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Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the Genus Rosa

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What this work says

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

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History and utilization ofRosa damascena
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DNA amounts of roses (Rosa L.) and their use in attributing ploidy levels
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Evolutionary patterns and processes in the genus Rosa (Rosaceae) and their implications for host-parasite co-evolution
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Untangling the hybrid origin of the Chinese tea roses: evidence from DNA sequences of single-copy nuclear and chloroplast genes
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CLASSIFICATION | Conventional Taxonomy (Wild Roses)
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Conventional Taxonomy (Wild Roses) ☆
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Phylogenetic relationships of wild roses in China based on nrDNA and matK data
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Hybridization as an invasion of the genome
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Diversification of almonds, peaches, plums and cherries – Molecular systematics and biogeographic history of Prunus (Rosaceae)
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Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences
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Phylogeny of Rosa sections Chinenses and Synstylae (Rosaceae) based on chloroplast and nuclear markers
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Reconstructing the origins and the biogeography of species’ genomes in the highly reticulate allopolyploid-rich model grass genus Brachypodium using minimum evolution, coalescence and maximum likelihood approaches
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Hybridization preceded radiation in diploid wheats
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Phylogenetic analyses of the genus Rosa using the matK sequence: molecular evidence for the narrow genetic background of modern roses
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Triparental origin of Damask roses
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Stepwise transition from the Eocene greenhouse to the Oligocene icehouse
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jModelTest 2: more models, new heuristics and parallel computing
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A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits
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Microsatellite DNA marker inheritance indicates preferential pairing between two highly homologous genomes in polyploid and hemisexual dog-roses, Rosa L. Sect. Caninae DC.
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The frequency of polyploid speciation in vascular plants
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Maximum likelihood inference of reticulate evolutionary histories
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Decaploidy inRosa praelucensByhouwer (Rosaceae) Endemic to Zhongdian Plateau, Yunnan, China
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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
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Species Concepts and Species Delimitation
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Phylogenetic analysis of Japanese Rosa species using DNA sequences of nuclear ribosomal internal transcribed spacers (ITS)
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Phylogeny and biogeography of wild roses with specific attention to polyploids
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MRBAYES: Bayesian inference of phylogenetic trees
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FLASH: fast length adjustment of short reads to improve genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btu530openalex-snapshot
Quartet Inference from SNP Data Under the Coalescent Model
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ploidyNGS: visually exploring ploidy with Next Generation Sequencing data
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A divide-and-conquer method for scalable phylogenetic network inference from multilocus data
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Cytological, genetic and morphological variation in mixed stands of dogroses (Rosa section Caninae; Rosaceae) in Germany with a focus on the hybridogenic R. micrantha
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Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry ( Fragaria vesca ) with chromosome-scale contiguity
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Evolution by Reticulation: European Dogroses Originated by Multiple Hybridization Across the Genus Rosa
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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
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Application of Phylogenetic Networks in Evolutionary Studies
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication
inferredcites →https://doi.org/10.1093/molbev/msx093openalex-snapshot
Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication
inferredcites →https://doi.org/10.1093/molbev/msx235openalex-snapshot
PhyloNetworks: A Package for Phylogenetic Networks
inferredcites →https://doi.org/10.1093/sysbio/46.3.523openalex-snapshot
Gene Trees in Species Trees
inferredcites →https://doi.org/10.1093/sysbio/syr096openalex-snapshot
Inferring Species Networks from Gene Trees in High-Polyploid North American and Hawaiian Violets (Viola, Violaceae)
inferredcites →https://doi.org/10.1093/sysbio/sys062openalex-snapshot
Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks
inferredcites →https://doi.org/10.1093/sysbio/syv068openalex-snapshot
Fast Dating Using Least-Squares Criteria and Algorithms
inferredcites →https://doi.org/10.1093/sysbio/syx085openalex-snapshot
Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data
inferredcites →https://doi.org/10.1093/sysbio/syy015openalex-snapshot
Inferring Phylogenetic Networks Using PhyloNet
inferredcites →https://doi.org/10.1093/sysbio/syy032openalex-snapshot
Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7
inferredcites →https://doi.org/10.1101/746362openalex-snapshot
Practical Aspects of Phylogenetic Network Analysis Using PhyloNet
inferredcites →https://doi.org/10.1111/1755-0998.12657openalex-snapshot
Detection of individual ploidy levels with genotyping‐by‐sequencing (GBS) analysis
inferredcites →https://doi.org/10.1111/1755-0998.13073openalex-snapshot
Differentiating diploid and triploid individuals using single nucleotide polymorphisms genotyped by amplicon sequencing
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The role of the uplift of the Qinghai‐Tibetan Plateau for the evolution of Tibetan biotas
inferredcites →https://doi.org/10.1111/j.1095-8339.1977.tb01184.xopenalex-snapshot
Relationship between species in the genus Rosa, section Pimpinellifoliae
inferredcites →https://doi.org/10.1111/j.1095-8339.2005.00368.xopenalex-snapshot
The genus Rosa (Rosoideae, Rosaceae) revisited: molecular analysis of nrITS-1 and atpB-rbcL intergenic spacer (IGS) versus conventional taxonomy
inferredcites →https://doi.org/10.1111/j.1558-5646.2010.01063.xopenalex-snapshot
RECONSTRUCTING RETICULATION HISTORY IN A PHYLOGENETIC FRAMEWORK AND THE POTENTIAL OF ALLOPATRIC SPECIATION DRIVEN BY POLYPLOIDY IN AN AGAMIC COMPLEX IN CRATAEGUS (ROSACEAE)
inferredcites →https://doi.org/10.1111/nph.14111openalex-snapshot
Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing
inferredcites →https://doi.org/10.1111/nph.14461openalex-snapshot
Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics
inferredcites →https://doi.org/10.1111/nph.16215openalex-snapshot
Phylogenomics of the genusPopulusreveals extensive interspecific gene flow and balancing selection
inferredcites →https://doi.org/10.1111/nph.17105openalex-snapshot
Polyploid phylogenetics
inferredcites →https://doi.org/10.1111/tpj.14641openalex-snapshot
Genome‐wide sequence information reveals recurrent hybridization among diploid wheat wild relatives
inferredcites →https://doi.org/10.1126/sciadv.aav9188openalex-snapshot
Pervasive hybridizations in the history of wheat relatives
inferredcites →https://doi.org/10.1126/science.1166368openalex-snapshot
Global Cooling During the Eocene-Oligocene Climate Transition
inferredcites →https://doi.org/10.1155/2018/7627191openalex-snapshot
Phylogeny of Maleae (Rosaceae) Based on Multiple Chloroplast Regions: Implications to Genera Circumscription
inferredcites →https://doi.org/10.1159/000360437openalex-snapshot
High Penetrance of a Pan-Canina Type rDNA Family in Intersection Rosa Hybrids Suggests Strong Selection of Bivalent Chromosomes in the Section Caninae
inferredcites →https://doi.org/10.11646/phytotaxa.411.1.2openalex-snapshot
Origin of Rosa x binaloudensis (Rosaceae), a new natural hybrid species from Iran
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Multimodel Inference
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/10.1186/1471-2148-12-70openalex-snapshot
Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota)
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A maximum pseudo-likelihood approach for phylogenetic networks
inferredcites →https://doi.org/10.1186/s12859-018-2129-yopenalex-snapshot
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
inferredcites →https://doi.org/10.1186/s12862-015-0423-0openalex-snapshot
Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
inferredcites →https://doi.org/10.1186/s12862-017-1019-7openalex-snapshot
Evaluating allopolyploid origins in strawberries (Fragaria) using haplotypes generated from target capture sequencing
inferredcites →https://doi.org/10.1186/s12862-019-1479-zopenalex-snapshot
Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)
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Retrieval of hundreds of nuclear loci from herbarium specimens
inferredcites →https://doi.org/10.1600/036364407781179653openalex-snapshot
Phylogenetic Relationships in the Genus Rosa: New Evidence from Chloroplast DNA Sequences and an Appraisal of Current Knowledge
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A Diploids-First Approach to Species Delimitation and Interpreting Polyploid Evolution in the Fern Genus Astrolepis (Pteridaceae)
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PHYLOGENETIC ANALYSES OF THE SUBGENUS EUROSA USING THE ITS NRDNA SEQUENCE
inferredcites →https://doi.org/10.21273/hortsci.34.2.341openalex-snapshot
Rose Germplasm Analysis with RAPD Markers
inferredcites →https://doi.org/10.21273/hortsci.48.12.1445openalex-snapshot
Genetic Relationships of Wild Roses, Old Garden Roses, and Modern Roses Based on Internal Transcribed Spacers and matK Sequences
inferredcites →https://doi.org/10.21273/jashs.131.1.66openalex-snapshot
Characterization and Genetic Relationships of Wild Species and Old Garden Roses Based on Microsatellite Analysis
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Biotechnology of Scented Roses: A Review
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Hierarchical models, reticulate evolution and the inevitability of paraphyletic supraspecific taxa
inferredcites →https://doi.org/10.2307/1224295openalex-snapshot
Paraphyletic groups or what should a classification entail
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How to chop up a tree
inferredcites →https://doi.org/10.2307/2394865openalex-snapshot
Monograph of Rosa in North America. V. Subgenus Hesperhodos
inferredcites →https://doi.org/10.2307/2419070openalex-snapshot
Gene Trees and Species Trees: Molecular Systematics as One-Character Taxonomy
inferredcites →https://doi.org/10.2307/25065631openalex-snapshot
Paraphyletic versus monophyletic taxa—evolutionary versus cladistic classifications
inferredcites →https://doi.org/10.2307/2805073openalex-snapshot
A Monograph of the Genus Rosa in North America. I. R. Acicularis
inferredcites →https://doi.org/10.3389/fpls.2019.01615openalex-snapshot
Target Capture Sequencing Unravels Rubus Evolution
inferredcites →https://doi.org/10.3389/fpls.2020.01077openalex-snapshot
Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing Data
inferredcites →https://doi.org/10.3732/ajb.1400106openalex-snapshot
Phylogenomics of the carrot genus (Daucus, Apiaceae)
inferredcites →https://doi.org/10.3732/ajb.1500330openalex-snapshot
Understanding diploid diversity: A first step in unraveling polyploid, apomictic complexity in Amelanchier
inferredcites →https://doi.org/10.3732/ajb.93.3.412openalex-snapshot
Polyploid and hybrid evolution in roses east of the Rocky Mountains
inferredcites →https://doi.org/10.3732/ajb.95.3.353openalex-snapshot
AFLP markers as a tool to reconstruct complex relationships: A case study in Rosa (Rosaceae)
inferredcites →https://doi.org/10.3732/apps.1300083openalex-snapshot
2matrix: A utility for indel coding and phylogenetic matrix concatenation1

What points at this work

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

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Integrative morphological and genomic analyses reveal diversity, reticulate evolution, and adaptation in diploid and tetraploid Rosa species from Xinjiang
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Phenotypic and genomic signatures across wild Rosa species open new horizons for modern rose breeding
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Comparative analysis of the chloroplast genomes of Rosa species and RNA editing analysis
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Plastid genomic features and phylogenetic placement in Rosa (Rosaceae) through comparative analysis
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Chloroplast genome and haplotype relationships unravel the genetic introgression and complex evolutionary history of East Asian Rosa section Synstylae roses (Rosaceae)
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Power and Weakness of Repetition – Evaluating the Phylogenetic Signal From Repeatomes in the Family Rosaceae With Two Case Studies From Genera Prone to Polyploidy and Hybridization (Rosa and Fragaria)
inferred← citeshttps://doi.org/10.3390/biology15151247openalex-snapshot
Edaphic Niche Differentiation Exceeds Field Ecophysiological Divergence Among Wild Rosa Species Across the Mountain Systems of Eastern Kazakhstan
inferred← citeshttps://doi.org/10.3390/genes16080852openalex-snapshot
Characterization of the Four Rosa L. Species from Kazakhstan Based on Complete Plastomes and Nuclear Ribosomal Internal Transcribed Spacer (ITS) Sequences
inferred← citeshttps://doi.org/10.3897/phytokeys.205.85866openalex-snapshot
Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae)
inferred← citeshttps://doi.org/10.48130/opr-0026-0012openalex-snapshot
Genus Rosa L. in China: advances in resources and taxonomy
inferred← citeshttps://doi.org/10.6084/m9.figshare.23520152openalex-snapshot
Additional file 1 of Comparative analysis of the chloroplast genomes of Rosa species and RNA editing analysis
inferred← citeshttps://doi.org/10.6084/m9.figshare.23520155openalex-snapshot
Additional file 2 of Comparative analysis of the chloroplast genomes of Rosa species and RNA editing analysis
inferred← citeshttps://doi.org/10.61215/auofb.2026.1.03openalex-snapshot
COMPARATIVE CHLOROPLAST GENOME ANALYSIS AND PHYLOGENY OF THE GENUS Rosa (ROSACEAE)
inferred← citeshttps://doi.org/10.70675/40a94106z14b5z4bbdza30fz4485bdc8fc10openalex-snapshot
Pourquoi aimons-nous tant le parfum de la rose ?
inferred← citeshttps://doi.org/10.70675/cfbb80f0z986fz48a4zb776z47eba525d4d6openalex-snapshot
Caractérisation multiomique dans la compréhension des mécanismes contrôlant les traits floraux majeurs chez Rosa x damascena
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