution of Pinaceae
inferred← citeshttps://doi.org/10.1086/321929openalex-snapshot
Thrips and Weevils as Dual, Specialist Pollinators of the Australian CycadMacrozamia communis(Zamiaceae)
inferred← citeshttps://doi.org/10.1086/323417openalex-snapshot
Characterization of aFLORICAULA/LEAFYHomologue ofGnetum parvifoliumand Its Implications for the Evolution of Reproductive Organs in Seed Plants
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