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Convergence and novelty in adaptation to whole genome duplication in three independent polyploids

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

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Mid‐Miocene divergence of Ionopsidium and Cochlearia and its impact on the systematics and biogeography of the tribe Cochlearieae (Brassicaceae)
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BUSCO: Assessing Genome Assembly and Annotation Completeness
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Cytogenetic studies in Cochlearia L. (Cruciferae). The origins of C. officinalis L. and C. micacea Marshall
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Cytogenetic studies in Cochlearia L. (Cruciferae). The chromosomal constitution of C. danica L.
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Suppression of multivalent formation by B chromosomes in natural and artificial autopolyploids of scurvy-grass (Cochlearia L.)
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Molecular phylogenetics ofCochlearia (Brassicaceae) and allied genera based on nuclear ribosomal ITS DNA sequence analysis contradict traditional concepts of their evolutionary relationship
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Chromosomal passengers: the four-dimensional regulation of mitotic events
inferredcites →https://doi.org/10.1007/s00412-015-0571-4openalex-snapshot
The challenge of evolving stable polyploidy: could an increase in “crossover interference distance” play a central role?
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Cochlearia macrorrhiza (Brassicaceae): A bridging species between Cochlearia taxa from the Eastern Alps and the Carpathians?
inferredcites →https://doi.org/10.1007/s006060200025openalex-snapshot
Genetic differentiation and speciation in prealpine Cochlearia : Allohexaploid Cochlearia bavarica Vogt (Brassicaceae) compared to its diploid ancestor Cochlearia pyrenaica DC. in Germany and Austria
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Functional Consequences of Subunit Diversity in RNA Polymerases II and V
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Meiotic Adaptation to Genome Duplication in Arabidopsis arenosa
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Meiosis in autopolyploid and allopolyploid Arabidopsis
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Salt and heavy metal tolerance and expression levels of candidate tolerance genes among four extremophile Cochlearia species with contrasting habitat preferences
inferredcites →https://doi.org/10.1038/nature03667openalex-snapshot
An Arabidopsis hAT-like transposase is essential for plant development
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Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis
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Inference of population splits and mixtures from genome-wide allele frequency data
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The evolutionary significance of polyploidy
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Chromosomal passengers: conducting cell division
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Interspecific introgression mediates adaptation to whole genome duplication
inferredcites →https://doi.org/10.1038/s41559-019-0807-4openalex-snapshot
Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa
inferredcites →https://doi.org/10.1038/s41598-017-05794-zopenalex-snapshot
RADseq provides evidence for parallel ecotypic divergence in the autotetraploid Cochlearia officinalis in Northern Norway
inferredcites →https://doi.org/10.1038/sj.emboj.7600992openalex-snapshot
Reduced meiotic crossovers and delayed prophase I progression in AtMLH3‐deficient Arabidopsis
inferredcites →https://doi.org/10.1038/sj.emboj.7601750openalex-snapshot
Constitutive activation of a plasma membrane H+‐ATPase prevents abscisic acid‐mediated stomatal closure
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Identification of Ku70 and Ku80 homologues in Arabidopsis thaliana: evidence for a role in the repair of DNA double‐strand breaks
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Effect of ploidy level on fruit morphology, seed germination and juvenile growth in scurvy grass ( Cochlearia officinalis L. s.l., Brassicaceae)
inferredcites →https://doi.org/10.1071/fp07249openalex-snapshot
Regulation of Ku gene promoters in Arabidopsis by hormones and stress
inferredcites →https://doi.org/10.1073/pnas.0511330103openalex-snapshot
RNA polymerase II subunit Rpb9 is important for transcriptional fidelity in vivo
inferredcites →https://doi.org/10.1073/pnas.120170197openalex-snapshot
The Arabidopsis thaliana salt tolerance gene SOS1 encodes a putative Na + /H + antiporter
inferredcites →https://doi.org/10.1073/pnas.1600405113openalex-snapshot
Borrowed alleles and convergence in serpentine adaptation
inferredcites →https://doi.org/10.1073/pnas.1615123114openalex-snapshot
Endosperm-based hybridization barriers explain the pattern of gene flow between Arabidopsis lyrata and Arabidopsis arenosa in Central Europe
inferredcites →https://doi.org/10.1073/pnas.1715903115openalex-snapshot
Arabidopsis TSO1 and MYB3R1 form a regulatory module to coordinate cell proliferation with differentiation in shoot and root
inferredcites →https://doi.org/10.1074/jbc.m004721200openalex-snapshot
RNA Polymerase II Subunit Rpb9 Regulates Transcription Elongation in Vivo
inferredcites →https://doi.org/10.1074/jbc.m804080200openalex-snapshot
Microcephalin/MCPH1 Associates with the Condensin II Complex to Function in Homologous Recombination Repair
inferredcites →https://doi.org/10.1080/19491034.2019.1616507openalex-snapshot
Plant condensin II is required for the correct spatial relationship between centromeres and rDNA arrays
inferredcites →https://doi.org/10.1086/282771openalex-snapshot
Genetic Distance between Populations
inferredcites →https://doi.org/10.1086/700636openalex-snapshot
Polyploidy, the Nucleotype, and Novelty: The Impact of Genome Doubling on the Biology of the Cell
inferredcites →https://doi.org/10.1093/aob/mcaa053openalex-snapshot
The Quaternary evolutionary history of Bristol rock cress (Arabis scabra, Brassicaceae), a Mediterranean element with an outpost in the north-western Atlantic region
inferredcites →https://doi.org/10.1093/aob/mcz123openalex-snapshot
Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events
inferredcites →https://doi.org/10.1093/bioinformatics/btg1080openalex-snapshot
Gene prediction with a hidden Markov model and a new intron submodel
inferredcites →https://doi.org/10.1093/bioinformatics/btm440openalex-snapshot
Improved detection of overrepresentation of Gene-Ontology annotations with parent–child analysis
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/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btq228openalex-snapshot
DendroPy: a Python library for phylogenetic computing
inferredcites →https://doi.org/10.1093/bioinformatics/btr521openalex-snapshot
adegenet 1.3-1 : new tools for the analysis of genome-wide SNP data
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/genetics/132.2.583openalex-snapshot
Estimation of levels of gene flow from DNA sequence data.
inferredcites →https://doi.org/10.1093/genetics/150.2.921openalex-snapshot
Analysis of Population Structure in Autotetraploid Species
inferredcites →https://doi.org/10.1093/molbev/msj030openalex-snapshot
Application of Phylogenetic Networks in Evolutionary Studies
inferredcites →https://doi.org/10.1093/molbev/msn223openalex-snapshot
The Dynamic Ups and Downs of Genome Size Evolution in Brassicaceae
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/oxfordjournals.aob.a084558openalex-snapshot
Cytogenetic Studies in Cochlearia L. The chromosomal homogeneity within both the 2n = 12 diploids and the 2n = 14 diploids and the cytogenetic relationship between the two chromosome levels
inferredcites →https://doi.org/10.1093/pcp/pcn125openalex-snapshot
Functional Characterization of DEAD-Box RNA Helicases in Arabidopsis thaliana under Abiotic Stress Conditions
inferredcites →https://doi.org/10.1098/rstb.2019.0102openalex-snapshot
Convergent evolution in the genomics era: new insights and directions
inferredcites →https://doi.org/10.1101/2020.01.31.929109openalex-snapshot
Genomic novelty and process-level convergence in adaptation to whole genome duplication
inferredcites →https://doi.org/10.1101/gad.271072.115openalex-snapshot
Genome management and mismanagement—cell-level opportunities and challenges of whole-genome duplication
inferredcites →https://doi.org/10.1101/gad.9.4.481openalex-snapshot
RNA polymerase II subunit RPB9 is required for accurate start site selection.
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.154831.113openalex-snapshot
Estimating and interpreting F ST : The impact of rare variants
inferredcites →https://doi.org/10.1104/pp.107.099895openalex-snapshot
STRESS RESPONSE SUPPRESSOR1 and STRESS RESPONSE SUPPRESSOR2, Two DEAD-Box RNA Helicases That Attenuate Arabidopsis Responses to Multiple Abiotic Stresses
inferredcites →https://doi.org/10.1105/tpc.111.086314openalex-snapshot
Condensin II Alleviates DNA Damage and Is Essential for Tolerance of Boron Overload Stress in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.15.00482openalex-snapshot
A Time-Calibrated Road Map of Brassicaceae Species Radiation and Evolutionary History
inferredcites →https://doi.org/10.1105/tpc.16.00720openalex-snapshot
Targeting of Arabidopsis KNL2 to Centromeres Depends on the Conserved CENPC-k Motif in Its C Terminus
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Isozymes, Speciation and Evolution in the Polyploid Complex Cochlearia L. (Brassicaceae)
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A MORPHOLOGICAL AND CYTOLOGICAL INVESTIGATION OF COCHLEARIA POPULATIONS ON THE GOWER PENINSULA, GLAMORGAN
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ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE
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CYTO-GENETICAL STUDIES IN THE COCHLEARIA OFFICINALIS COMPLEX
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Chloroplast DNA restriction site variation and RAPD‐analyses in Cochlearia (Brassicaceae): Biosystematics and speciation
inferredcites →https://doi.org/10.1111/mec.12796openalex-snapshot
Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow
inferredcites →https://doi.org/10.1111/nph.13499openalex-snapshot
Meiosis evolves: adaptation to external and internal environments
inferredcites →https://doi.org/10.1111/pce.12021openalex-snapshot
Tetraploid Rangpur lime rootstock increases drought tolerance via enhanced constitutive root abscisic acid production
inferredcites →https://doi.org/10.1111/pce.12344openalex-snapshot
Deciphering the molecular bases for drought tolerance in A rabidopsis autotetraploids
inferredcites →https://doi.org/10.1111/tpj.12533openalex-snapshot
The A rabidopsis STRESS RESPONSE SUPPRESSOR DEAD ‐box RNA helicases are nucleolar‐ and chromocenter‐localized proteins that undergo stress‐mediated relocalization and are involved in epigenetic gene silencing
inferredcites →https://doi.org/10.1126/science.1226630openalex-snapshot
Parallel Molecular Evolution in an Herbivore Community
inferredcites →https://doi.org/10.1126/science.1240561openalex-snapshot
Polyploids Exhibit Higher Potassium Uptake and Salinity Tolerance in Arabidopsis
inferredcites →https://doi.org/10.1126/science.aat7244openalex-snapshot
Convergent regulatory evolution and loss of flight in paleognathous birds
inferredcites →https://doi.org/10.1128/mcb.01656-06openalex-snapshot
Evidence that the Transcription Elongation Function of Rpb9 Is Involved in Transcription-Coupled DNA Repair in Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1186/1471-2229-14-150openalex-snapshot
Arabidopsis AtHB7 and AtHB12evolved divergently to fine tune processes associated with growth and responses to water stress
inferredcites →https://doi.org/10.1186/s12864-017-3555-3openalex-snapshot
Plastome phylogeny and early diversification of Brassicaceae
inferredcites →https://doi.org/10.1186/s13059-017-1380-2openalex-snapshot
FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations
inferredcites →https://doi.org/10.1186/s13059-019-1832-yopenalex-snapshot
OrthoFinder: phylogenetic orthology inference for comparative genomics
inferredcites →https://doi.org/10.1242/dev.060384openalex-snapshot
Female gametophytic cell specification and seed development require the function of the putativeArabidopsisINCENP orthologWYRD
inferredcites →https://doi.org/10.1266/ggs.79.139openalex-snapshot
Characterization of a CENP-C homolog in Arabidopsis thaliana
inferredcites →https://doi.org/10.1371/journal.pgen.1002967openalex-snapshot
Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
inferredcites →https://doi.org/10.1371/journal.pgen.1003093openalex-snapshot
Genetic Adaptation Associated with Genome-Doubling in Autotetraploid Arabidopsis arenosa
inferredcites →https://doi.org/10.1371/journal.pgen.1005397openalex-snapshot
Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference
inferredcites →https://doi.org/10.1371/journal.pgen.1008900openalex-snapshot
A novel allele of ASY3 is associated with greater meiotic stability in autotetraploid Arabidopsis lyrata
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.1534/genetics.114.164350openalex-snapshot
fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets
inferredcites →https://doi.org/10.2307/4117308openalex-snapshot
Hybridization and the Flora of the British Isles
inferredcites →https://doi.org/10.23855/preslia.2018.023openalex-snapshot
A hitchhiker from the beach
inferredcites →https://doi.org/10.3389/fevo.2018.00117openalex-snapshot
The “Polyploid Hop”: Shifting Challenges and Opportunities Over the Evolutionary Lifespan of Genome Duplications
inferredcites →https://doi.org/10.3389/fpls.2015.00825openalex-snapshot
Down-regulation of multiple CDK inhibitor ICK/KRP genes promotes cell proliferation, callus induction and plant regeneration in Arabidopsis

What points at this work

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

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Population Genomic Analysis of Diploid-Autopolyploid Species
inferred← citeshttps://doi.org/10.1007/s00497-022-00451-6openalex-snapshot
Ancestral self-compatibility facilitates the establishment of allopolyploids in Brassicaceae
inferred← citeshttps://doi.org/10.1016/j.ppees.2023.125728openalex-snapshot
Evolutionary footprints of cold adaptation in arctic-alpine Cochlearia (Brassicaceae) – Evidence from freezing experiments and electrolyte leakage
inferred← citeshttps://doi.org/10.1016/j.xplc.2023.100571openalex-snapshot
Chasing the mechanisms of ecologically adaptive salinity tolerance
inferred← citeshttps://doi.org/10.1038/s41467-024-49679-yopenalex-snapshot
Impact of whole-genome duplications on structural variant evolution in Cochlearia
inferred← citeshttps://doi.org/10.1098/rspb.2020.2154openalex-snapshot
When everything changes at once: finding a new normal after genome duplication
inferred← citeshttps://doi.org/10.1101/2023.01.11.523565openalex-snapshot
Novel reassortments of variation underlie repeated adaptation to whole genome duplication in two outcrossing Arabidopsis species
inferred← citeshttps://doi.org/10.3390/ijms25041957openalex-snapshot
Polyploidization: A Biological Force That Enhances Stress Resistance
inferred← citeshttps://doi.org/10.7554/elife.71572openalex-snapshot
Evolutionary footprints of a cold relic in a rapidly warming world
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