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Biased gene retention in the face of massive nuclear introgression obscures species relationships

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Arabidopsis family ties: molecular phylogeny and age estimates in Brassicaceae
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The shrunken genome of Arabidopsis thaliana
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ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments
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Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
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Butterfly genome reveals promiscuous exchange of mimicry adaptations among species
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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
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The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure
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The Capsella rubella genome and the genomic consequences of rapid mating system evolution
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The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
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Recombination and linkage disequilibrium in Arabidopsis thaliana
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The Cardamine hirsuta genome offers insight into the evolution of morphological diversity
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Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
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Young inversion with multiple linked QTLs under selection in a hybrid zone
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Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana
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Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins
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Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants
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Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti
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A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting
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APE: Analyses of Phylogenetics and Evolution in R language
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The Sequence Alignment/Map format and SAMtools
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phangorn: phylogenetic analysis in R
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Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
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Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
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D obzhansky , B ateson , and the Genetics of Speciation
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Toward a Global Phylogeny of the Brassicaceae
inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/msp202openalex-snapshot
Molecular Phylogenetics, Temporal Diversification, and Principles of Evolution in the Mustard Family (Brassicaceae)
inferredcites →https://doi.org/10.1093/molbev/msr048openalex-snapshot
Testing for Ancient Admixture between Closely Related Populations
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/msu269openalex-snapshot
Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci
inferredcites →https://doi.org/10.1093/molbev/msv226openalex-snapshot
Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution
inferredcites →https://doi.org/10.1093/nar/gkr1090openalex-snapshot
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
inferredcites →https://doi.org/10.1093/nar/gkr944openalex-snapshot
Phytozome: a comparative platform for green plant genomics
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Gene Ontology Consortium: going forward
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Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach
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A Linear-Time Algorithm for Gaussian and Non-Gaussian Trait Evolution Models
inferredcites →https://doi.org/10.1093/sysbio/syv023openalex-snapshot
Detection and Polarization of Introgression in a Five-Taxon Phylogeny
inferredcites →https://doi.org/10.1093/sysbio/syv039openalex-snapshot
Exploring Tree-Like and Non-Tree-Like Patterns Using Genome Sequences: An Example Using the Inbreeding Plant SpeciesArabidopsis thaliana(L.) Heynh
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Mixing patterns in networks
inferredcites →https://doi.org/10.1104/pp.107.096685openalex-snapshot
Comparative Genetic Mapping inBoechera stricta, a Close Relative of Arabidopsis
inferredcites →https://doi.org/10.1111/j.1096-0031.2010.00329.xopenalex-snapshot
SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information
inferredcites →https://doi.org/10.1111/j.1438-8677.1996.tb00515.xopenalex-snapshot
Molecular marker incongruence in plant hybrid zones and phylogenetic trees
inferredcites →https://doi.org/10.1111/j.2041-210x.2011.00169.xopenalex-snapshot
phytools: an R package for phylogenetic comparative biology (and other things)
inferredcites →https://doi.org/10.1111/mec.13544openalex-snapshot
Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis
inferredcites →https://doi.org/10.1111/mec.13610openalex-snapshot
Powerful methods for detecting introgressed regions from population genomic data
inferredcites →https://doi.org/10.1111/mec.13959openalex-snapshot
The on‐again, off‐again relationship between mitochondrial genomes and species boundaries
inferredcites →https://doi.org/10.1111/nph.15386openalex-snapshot
An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers ( Helianthus )
inferredcites →https://doi.org/10.1126/science.1188021openalex-snapshot
A Draft Sequence of the Neandertal Genome
inferredcites →https://doi.org/10.1126/science.1258522openalex-snapshot
Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes
inferredcites →https://doi.org/10.1126/science.1258524openalex-snapshot
Extensive introgression in a malaria vector species complex revealed by phylogenomics
inferredcites →https://doi.org/10.1186/1471-2105-10-454openalex-snapshot
AtPIN: Arabidopsis thaliana Protein Interaction Network
inferredcites →https://doi.org/10.1186/1471-2105-9-322openalex-snapshot
PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships
inferredcites →https://doi.org/10.1186/1471-2148-10-61openalex-snapshot
Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryzaand their phylogenetic utility across various taxonomic levels
inferredcites →https://doi.org/10.1186/gb-2004-5-10-r80openalex-snapshot
Bioconductor: open software development for computational biology and bioinformatics
inferredcites →https://doi.org/10.1186/s12859-017-2002-4openalex-snapshot
Gene flow analysis method, the D-statistic, is robust in a wide parameter space
inferredcites →https://doi.org/10.1186/s12859-018-2111-8openalex-snapshot
ATMAD: robust image analysis for Automatic Tissue MicroArray De-arraying
inferredcites →https://doi.org/10.1186/s13059-015-0721-2openalex-snapshot
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
inferredcites →https://doi.org/10.1371/journal.pbio.1002342openalex-snapshot
The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences
inferredcites →https://doi.org/10.1371/journal.pbio.1002469openalex-snapshot
Distinct Global Brain Dynamics and Spatiotemporal Organization of the Salience Network
inferredcites →https://doi.org/10.1371/journal.pgen.0020105openalex-snapshot
Possible Ancestral Structure in Human Populations
inferredcites →https://doi.org/10.1534/genetics.108.095364openalex-snapshot
Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium inBoechera stricta, a Wild Relative of Arabidopsis
inferredcites →https://doi.org/10.1534/genetics.114.162396openalex-snapshot
Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes
inferredcites →https://doi.org/10.1600/036364407780360166openalex-snapshot
Generic Limits in Tribe Halimolobeae and Description of the New Genus Exhalimolobos (Brassicaceae)
inferredcites →https://doi.org/10.1600/036364410792495926openalex-snapshot
Molecular Phylogenetics and Taxonomy of the Genus Thysanocarpus (Brassicaceae)
inferredcites →https://doi.org/10.2307/1218589openalex-snapshot
THE SIGNIFICANCE OF HYBRIDIZATION FOR PLANT TAXONOMY AND EVOLUTION
inferredcites →https://doi.org/10.2307/2657117openalex-snapshot
Molecular systematics of the Brassicaceae: evidence from coding plastidic matK and nuclear Chs sequences
inferredcites →https://doi.org/10.3389/fpls.2013.00046openalex-snapshot
The Reference Genome of the Halophytic Plant Eutrema salsugineum
inferredcites →https://doi.org/10.3389/fpls.2013.00366openalex-snapshot
Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes
inferredcites →https://doi.org/10.3732/ajb.0800065openalex-snapshot
Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited
inferredcites →https://doi.org/10.3732/ajb.1400201openalex-snapshot
The role of homoploid hybridization in evolution: A century of studies synthesizing genetics and ecology
inferredcites →https://doi.org/10.3732/ajb.93.11.1714openalex-snapshot
Intrageneric phylogeny of Capsella (Brassicaceae) and the origin of the tetraploid C. bursa‐pastoris based on chloroplast and nuclear DNA sequences
inferredcites →https://doi.org/10.3732/ajb.93.4.607openalex-snapshot
Brassicaceae phylogeny and trichome evolution
inferredcites →https://doi.org/10.4236/ajps.2015.68122openalex-snapshot
Genomic Fingerprinting of Camelina Species Using cTBP as Molecular Marker

What points at this work

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

inferred← citeshttps://doi.org/10.1002/ajb2.1514openalex-snapshot
Phylogeny and multiple independent whole‐genome duplication events in the Brassicales
inferred← citeshttps://doi.org/10.1038/s41467-020-17605-7openalex-snapshot
Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae
inferred← citeshttps://doi.org/10.1093/gbe/evaa053openalex-snapshot
Divergence-Based Introgression Polarization
inferred← citeshttps://doi.org/10.1093/gbe/evz144openalex-snapshot
CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis
inferred← citeshttps://doi.org/10.1101/2020.01.15.908376openalex-snapshot
Novel phylogeny of angiosperms inferred from whole-genome microsynteny analysis
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