Research graph
References from Unravelling Complex Hybrid and Polyploid Evolutionary Relationships Using Phylogenetic Placement of Homologous Gene Copies from Target Enrichment Data. Local targets link to admitted publications; unresolved targets remain external evidence.
Single geographic origin of a widespread autotetraploid Arabidopsis arenosa lineage followed by interploidy admixture
10.1093/molbev/msv089 · 2015 · External reference
ggExtra: add marginal histograms to “ggplot2”, and more “ggplot2” enhancements
2023 · External reference
Paleopolyploidy in the Brassicales: analyses of the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and other Brassicales
10.1093/gbe/evp040 · 2009 · External reference
Sequence capture: obsolete or irreplaceable? A thorough validation across phylogenetic distances and its applicability to hybrids and allopolyploids
10.1111/1755-0998.13806 · 2023 · External reference
MoreTreeTools: tools for manipulating phylogenetic trees
2014 · External reference
Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood
10.1093/sysbio/syr010 · 2011 · External reference
Trimmomatic: a flexible trimmer for Illumina sequence data
10.1093/bioinformatics/btu170 · 2014 · External reference
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
10.1038/nature01521 · 2003 · External reference
Package “ggalluvial.”
2019 · External reference
Gradual evolution of allopolyploidy in Arabidopsis suecica
10.1038/s41559-021-01525-w · 2021 · External reference
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
10.1093/bioinformatics/btp348 · 2009 · External reference
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
10.1126/science.1253435 · 2014 · External reference
Ghost introgression facilitates genomic divergence of a sympatric cryptic lineage in Cycas revoluta
10.1002/ece3.10435 · 2023 · External reference
SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis
10.1007/978-3-540-35306-5_10 · 2007 · External reference
Gene retention, fractionation and subgenome differences in polyploid plants
10.1038/s41477-018-0136-7 · 2018 · External reference
Whole-genome duplication and plant macroevolution
10.1016/j.tplants.2018.07.006 · 2018 · External reference
Metagenomic analysis using phylogenetic placement—a review of the first decade
10.3389/fbinf.2022.871393 · 2022 · External reference
Unveiling the patterns of reticulated evolutionary processes with phylogenomics: hybridization and polyploidy in the genus Rosa
10.1093/sysbio/syab064 · 2022 · External reference
Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants
10.1073/pnas.1300127110 · 2013 · External reference
Is post-polyploidization diploidization the key to the evolutionary success of angiosperms?: diploidization in polyploid angiosperms
10.1111/boj.12357 · 2016 · External reference
Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family
10.1186/s12915-022-01297-0 · 2022 · External reference
Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization
10.1371/journal.pgen.1007267 · 2018 · External reference
Phylogenomics of neogastropoda: the backbone hidden in the bush
10.1093/sysbio/syae010 · 2024 · External reference
Distinguishing homologous from analogous proteins
10.2307/2412448 · 1970 · External reference
homologizer: phylogenetic phasing of gene copies into polyploid subgenomes
10.1111/2041-210x.14072 · 2023 · External reference
10.1093/sysbio/syad076
10.1093/sysbio/syad076 · External reference
Phylogenomic analysis of the hemp family (Cannabaceae) reveals deep cyto-nuclear discordance and provides new insights into generic relationships
10.1111/jse.12920 · 2023 · External reference
viridis(Lite)—colorblind-friendly color maps for R
2023 · External reference
nQuack: an R package for predicting ploidal level from sequence data using site-based heterozygosity
10.1002/aps3.11606 · 2024 · External reference
Shehbazia (Shehbazieae, Cruciferae), a new monotypic genus and tribe of hybrid origin from Tibet
10.14258/turczaninowia.17.4.3 · 2014 · External reference
An updated classification of the Brassicaceae (Cruciferae)
10.3897/phytokeys.220.97724 · 2023 · External reference
Homoeologs: what are they and how do we infer them?
10.1016/j.tplants.2016.02.005 · 2016 · External reference
Linked by ancestral bonds: multiple whole-genome duplications and reticulate evolution in a Brassicaceae tribe
10.1093/molbev/msaa327 · 2021 · External reference
PloiDB : the plant ploidy database
2023 · External reference
A Hyb-Seq phylogeny of Boechera and related genera using a combination of Angiosperms353 and Brassicaceae-specific bait sets
10.1002/ajb2.16226 · 2023 · External reference
10.1016/j.cub.2023.08.026
10.1016/j.cub.2023.08.026 · External reference
The best of both worlds: combining lineage-specific and universal bait sets in target-enrichment hybridization reactions
10.1002/aps3.11438 · 2021 · External reference
The Gynandropsis gynandra genome provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae
10.1093/plcell/koad018 · 2023 · External reference
Expanding the triangle of U: comparative analysis of the Hirschfeldia incana genome provides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits
10.1093/aob/mcae179 · 2024 · External reference
An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes
10.1186/s12864-017-4220-6 · 2017 · External reference
Taming the wild: resolving the gene pools of non-model Arabidopsis lineages
10.1186/s12862-014-0224-x · 2014 · External reference
A time-calibrated road map of Brassicaceae species radiation and evolutionary history
2015 · External reference
Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events
10.1093/aob/mcz123 · 2020 · External reference
Application of phylogenetic networks in evolutionary studies
10.1093/molbev/msj030 · 2006 · External reference
A unique recent origin of the allotetraploid species Arabidopsis suecica: evidence from nuclear DNA markers
10.1093/molbev/msk006 · 2006 · External reference
Nightmare or delight: taxonomic circumscription meets reticulate evolution in the phylogenomic era
10.1016/j.ympev.2023.107914 · 2023 · External reference
HybPiper: extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment
10.3732/apps.1600016 · 2016 · 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
Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting
10.1093/sysbio/syt012 · 2013 · External reference
Molecular phylogeny and systematics of the genus Draba (Brassicaceae) and identification of its most closely related genera
10.1016/j.ympev.2010.02.012 · 2010 · External reference
Navigating phylogenetic conflict and evolutionary inference in plants with target-capture data
10.1071/sb24011 · 2025 · External reference
The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell
10.1093/bioinformatics/btq243 · 2010 · External reference
Systematics and evolution of arctic-alpine Arabis alpina (Brassicaceae) and its closest relatives in the eastern Mediterranean
10.3732/ajb.1100447 · 2012 · 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
Phylogenetic signatures of adaptation: the Arabis hirsuta species aggregate (Brassicaceae) revisited
10.1016/j.ppees.2014.06.001 · 2014 · External reference
ggpubr: “ggplot2” based publication ready plots
2023 · External reference
Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus
10.1002/ajb2.1068 · 2018 · External reference
MAFFT multiple sequence alignment software version 7: improvements in performance and usability
10.1093/molbev/mst010 · 2013 · External reference
The spatio-temporal diversification of SRK alleles in an Arabidopsis polyploid hybrid and introgression zone
10.1016/j.ppees.2023.125760 · 2023 · External reference
Divergence of annual and perennial species in the Brassicaceae and the contribution of cis-acting variation at flc orthologues
10.1111/mec.14084 · 2017 · External reference
Capacity building in crucifer research—from BrassiBase to a taxonomic expert network (BrassiTEN)
10.1007/s00606-025-01964-z · 2025 · External reference
BrassiBase: introduction to a novel knowledge database on Brassicaceae evolution
10.1093/pcp/pct158 · 2014 · External reference
Molecular data indicate complex intra- and intercontinental differentiation of American Draba (Brassicaceae)
10.2307/3298659 · 2002 · External reference
The plant model system Arabidopsis set into an evolutionary, systematic and spatio-temporal context
2018 · External reference
Database taxonomics as key to modern plant biology
10.1016/j.tplants.2017.10.005 · 2018 · External reference
East Asian Arabis species (Brassicaceae) exemplify past hybridization and subsequent emergence of three main evolutionary lineages in East Asia, America and the amphi-Beringian region
10.1093/botlinnean/box020 · 2017 · External reference
Underexplored biodiversity of Eastern Mediterranean biota: systematics and evolutionary history of the genus Aubrieta (Brassicaceae)
10.1093/aob/mcw204 · 2017 · External reference
Systematics, taxonomy and biogeography of three new Asian genera of Brassicaceae tribe Arabideae: an ancient distribution circle around the Asian high mountains
10.1002/tax.615003 · 2012 · External reference
Colonizing the American continent: systematics of the genus Arabis in North America (Brassicaceae)
10.3732/ajb.0900366 · 2010 · External reference
Three times out of Asia Minor: the phylogeography of Arabis alpina L. (Brassicaceae)
10.1111/j.1365-294x.2005.02848.x · 2006 · External reference
KMC 3: counting and manipulating k-mer statistics
10.1093/bioinformatics/btx304 · 2017 · External reference
Orthologs, paralogs, and evolutionary genomics
10.1146/annurev.genet.39.073003.114725 · 2005 · External reference
ggpointdensity: a cross between a 2D density plot and a scatter plot
10.32614/cran.package.ggpointdensity · 2019 · External reference
Phylogenetic analysis of allotetraploid species using polarized genomic sequences
10.1093/sysbio/syad009 · 2023 · External reference
BoSSA: a bunch of structure and sequence analysis
2020 · External reference
Reticulate evolution of the tertiary relict Osmanthus
2023 · External reference
Gene duplicability of core genes is highly consistent across all angiosperms
10.1105/tpc.15.00877 · 2016 · External reference
Chasing ghosts: allopolyploid origin of Oxyria sinensis (Polygonaceae) from its only diploid congener and an unknown ancestor
10.1111/mec.14097 · 2017 · External reference
Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering
10.1073/pnas.2109204118 · 2021 · External reference
Dsuite—fast D-statistics and related admixture evidence from VCF files
10.1111/1755-0998.13265 · 2021 · External reference
Hybridization-facilitated genome merger and repeated chromosome fusion after 8 million years
10.1111/tpj.14065 · 2018 · External reference
Genome evolution in Arabideae was marked by frequent centromere repositioning
10.1105/tpc.19.00557 · 2020 · External reference
Recently formed polyploid plants diversify at lower rates
10.1126/science.1207205 · 2011 · External reference
Target capture methods offer insight into the evolution of rapidly diverged taxa and resolve allopolyploid homeologs in the fern genus Polypodium s.s
10.1600/036364423x16758873924135 · 2023 · External reference
Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae)
10.1093/sysbio/syab032 · 2021 · External reference
HybPhaser: a workflow for the detection and phasing of hybrids in target capture data sets
10.1002/aps3.11441 · 2021 · External reference
Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity
10.1111/nph.15732 · 2019 · External reference
Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism
10.1038/ng.3617 · 2016 · External reference
Genome sequencing reveals the origin of the allotetraploid Arabidopsis suecica
10.1093/molbev/msw299 · 2017 · External reference
The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic
10.1111/1755-0998.13280 · 2021 · External reference
One thousand plant transcriptomes and the phylogenomics of green plants
10.1038/s41586-019-1693-2 · 2019 · External reference
Hybridization and introgression are prevalent in Southern European Erysimum (Brassicaceae) species
10.1093/aob/mcac048 · 2023 · External reference
Phylogenetics of allopolyploids
10.1146/annurev-ecolsys-110316-022729 · 2017 · External reference
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
10.1093/bioinformatics/bty633 · 2019 · External reference
Frequent allopolyploidy with distant progenitors in the moss genera Physcomitrium and Entosthodon (Funariaceae) identified via subgenome phasing of targeted nuclear genes
10.1093/evolut/qpad171 · 2023 · External reference
10.1016/j.csbj.2022.06.026 · 2022 · Admitted local publication
Unresolved reference
2022 · External reference
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
10.1038/s41467-020-14998-3 · 2020 · External reference
MACSE v2: toolkit for the alignment of coding sequences accounting for frameshifts and stop codons
10.1093/molbev/msy159 · 2018 · External reference
phytools: an R package for phylogenetic comparative biology (and other things): phytools: R package
10.1111/j.2041-210x.2011.00169.x · 2012 · External reference
Polyploid phylogenetics
10.1111/nph.17105 · 2021 · External reference
Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing
10.1111/nph.14111 · 2017 · External reference
Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process
10.1111/mec.14909 · 2018 · External reference
Chloroplast DNA indicates a single origin of the allotetraploid Arabidopsis suecica
10.1046/j.1420-9101.2003.00554.x · 2003 · External reference
Tracking the ancestry of known and “ghost” homeologous subgenomes in model grass Brachypodium polyploids
10.1111/tpj.15650 · 2022 · External reference
Nano-Strainer: a workflow for the identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads
10.1002/ece3.10190 · 2023 · External reference
Arabidopsis hybrid speciation processes
10.1073/pnas.1104212108 · 2011 · External reference
The evolutionary history of the Arabidopsis arenosa complex: diverse tetraploids mask the Western Carpathian center of species and genetic diversity
10.1371/journal.pone.0042691 · 2012 · External reference
The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri
10.1111/j.1365-294x.2009.04329.x · 2009 · External reference
The hidden duplication past of Arabidopsis thaliana
10.1073/pnas.212522399 · 2002 · External reference
Revisiting the bicontinental allopolyploid origin of Australasian Lepidium species with amplicon sequencing of 15 nuclear genes
10.1007/s00606-024-01899-x · 2024 · External reference
Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting
10.1371/journal.pgen.1005896 · 2016 · External reference
PhyloNetworks: a package for phylogenetic networks
10.1093/molbev/msx235 · 2017 · External reference
Polyploidy and angiosperm diversification
10.3732/ajb.0800079 · 2009 · External reference
Ancient WGD events as drivers of key innovations in angiosperms
10.1016/j.pbi.2016.03.015 · 2016 · External reference
Plant genomes: markers of evolutionary history and drivers of evolutionary change
10.1002/ppp3.10159 · 2021 · External reference
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
10.1093/bioinformatics/btu033 · 2014 · External reference
Deep reticulation: the long legacy of hybridization in vascular plant evolution
10.1111/tpj.16142 · 2023 · External reference
Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms
10.1038/s41477-021-00964-4 · 2021 · External reference
Gene-tree reconciliation with MUL-trees to resolve polyploidy events
10.1093/sysbio/syx044 · 2017 · External reference
Benefits and limits of phasing alleles for network inference of allopolyploid complexes
10.1093/sysbio/syae024 · 2024 · External reference
The role of deep hybridization in fern speciation: examples from the Thelypteridaceae
10.1002/ajb2.16388 · 2024 · External reference
Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
10.1101/gr.168997.113 · 2014 · External reference
A target capture-based method to estimate ploidy from herbarium specimens
10.3389/fpls.2019.00937 · 2019 · External reference
ggdendro: create Dendrograms and Tree Diagrams Using “ggplot2.”
2022 · External reference
Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae
10.1038/s41467-020-17605-7 · 2020 · External reference
Synteny identifies reliable orthologs for phylogenomics and comparative genomics of the Brassicaceae
10.1093/gbe/evad034 · 2023 · External reference
Treeio: an R package for phylogenetic tree input and output with richly annotated and associated data
10.1093/molbev/msz240 · 2020 · External reference
Phylogenomic assessment of the role of hybridization and introgression in trait evolution
10.1371/journal.pgen.1009701 · 2021 · External reference
nQuire: a statistical framework for ploidy estimation using next generation sequencing
10.1186/s12859-018-2128-z · 2018 · External reference
10.1007/978-3-319-24277-4
10.1007/978-3-319-24277-4 · 2016 · External reference
stringr: simple, consistent wrappers for common string operations
2022 · External reference
ggridges: ridgeline plots in “ggplot2.”
2022 · External reference
Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
10.1038/nplants.2014.23 · 2015 · External reference
Arabis alpina: a perennial model plant for ecological genomics and life-history evolution
10.1111/1755-0998.13490 · 2022 · External reference
Species tree estimation and the impact of gene loss following whole-genome duplication
10.1093/sysbio/syac040 · 2022 · External reference
Maximum parsimony inference of phylogenetic networks in the presence of polyploid complexes
10.1093/sysbio/syab081 · 2022 · External reference
ggtree : an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data
10.1111/2041-210x.12628 · 2017 · External reference
ASTRAL-Pro: quartet-based species-tree inference despite paralogy
10.1093/molbev/msaa139 · 2020 · External reference
Using nuclear gene data for plant phylogenetics: progress and prospects II. Next-gen approaches
10.1111/jse.12174 · 2015 · External reference
Phylogenomics and the rise of the angiosperms
10.1038/s41586-024-07324-0 · 2024 · External reference
Inference of ancient whole genome duplications and the evolution of the gene duplication and loss rate
10.1093/molbev/msz088 · 2019 · External reference
