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References from Simultaneous Inference of Flora‐Wide Nuclear and Plastid Phylogenies Using Angiosperms353 Sequence Capture Data. Local targets link to admitted publications; unresolved targets remain external evidence.
Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates
10.1016/j.isci.2018.12.002 · 2019 · External reference
Using Ancient Sedimentary DNA to Forecast Ecosystem Trajectories Under Climate Change
10.1098/rstb.2023.0017 · 2024 · External reference
The Treasure Vault Can Be Opened: Large‐Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material
10.3390/plants9040432 · 2020 · External reference
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project
10.3389/fgene.2019.01407 · 2020 · External reference
Unresolved reference
External reference
Settling a Family Feud: A High‐Level Phylogenomic Framework for the Gentianales Based on 353 Nuclear Genes and Partial Plastomes
10.1002/ajb2.1697 · 2021 · External reference
Amazonia Is the Primary Source of Neotropical Biodiversity
10.1073/pnas.1713819115 · 2018 · External reference
A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life
10.1093/sysbio/syab035 · 2022 · External reference
Exploring Angiosperms353: An Open, Community Toolkit for Collaborative Phylogenomic Research on Flowering Plants
10.1002/ajb2.1703 · 2021 · External reference
Molecular Phylogenetics and Evolution of Orchidinae and Selected Habenariinae (Orchidaceae)
10.1046/j.1095-8339.2003.00157.x · 2003 · External reference
Unresolved reference
External reference
Trimmomatic: A Flexible Trimmer for Illumina Sequence Data
10.1093/bioinformatics/btu170 · 2014 · External reference
Unresolved reference
2016 · External reference
Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms
10.3389/fpls.2019.01102 · 2019 · External reference
Evolutionary Histories Determine DNA Barcoding Success in Vascular Plants: Seven Case Studies Using Intraspecific Broad Sampling of Closely Related Species
10.1186/s12862-016-0678-0 · 2016 · External reference
Recent and Local Diversification of Central American Understorey Palms
10.1111/geb.13521 · 2022 · External reference
Target Capture Sequencing Unravels Rubus Evolution
10.3389/fpls.2019.01615 · 2019 · External reference
The Merging of Community Ecology and Phylogenetic Biology
10.1111/j.1461-0248.2009.01314.x · 2009 · External reference
Phylogenetic Analysis in the Festuca‐Lolium Complex Using Molecular Markers and ITS rDNA
10.1007/s001220050512 · 1997 · External reference
From Barcodes to Genomes: Extending the Concept of DNA Barcoding
10.1111/mec.13549 · 2016 · External reference
Phylogeny of Campanuloideae (Campanulaceae) With Emphasis on the Utility of Nuclear Pentatricopeptide Repeat (PPR) Genes (EJ Louis, ed.)
10.1371/journal.pone.0094199 · 2014 · External reference
The Hidden Side of Invasions: Massive Introgression by Local Genes
2008 · External reference
Twelve Years of SAMtools and BCFtools
10.1093/gigascience/giab008 · 2021 · External reference
A Dedicated Target Capture Approach Reveals Variable Genetic Markers Across Micro‐ and Macro‐Evolutionary Time Scales in Palms
10.1111/1755-0998.12945 · 2019 · External reference
Dispersal Assembly of Rain Forest Tree Communities Across the Amazon Basin
10.1073/pnas.1613655114 · 2017 · External reference
Hyb‐Seq for Flowering Plant Systematics
10.1016/j.tplants.2019.07.011 · 2019 · External reference
A Rapid DNA Isolation Procedure for Small Quantities of Fresh Leaf Tissue
1987 · External reference
BEAST: Bayesian Evolutionary Analysis by Sampling Trees
10.1186/1471-2148-7-214 · 2007 · External reference
MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report
10.1093/bioinformatics/btw354 · 2016 · External reference
Unresolved reference
External reference
Preserving the Evolutionary Potential of Floras in Biodiversity Hotspots
10.1038/nature05587 · 2007 · External reference
Gymnosperms on the EDGE
10.1038/s41598-018-24365-4 · 2018 · External reference
Predicting Regional Hotspots of Phylogenetic Diversity Across Multiple Species Groups
10.1111/ddi.13125 · 2020 · External reference
A Novel Phylogeny‐Based Generic Classification for Chenopodium Sensu Lato, and a Tribal Rearrangement of Chenopodioideae (Chenopodiaceae)
10.3372/wi.42.42101 · 2012 · External reference
Phylogenetic Relationships and Genetic Diversity Among Members of the Festuca‐Lolium Complex (Poaceae) Based on ITS Sequence Data
10.1007/bf00985265 · 2000 · External reference
Parallel and Convergent Diversification in Two Northern Hemispheric Species‐Rich Carex Lineages (Cyperaceae)
10.1007/s13127-014-0171-9 · 2014 · External reference
A Nuclear Phylogenomic Tree of Grasses (Poaceae) Recovers Current Classification Despite Gene Tree Incongruence
10.1111/nph.20263 · 2025 · External reference
Chloranthus Genome Provides Insights Into the Early Diversification of Angiosperms
10.1038/s41467-021-26922-4 · 2021 · External reference
Target Sequence Data Shed New Light on the Infrafamilial Classification of Araceae
10.1002/ajb2.16117 · 2023 · External reference
Strategies for Reducing Per‐Sample Costs in Target Capture Sequencing for Phylogenomics and Population Genomics in Plants
10.1002/aps3.11337 · 2020 · External reference
Bayesian Inference of Species Trees From Multilocus Data
10.1093/molbev/msp274 · 2010 · External reference
Some Limitations of Public Sequence Data for Phylogenetic Inference (In Plants)
10.1371/journal.pone.0098986 · 2014 · External reference
Implementing Green Infrastructure for the Spatial Planning of Peri‐Urban Areas in Geneva, Switzerland
10.3390/su12041387 · 2020 · External reference
Phylogenetics of Tribe Orchideae (Orchidaceae: Orchidoideae) Based on Combined DNA Matrices: Inferences Regarding Timing of Diversification and Evolution of Pollination Syndromes
10.1093/aob/mcs083 · 2012 · External reference
Effects of Taxon Sampling and Tree Reconstruction Methods on Phylodiversity Metrics
10.1002/ece3.5425 · 2019 · External reference
V.PhyloMaker2: An Updated and Enlarged R Package That Can Generate Very Large Phylogenies for Vascular Plants
10.1016/j.pld.2022.05.005 · 2022 · External reference
A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes From Any Flowering Plant Designed Using k‐Medoids Clustering
10.1093/sysbio/syy086 · 2019 · External reference
Unresolved reference
External reference
A World‐Wide Perspective on Crucifer Speciation and Evolution: Phylogenetics, Biogeography and Trait Evolution in Tribe Arabideae
10.1093/aob/mct165 · 2013 · External reference
Molecular Phylogeny of Persicaria (Persicarieae, Polygonaceae)
10.1600/036364408783887302 · 2008 · External reference
Challenging Urban Species Diversity: Contrasting Phylogenetic Patterns Across Plant Functional Groups in Germany
10.1111/j.1461-0248.2008.01217.x · 2008 · External reference
Towards a Comprehensive Barcoding and Phylogenomic Reference for the European Arctic‐Alpine Flora
10.1080/23818107.2025.2549565 · 2025 · External reference
Reconstructing Dipsacales Phylogeny Using Angiosperms353: Issues and Insights
10.1002/ajb2.1695 · 2021 · External reference
Interactive Tree of Life (iTOL) v5: An Online Tool for Phylogenetic Tree Display and Annotation
10.1093/nar/gkab301 · 2021 · External reference
For Common Community Phylogenetic Analyses, Go Ahead and Use Synthesis Phylogenies
10.1002/ecy.2788 · 2019 · External reference
Fast and Accurate Short Read Alignment With Burrows–Wheeler Transform
10.1093/bioinformatics/btp324 · 2009 · External reference
Capturing Single‐Copy Nuclear Genes, Organellar Genomes, and Nuclear Ribosomal DNA from Deep Genome Skimming Data for Plant Phylogenetics: A Case Study in Vitaceae
10.1111/jse.12806 · 2021 · External reference
Phylogenetic Relationships and Chloroplast Capture in the Amelanchier‐Malacomeles‐Peraphyllum Clade (Maleae, Rosaceae): Evidence From Chloroplast Genome and Nuclear Ribosomal DNA Data Using Genome Skimming
10.1016/j.ympev.2020.106784 · 2020 · External reference
Expanded Phylogenetic and Dating Analyses of the Apples and Their Relatives (Pyreae, Rosaceae)
10.1016/j.ympev.2011.10.005 · 2012 · External reference
A Metacalibrated Time‐Tree Documents the Early Rise of Flowering Plant Phylogenetic Diversity
10.1111/nph.13264 · 2015 · External reference
TreeShrink: Fast and Accurate Detection of Outlier Long Branches in Collections of Phylogenetic Trees
10.1186/s12864-018-4620-2 · 2018 · External reference
How to Handle Speciose Clades? Mass Taxon‐Sampling as a Strategy Towards Illuminating the Natural History of Campanula (Campanuloideae)
10.1371/journal.pone.0050076 · 2012 · External reference
A Tale of Worldwide Success: Behind the Scenes of Carex (Cyperaceae) Biogeography and Diversification
10.1111/jse.12549 · 2019 · External reference
A Nuclear Phylogenomic Study of the Angiosperm Order Myrtales, Exploring the Potential and Limitations of the Universal Angiosperms353 Probe Set
10.1002/ajb2.1699 · 2021 · External reference
Exploring Angiosperms353: Developing and Applying a Universal Toolkit for Flowering Plant Phylogenomics
10.1002/aps3.11443 · 2021 · External reference
New Targets Acquired: Improving Locus Recovery From the Angiosperms353 Probe Set
10.1002/aps3.11420 · 2021 · External reference
Phylogenomic Analyses Based on Genome‐Skimming Data Reveal Cyto‐Nuclear Discordance in the Evolutionary History of Cotoneaster (Rosaceae)
10.1016/j.ympev.2021.107083 · 2021 · External reference
Evolution of Endemism on a Young Tropical Mountain
10.1038/nature14949 · 2015 · External reference
IQ‐TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
10.1093/molbev/msaa015 · 2020 · External reference
Phylogenetic Measures of Biodiversity and Neo‐ and Paleo‐Endemism in Australian Acacia
10.1038/ncomms5473 · 2014 · External reference
Evaluating the Utility of Deep Genome Skimming for Phylogenomic Analyses: A Case Study in the Species‐Rich Genus Rhododendron
10.1016/j.pld.2025.04.006 · 2025 · External reference
Phylogenetic Patterns of Extinction Risk in the Endemic Flora of a Mediterranean Hotspot as a Guiding Tool for Preemptive Conservation Actions
10.3389/fevo.2020.571587 · 2020 · External reference
Unresolved reference
External reference
Plant DNA Barcodes and the Influence of Gene Flow
10.1111/j.1755-0998.2012.03130.x · 2012 · External reference
Species Delimitation and Relationships: The Dance of the Seven Veils
10.12705/641.24 · 2015 · External reference
The Genetics of Evolutionary Radiations
10.1111/brv.12598 · 2020 · External reference
Unresolved reference
External reference
Unresolved reference
2022 · External reference
One Thousand Plant Transcriptomes and the Phylogenomics of Green Plants
10.1038/s41586-019-1693-2 · 2019 · External reference
The Andes Through Time: Evolution and Distribution of Andean Floras
10.1016/j.tplants.2021.09.010 · 2022 · External reference
Advancing EDGE Zones to Identify Spatial Conservation Priorities of Tetrapod Evolutionary History
10.1038/s41467-024-51992-5 · 2024 · External reference
REFMAKER: Make Your Own Reference to Target Nuclear Loci in Low Coverage Genome Skimming Libraries. Phylogenomic Application in Sapotaceae
10.1016/j.ympev.2023.107826 · 2023 · External reference
ORTHOSKIM: In Silico Sequence Capture From Genomic and Transcriptomic Libraries for Phylogenomic and Barcoding Applications
10.1111/1755-0998.13584 · 2022 · External reference
An Updated Megaphylogeny of Plants, a Tool for Generating Plant Phylogenies and an Analysis of Phylogenetic Community Structure
10.1093/jpe/rtv047 · 2016 · External reference
Are Phylogenies Resolved at the Genus Level Appropriate for Studies on Phylogenetic Structure of Species Assemblages?
10.1016/j.pld.2020.11.005 · 2021 · External reference
Evolutionary Assembly of Flowering Plants Into Sky Islands
10.1038/s41559-021-01423-1 · 2021 · External reference
The Delayed and Geographically Heterogeneous Diversification of Flowering Plant Families
10.1038/s41559-020-1241-3 · 2020 · External reference
BOLD: The Barcode of Life Data System
10.1111/j.1471-8286.2007.01678.x · 2007 · External reference
Phytools: An R Package for Phylogenetic Comparative Biology (and Other Things)
10.1111/j.2041-210x.2011.00169.x · 2012 · External reference
Phylogenetic Consequences of Cytoplasmic Gene Flow in Plants
1991 · External reference
Cost‐Effective, High‐Throughput DNA Sequencing Libraries for Multiplexed Target Capture
10.1101/gr.128124.111 · 2012 · External reference
Rapid Climate Change Results in Long‐Lasting Spatial Homogenization of Phylogenetic Diversity
10.1038/s41467-020-18343-6 · 2020 · External reference
Testing the Impact of Calibration on Molecular Divergence Times Using a Fossil‐Rich Group: The Case of Nothofagus (Fagales)
10.1093/sysbio/syr116 · 2012 · External reference
What Is the Age of Flowering Plants?
10.1093/jxb/erac130 · 2022 · External reference
Contrasted Patterns of Hyperdiversification in Mediterranean Hotspots
10.1073/pnas.0805607106 · 2009 · External reference
Systematics, Biogeography, and Character Evolution of the Legume Tribe Fabeae With Special Focus on the Middle‐Atlantic Island Lineages
10.1186/1471-2148-12-250 · 2012 · External reference
BUSCO: Assessing Genome Assembly and Annotation Completeness With Single‐Copy Orthologs
10.1093/bioinformatics/btv351 · 2015 · External reference
Recent Assembly of the Cerrado, a Neotropical Plant Diversity Hotspot, by In Situ Evolution of Adaptations to Fire
10.1073/pnas.0903410106 · 2009 · External reference
The Genomics for Australian Plants (GAP) Framework Initiative—Developing Genomic Resources for Understanding the Evolution and Conservation of the Australian Flora
10.1071/sb24022 · 2024 · External reference
On the Potential of Angiosperms353 for Population Genomic Studies
10.1002/aps3.11419 · 2021 · External reference
Use of Nuclear Genes for Phylogeny Reconstruction in Plants
10.1071/sb03015 · 2004 · External reference
Constructing a Broadly Inclusive Seed Plant Phylogeny
10.1002/ajb2.1019 · 2018 · External reference
treePL: Divergence Time Estimation Using Penalized Likelihood for Large Phylogenies
10.1093/bioinformatics/bts492 · 2012 · External reference
Tempo and Drivers of Plant Diversification in the European Mountain System
10.1038/s41467-022-30394-5 · 2022 · External reference
How Just a Few Makes a Lot: Speciation via Reticulation and Apomixis on Example of European Brambles (Rubus Subgen. Rubus, Rosaceae)
10.1016/j.ympev.2015.04.007 · 2015 · External reference
Discordance Between Nuclear and Chloroplast Phylogenies in the Heuchera Group (Saxifragaceae)
10.1111/j.1558-5646.1995.tb02309.x · 1995 · External reference
Spatial Phylogenetics Reveals Evolutionary Constraints on the Assembly of a Large Regional Flora
10.1002/ajb2.1191 · 2018 · External reference
Polyploidy, Hybridization, and the Invasion of New Habitats
10.2307/2399224 · 1985 · External reference
Genetic Divergence of Clematis alpina in the Swiss Prealps: A Tale of the Margins
10.1007/s00035-025-00333-3 · 2025 · External reference
Nuclear Phylogenomic Analyses of Asterids Conflict With Plastome Trees and Support Novel Relationships Among Major Lineages
10.1002/ajb2.1468 · 2020 · External reference
Megaphylogenetic Specimen‐Level Approaches to the Carex (Cyperaceae) Phylogeny Using ITS, ETS, and matK Sequences: Implications for Classification
10.1600/036364416x692497 · 2016 · External reference
Comprehending Cornales: Phylogenetic Reconstruction of the Order Using the Angiosperms353 Probe Set
10.1002/ajb2.1696 · 2021 · External reference
Spatial Phylogenetics of the Native California Flora
10.1186/s12915-017-0435-x · 2017 · External reference
Continental‐Scale Spatial Phylogenetics of Australian Angiosperms Provides Insights Into Ecology, Evolution and Conservation
10.1111/jbi.12797 · 2016 · External reference
Consequences of Climate Change on the Tree of Life in Europe
10.1038/nature09705 · 2011 · External reference
Phylogeny of Broad‐Leaved and Fine‐Leaved Festuca Lineages (Poaceae) Based on Nuclear ITS Sequences
2002 · External reference
A Model for Chloroplast Capture
10.1111/j.0014-3820.2003.tb00585.x · 2003 · External reference
SILEX: A Fast and Inexpensive High‐Quality DNA Extraction Method Suitable for Multiple Sequencing Platforms and Recalcitrant Plant Species
10.1186/s13007-020-00652-y · 2020 · External reference
From Cacti to Carnivores: Improved Phylotranscriptomic Sampling and Hierarchical Homology Inference Provide Further Insight Into the Evolution of Caryophyllales
10.1002/ajb2.1069 · 2018 · External reference
Unresolved reference
2009 · External reference
Exploring the Phylogenetic Structure of Ecological Communities: An Example for Rain Forest Trees
10.1086/303378 · 2000 · External reference
Catalogue Dynamique de la Flore de Genève
1966 · External reference
Plant Extinctions and Introductions Lead to Phylogenetic and Taxonomic Homogenization of the European Flora
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Uplift‐Driven Diversification in the Hengduan Mountains, a Temperate Biodiversity Hotspot
2017 · External reference
Phylogenetic Analyses Confirm Polyphyly of the Genus Campanula (Campanulaceae s. Str.), Leading to a Proposal for Generic Reappraisal
10.1111/jse.12586 · 2021 · External reference
Phylogenomic Insights Into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling
10.1016/j.xplc.2020.100027 · 2020 · External reference
Three Keys to the Radiation of Angiosperms Into Freezing Environments
10.1038/nature12872 · 2014 · External reference
Resolution of Deep Angiosperm Phylogeny Using Conserved Nuclear Genes and Estimates of Early Divergence Times
10.1038/ncomms5956 · 2014 · External reference
Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet‐Based Species Trees
10.1093/molbev/msac215 · 2022 · External reference
Nuclear Phylogenomics of Asteraceae With Increased Sampling Provides New Insights Into Convergent Morphological and Molecular Evolution
10.1016/j.xplc.2024.100851 · 2024 · External reference
Phylogenomics and the Rise of the Angiosperms
10.1038/s41586-024-07324-0 · 2024 · External reference
