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Exploring the phylogeny of rosids with a five-locus supermatrix from GenBank

https://doi.org/10.1101/694950
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Outgoing claims: the papers this work cites, builds on, or argues with.

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A roadmap for global synthesis of the plant tree of life
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Model clades are vital for comparative biology, and ascertainment bias is not a problem in practice: a response to Beaulieu and O'Meara (2018)
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THE RELATIONSHIP BETWEEN HOMOPLASY AND CONFIDENCE IN A PHYLOGENETIC TREE
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Deep phylogenetic incongruence in the angiosperm clade Rosidae
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Another look at the phylogenetic position of the grape order Vitales: Chloroplast phylogenomics with an expanded sampling of key lineages
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Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids
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Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
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Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots
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Improved Bootstrap Confidence Limits in Large-Scale Phylogenies, with an Example from Neo-Astragalus (Leguminosae)
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Explosive Radiation of Malpighiales Supports a Mid‐Cretaceous Origin of Modern Tropical Rain Forests
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A 567‐Taxon Data Set for Angiosperms: The Challenges Posed by Bayesian Analyses of Large Data Sets
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Ferns in an Angiosperm World: Cretaceous Radiation into the Epiphytic Niche and Diversification on the Forest Floor
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How Many Bootstrap Replicates Are Necessary?
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The Newick utilities: high-throughput phylogenetic tree processing in the U nix shell
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treePL: divergence time estimation using penalized likelihood for large phylogenies
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees
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Genome Structure of the Legume, Lotus japonicus
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MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
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MAFFT version 5: improvement in accuracy of multiple sequence alignment
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Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
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Testing the Impact of Calibration on Molecular Divergence Times Using a Fossil-Rich Group: The Case of Nothofagus (Fagales)
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Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks
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Evolution of the angiosperms: calibrating the family tree
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PASTIS : an R package to facilitate phylogenetic assembly with soft taxonomic inferences
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An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV
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TESTING THE MUSEUM VERSUS CRADLE TROPICAL BIOLOGICAL DIVERSITY HYPOTHESIS: PHYLOGENY, DIVERSIFICATION, AND ANCESTRAL BIOGEOGRAPHIC RANGE EVOLUTION OF THE ANTS
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No substitute for real data: A cautionary note on the use of phylogenies from birth-death polytomy resolvers for downstream comparative analyses
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An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III
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Highly conserved low‐copy nuclear genes as effective markers for phylogenetic analyses in angiosperms
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Phylogenetics of early branching eudicots: Comparing phylogenetic signal across plastid introns, spacers, and genes
inferredcites →https://doi.org/10.1111/j.2041-210x.2012.00232.xopenalex-snapshot
taxonstand: An r package for species names standardisation in vegetation databases
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Phylogeny of the Rosidae: A dense taxon sampling analysis
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A metacalibrated time‐tree documents the early rise of flowering plant phylogenetic diversity
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Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets
inferredcites →https://doi.org/10.1126/science.1100671openalex-snapshot
Host-to-Parasite Gene Transfer in Flowering Plants: Phylogenetic Evidence from Malpighiales
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Phylogeny of the Ants: Diversification in the Age of Angiosperms
inferredcites →https://doi.org/10.1126/science.281.5376.555openalex-snapshot
"Inordinate Fondness" Explained: Why Are There So Many Beetles?
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Timing the Radiations of Leaf Beetles: Hispines on Gingers from Latest Cretaceous to Recent
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MUSCLE: a multiple sequence alignment method with reduced time and space complexity
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From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
inferredcites →https://doi.org/10.1186/1471-2148-7-217openalex-snapshot
Mitochondrial matR sequences help to resolve deep phylogenetic relationships in rosids
inferredcites →https://doi.org/10.1186/1471-2148-9-37openalex-snapshot
Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches
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Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration
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The relative ages of ectomycorrhizal mushrooms and their plant hosts estimated using Bayesian relaxed molecular clock analyses
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Applying the Bootstrap in Phylogeny Reconstruction
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Some Limitations of Public Sequence Data for Phylogenetic Inference (in Plants)
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How many species of seed plants are there?
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Homoplasy. The Recurrence of Similarity in Evolution
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Parallel evolution of glucosinolate biosynthesis inferred from congruent nuclear and plastid gene phylogenies
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In defence of a conifer taxonomy which recognises evolution
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Phylogenetic Pattern, Diversity, and Diversification of Eudicots
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Assembling the Angiosperm Tree of Life: Progress and Future Prospects
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Angiosperms Helped Put the Rain in the Rainforests: The Impact of Plant Physiological Evolution on Tropical Biodiversity1
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inferredcites →https://doi.org/10.3732/ajb.1000404openalex-snapshot
Angiosperm phylogeny: 17 genes, 640 taxa
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The origin and diversification of angiosperms
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Phylogeny and Evolution of the Angiosperms

What points at this work

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

inferred← citeshttps://doi.org/10.1002/ajb2.1479openalex-snapshot
Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107287openalex-snapshot
Combining molecular and geographical data to infer the phylogeny of Lamiales and its dispersal patterns in and out of the tropics
inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108716openalex-snapshot
Complex evolutionary history of Rosales mediated by extensive incomplete lineage sorting and hybridization
inferred← citeshttps://doi.org/10.1038/s41467-020-17116-5openalex-snapshot
Recent accelerated diversification in rosids occurred outside the tropics
inferred← citeshttps://doi.org/10.1093/biolinnean/blaa058openalex-snapshot
Macroevolution and shifts in the feeding biology of the New World scarab beetle tribe Phanaeini (Coleoptera: Scarabaeidae: Scarabaeinae)
inferred← citeshttps://doi.org/10.1101/2022.09.27.509719openalex-snapshot
Testing the evolutionary drivers of nitrogen-fixing symbioses in challenging soil environments
inferred← citeshttps://doi.org/10.1111/jipb.13972openalex-snapshot
Nuclear phylogenomics provide evidence to clarify key morphological evolution and whole‐genome duplication across rosids
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