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A protocol for targeted enrichment of intron‐containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae)
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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CHLOROPLAST DNA VARIATION WITHIN AND AMONG GENERA OF THE HEUCHERA GROUP (SAXIFRAGACEAE): EVIDENCE FOR CHLOROPLAST TRANSFER AND PARAPHYLY
inferredcites →https://doi.org/10.1007/978-1-59745-251-9_3openalex-snapshot
Multiple Alignment of DNA Sequences with MAFFT
inferredcites →https://doi.org/10.1016/j.ympev.2011.12.007openalex-snapshot
Applications of next-generation sequencing to phylogeography and phylogenetics
inferredcites →https://doi.org/10.1016/j.ympev.2014.08.013openalex-snapshot
Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
inferredcites →https://doi.org/10.1016/j.ympev.2014.11.011openalex-snapshot
Phylogeny, divergence times, and historical biogeography of the angiosperm family Saxifragaceae
inferredcites →https://doi.org/10.1038/35048692openalex-snapshot
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
inferredcites →https://doi.org/10.1038/nbt.1523openalex-snapshot
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
inferredcites →https://doi.org/10.1038/ng.911openalex-snapshot
Whole-genome sequencing of multiple Arabidopsis thaliana populations
inferredcites →https://doi.org/10.1046/j.1365-294x.2001.01285.xopenalex-snapshot
Chloroplast microsatellites and mitochondrial nad1 intron 2 sequences indicate congruent phylogenetic relationships among Swiss stone pine (Pinus cembra), Siberian stone pine (Pinus sibirica), and Siberian dwarf pine (Pinus pumila)
inferredcites →https://doi.org/10.1073/pnas.1232297100openalex-snapshot
Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain
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
inferredcites →https://doi.org/10.1080/10409230290771474openalex-snapshot
Utility of Low-Copy Nuclear Gene Sequences in Plant Phylogenetics
inferredcites →https://doi.org/10.1080/10635150801888871openalex-snapshot
Resolving an Ancient, Rapid Radiation in Saxifragales
inferredcites →https://doi.org/10.1093/bioinformatics/bth058openalex-snapshot
Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus
inferredcites →https://doi.org/10.1093/bioinformatics/btl446openalex-snapshot
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/molbev/msn226openalex-snapshot
Mitochondrial DNA of Vitis vinifera and the Issue of Rampant Horizontal Gene Transfer
inferredcites →https://doi.org/10.1093/nar/gkt289openalex-snapshot
OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets
inferredcites →https://doi.org/10.1093/nar/gkt377openalex-snapshot
STRAW: Species TRee Analysis Web server
inferredcites →https://doi.org/10.1093/sysbio/syp031openalex-snapshot
Estimating Species Phylogenies Using Coalescence Times among Sequences
inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
inferredcites →https://doi.org/10.1101/gr.2289704openalex-snapshot
Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements
inferredcites →https://doi.org/10.1111/j.1365-294x.2007.03640.xopenalex-snapshot
Ancient hybridization and mitochondrial capture between two species of chipmunks
inferredcites →https://doi.org/10.1111/j.1558-5646.1995.tb02309.xopenalex-snapshot
DISCORDANCE BETWEEN NUCLEAR AND CHLOROPLAST PHYLOGENIES IN THE HEUCHERA GROUP (SAXIFRAGACEAE)
inferredcites →https://doi.org/10.1111/nph.12395openalex-snapshot
One ring to rule them all? Genome sequencing provides new insights into the ‘master circle’ model of plant mitochondrial DNA structure
inferredcites →https://doi.org/10.1186/1471-2148-10-302openalex-snapshot
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
inferredcites →https://doi.org/10.1186/1471-2148-14-23openalex-snapshot
From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
inferredcites →https://doi.org/10.1186/2047-217x-1-18openalex-snapshot
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
inferredcites →https://doi.org/10.1371/journal.pone.0016404openalex-snapshot
The Mitochondrial Genome of the Legume Vigna radiata and the Analysis of Recombination across Short Mitochondrial Repeats
inferredcites →https://doi.org/10.1371/journal.pone.0109704openalex-snapshot
Phylogenetic Properties of 50 Nuclear Loci in Medicago (Leguminosae) Generated Using Multiplexed Sequence Capture and Next-Generation Sequencing
inferredcites →https://doi.org/10.2307/25027594openalex-snapshot
A Revision of the Genus Heuchera (Saxifragaceae) in Eastern North America
inferredcites →https://doi.org/10.3732/ajb.1100335openalex-snapshot
Navigating the tip of the genomic iceberg: Next‐generation sequencing for plant systematics
inferredcites →https://doi.org/10.3732/ajb.1100356openalex-snapshot
Targeted enrichment strategies for next‐generation plant biology
inferredcites →https://doi.org/10.3732/ajb.1200275openalex-snapshot
Polyploidization in Heuchera cylindrica (Saxifragaceae) did not result in a shift in climatic requirements
inferredcites →https://doi.org/10.3732/ajb.1400290openalex-snapshot
Phylogenetic relationships and character evolution in Heuchera (Saxifragaceae) on the basis of multiple nuclear loci
inferredcites →https://doi.org/10.3732/ajb.1500026openalex-snapshot
Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species
inferredcites →https://doi.org/10.3732/apps.1300085openalex-snapshot
A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae
inferredcites →https://doi.org/10.3732/apps.1400040openalex-snapshot
Microsatellite primers for the gynodioecious grassland perennial Saxifraga granulata (Saxifragaceae)
inferredcites →https://doi.org/10.3732/apps.1400042openalex-snapshot
Hyb‐Seq: Combining target enrichment and genome skimming for plant phylogenomics
inferredcites →https://doi.org/10.3732/apps.1400062openalex-snapshot
Geneious! Simplified genome skimming methods for phylogenetic systematic studies: A case study in Oreocarya (Boraginaceae)
inferredcites →https://doi.org/10.48550/arxiv.1303.3997openalex-snapshot
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems
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Phylogenomics supported by geometric morphometrics reveals delimitation of sexual species within the polyploid apomictic Ranunculus auricomus complex (Ranunculaceae)
inferred← citeshttps://doi.org/10.1002/tax.12450openalex-snapshot
Biogeography and habitat evolution of Saxifragaceae, with a revision of generic limits and a new tribal system
inferred← citeshttps://doi.org/10.1007/978-1-0716-3838-5_11openalex-snapshot
A Guide to Phylogenomic Inference
inferred← citeshttps://doi.org/10.1007/s44281-023-00026-zopenalex-snapshot
Integrating genomic sequencing resources: an innovative perspective on recycling with universal Angiosperms353 probe sets
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Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)
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Pseudo-parallel patterns of disjunctions in an Arctic-alpine plant lineage
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Exploring data processing strategies in NGS target enrichment to disentangle radiations in the tribe Cardueae (Compositae)
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Resolving the rapid plant radiation of early diverging lineages in the tropical Zingiberales: Pushing the limits of genomic data
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Nuclear and plastid DNA phylogeny of tribe Cardueae (Compositae) with Hyb-Seq data: A new subtribal classification and a temporal diversification framework
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Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study
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Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana)
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107070openalex-snapshot
Molecular phylogeny and ancestral biogeographic reconstruction of Platanthera subgenus Limnorchis (Orchidaceae) using target capture methods
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Development and phylogenetic utilities of a new set of single-/low-copy nuclear genes in Senecioneae (Asteraceae), with new insights into the tribal position and the relationships within subtribe Tussilagininae
inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108445openalex-snapshot
Target sequence capture informs generic delimitation and hybridization in the tribe Lasiopetaleae (Malvaceae)
inferred← citeshttps://doi.org/10.1080/23802359.2025.2529830openalex-snapshot
The complete chloroplast genome of Mitella nuda (Saxifragaceae)
inferred← citeshttps://doi.org/10.1086/698120openalex-snapshot
Geographic Range Dynamics Drove Ancient Hybridization in a Lineage of Angiosperms
inferred← citeshttps://doi.org/10.1086/715636openalex-snapshot
Discordance in a South African Memecylon Clade (Melastomataceae): Evidence for Reticulate Evolution
inferred← citeshttps://doi.org/10.1093/botlinnean/boy012openalex-snapshot
Integrative identification of incipient lineages in Heuchera longiflora (Saxifragaceae)
inferred← citeshttps://doi.org/10.1093/gbe/evad070openalex-snapshot
Filtration of Gene Trees From 9,000 Exons, Introns, and UCEs Disentangles Conflicting Phylogenomic Relationships in Tree Frogs (Hylidae)
inferred← citeshttps://doi.org/10.1093/sysbio/syac032openalex-snapshot
Target Enrichment and Extensive Population Sampling Help Untangle the Recent, Rapid Radiation of Oenothera Sect. Calylophus
inferred← citeshttps://doi.org/10.1093/sysbio/syad018openalex-snapshot
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method
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Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms
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Unraveling Phylogenetic Relationships, Reticulate Evolution, and Genome Composition of Polyploid Plant Complexes by Rad-Seq and Hyb-Seq
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Optimization of capture protocols across species targeting up to 32000 genes and their extension to pooled DNA
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Identifying climatic drivers of hybridization in Heuchereae (Saxifragaceae)
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Species delimitation in the grey zone: introgression obfuscates phylogenetic inference and species boundaries in a cryptic frog complex (Ranidae: Pulchrana picturata )
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Chloroplast genome evolution in >i /i<
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HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees
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Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae)
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Morphometrics and Phylogenomics Reveal a New Species ofHeuchera(Saxifragaceae) in Northeastern México
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Heuchera tuckasegeensissp. nov. (Saxifragaceae), a New Species from Western North Carolina
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Phylogenomics Yields New Insight Into Relationships Within Vernonieae (Asteraceae)
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A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade Micranthes (Saxifragaceae)
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Plastome Evolution in Saxifragaceae and Multiple Plastid Capture Events Involving Heuchera and Tiarella
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New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq)
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Plastid phylogenomics clarifies broad-level relationships in Bulbophyllum (Orchidaceae) and provides insights into range evolution of Australasian section Adelopetalum
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The Mitogenome of Sedum plumbizincicola (Crassulaceae): Insights into RNA Editing, Lateral Gene Transfer, and Phylogenetic Implications
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Geometric Morphometric Versus Genomic Patterns in a Large Polyploid Plant Species Complex
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Chloroplast Genomes and Comparative Analyses among Thirteen Taxa within Myrsinaceae s.str. Clade (Myrsinoideae, Primulaceae)
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Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales
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HybPiper: Extracting coding sequence and introns for phylogenetics from high‐throughput sequencing reads using target enrichment
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Performance of intron 7 of the β-fibrinogen gene for phylogenetic analysis: An example using gladiator frogs, Boana Gray, 1825 (Anura, Hylidae, Cophomantinae)
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Investigating the landscape of plant-pollinator interactions in a hybrid zone
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The geographic structure of chloroplast capture in a hybrid zone
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Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”?
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