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Assessing Among‐Locus Variation in the Inference of Seed Plant Phylogeny

https://doi.org/10.1086/509586
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Genome-scale data, angiosperm relationships, and ‘ending incongruence’: a cautionary tale in phylogenetics
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Taxon sampling and seed plant phylogeny
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Seed plant phylogeny: Demise of the anthophyte hypothesis?
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The challenge of constructing large phylogenetic trees
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Molecular phylogenetics and the origins of placental mammals
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Genome-scale approaches to resolving incongruence in molecular phylogenies
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Phylogenomics and the reconstruction of the tree of life
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An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II
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The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium , Entamoeba , and Mastigamoeba
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Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data
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Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella
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Horizontal gene transfer from flowering plants to Gnetum
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Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny
inferredcites →https://doi.org/10.1073/pnas.97.8.4086openalex-snapshot
Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers
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Is Sparse Taxon Sampling a Problem for Phylogenetic Inference?
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Least and Most Powerful Phylogenetic Tests to Elucidate the Origin of the Seed Plants in the Presence of Conflicting Signals under Misspecified Models
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Supertree Bootstrapping Methods for Assessing Phylogenetic Variation among Genes in Genome-Scale Data Sets
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Missing the Forest for the Trees: Phylogenetic Compression and Its Implications for Inferring Complex Evolutionary Histories
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Hidden Likelihood Support in Genomic Data: Can Forty-Five Wrongs Make a Right?
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Is It Better to Add Taxa or Characters to a Difficult Phylogenetic Problem?
inferredcites →https://doi.org/10.1086/297401openalex-snapshot
Seed Plant Phylogeny and the Relationships of Gnetales
inferredcites →https://doi.org/10.1086/338321openalex-snapshot
Seed Plant Relationships and the Systematic Position of Gnetales Based on Nuclear and Chloroplast DNA: Conflicting Data, Rooting Problems, and the Monophyly of Conifers
inferredcites →https://doi.org/10.1086/509588openalex-snapshot
Assessing Systematic Error in the Inference of Seed Plant Phylogeny
inferredcites →https://doi.org/10.1093/bioinformatics/bti020openalex-snapshot
Clann: investigating phylogenetic information through supertree analyses
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HyPhy: hypothesis testing using phylogenies
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Genome-Scale Phylogeny and the Detection of Systematic Biases
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Covarion Structure in Plastid Genome Evolution: A New Statistical Test
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Multigene Analyses of Bilaterian Animals Corroborate the Monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia
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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
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Error, Bias, and Long-Branch Attraction in Data for Two Chloroplast Photosystem Genes in Seed Plants
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040258openalex-snapshot
Sampling properties of DNA sequence data in phylogenetic analysis.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040454openalex-snapshot
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
inferredcites →https://doi.org/10.1093/sysbio/42.3.384openalex-snapshot
Partitioning and Combining Data in Phylogenetic Analysis
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Weighting, Partitioning, and Combining Characters in Phylogenetic Analysis
inferredcites →https://doi.org/10.1111/boj.12385openalex-snapshot
An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV
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A phylogenetic analysis of the land plants
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CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
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PHOTOMORPHOGENESIS IN PLANTS
inferredcites →https://doi.org/10.1126/science.1102036openalex-snapshot
Prospects for Building the Tree of Life from Large Sequence Databases
inferredcites →https://doi.org/10.1146/annurev.es.09.110178.002053openalex-snapshot
Origin of Angiosperms
inferredcites →https://doi.org/10.1146/annurev.es.26.110195.003301openalex-snapshot
SEPARATE VERSUS COMBINED ANALYSIS OF PHYLOGENETIC EVIDENCE
inferredcites →https://doi.org/10.1186/1471-2148-4-35openalex-snapshot
Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?
inferredcites →https://doi.org/10.1600/0363644042451008openalex-snapshot
Recombination, Heteroplasmy, Haplotype Polymorphism, and Paralogy in Plastid Genes: Implications for Plant Molecular Systematics
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/10.2307/2656749openalex-snapshot
Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms
inferredcites →https://doi.org/10.2307/2666635openalex-snapshot
The Mostly Male Theory of Flower Evolutionary Origins: From Genes to Fossils
inferredcites →https://doi.org/10.2307/2992242openalex-snapshot
Against Consensus
inferredcites →https://doi.org/10.2307/3241484openalex-snapshot
Morphology of Vascular Plants
inferredcites →https://doi.org/10.3159/1095-5674(2006)133[119:patbos]2.0.co;2openalex-snapshot
Pteridosperms are the backbone of seed-plant phylogeny1
inferredcites →https://doi.org/10.3159/1095-5674(2006)133[169:sfatoo]2.0.co;2openalex-snapshot
Seed ferns and the origin of angiosperms
inferredcites →https://doi.org/10.3732/ajb.89.10.1670openalex-snapshot
Phylogeny of seed plants based on evidence from eight genes
inferredcites →https://doi.org/10.3732/ajb.89.12.1991openalex-snapshot
Relationships among seed plants inferred from highly conserved genes: sorting conflicting phylogenetic signals among ancient lineages
inferredcites →https://doi.org/10.3732/ajb.91.10.1437openalex-snapshot
The plant tree of life: an overview and some points of view
inferredcites →https://doi.org/10.3732/ajb.91.10.1599openalex-snapshot
Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life

What points at this work

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

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Conflict between morphological and molecular data: A case study of Ficus krishnae (Moraceae)
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Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny
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Fast evolution of the retroprocessed mitochondrial rps3 gene in Conifer II and further evidence for the phylogeny of gymnosperms
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After a dozen years of progress the origin of angiosperms is still a great mystery
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The PhyLoTA Browser: Processing GenBank for Molecular Phylogenetics Research
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Penalized Likelihood Phylogenetic Inference: Bridging the Parsimony-Likelihood Gap
inferred← citeshttps://doi.org/10.1086/509588openalex-snapshot
Assessing Systematic Error in the Inference of Seed Plant Phylogeny
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Evolutionary Relationships inEphedra(Gnetales), with Implications for Seed Plant Phylogeny
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Evolution and Phylogeny of Gnetophytes: Evidence from the Anatomically Preserved Seed Cone Protoephedrites eamesii gen. et sp. nov. and the Seeds of Several Bennettitalean Species
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Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships
inferred← citeshttps://doi.org/10.1098/rstb.2009.0233openalex-snapshot
A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants
inferred← citeshttps://doi.org/10.1111/cla.12191openalex-snapshot
Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)
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The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates
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Framing the Salmonidae Family Phylogenetic Portrait: A More Complete Picture from Increased Taxon Sampling
inferred← citeshttps://doi.org/10.1371/journal.pone.0080870openalex-snapshot
Phylogenomics and Coalescent Analyses Resolve Extant Seed Plant Relationships
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inferred← citeshttps://doi.org/10.7287/peerj.7747v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Characterizing gene tree conflict in plastome-inferred phylogenies (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.7747v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Characterizing gene tree conflict in plastome-inferred phylogenies (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.7747v0.1/reviews/3openalex-snapshot
Peer Review #3 of "Characterizing gene tree conflict in plastome-inferred phylogenies (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.7747v0.2/reviews/1openalex-snapshot
Peer Review #1 of "Characterizing gene tree conflict in plastome-inferred phylogenies (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.7747v0.2/reviews/2openalex-snapshot
Peer Review #2 of "Characterizing gene tree conflict in plastome-inferred phylogenies (v0.2)"
inferred← citeshttps://doi.org/10.7717/peerj.7747openalex-snapshot
Characterizing gene tree conflict in plastome-inferred phylogenies
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