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Phylogenomics insights into gene evolution, rapid species diversification, and morphological innovation of the apple tribe (Maleae, Rosaceae)

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

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Using MCL to Extract Clusters from Networks
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Phylogeny and classification of Rosaceae
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Phylogeny of subtribe Pyrinae (formerly the Maloideae, Rosaceae): Limited resolution of a complex evolutionary history
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TAIR: a resource for integrated Arabidopsis data
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Why are fruits colorful? The relative importance of achromatic and chromatic contrasts for detection by birds
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Genome sequence and transcriptome of Sorbus pohuashanensis provide insights into population evolution and leaf sunburn response
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Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms
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TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data
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Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model
inferredcites →https://doi.org/10.1016/j.ympev.2011.10.005openalex-snapshot
Expanded phylogenetic and dating analyses of the apples and their relatives (Pyreae, Rosaceae)
inferredcites →https://doi.org/10.1016/j.ympev.2020.106784openalex-snapshot
Phylogenetic relationships and chloroplast capture in the Amelanchier-Malacomeles-Peraphyllum clade (Maleae, Rosaceae): Evidence from chloroplast genome and nuclear ribosomal DNA data using genome skimming
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Arctic hydrology during global warming at the Palaeocene/Eocene thermal maximum
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Evolutionary history of the angiosperm flora of China
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Full-length transcriptome assembly from RNA-Seq data without a reference genome
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Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation
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Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times
inferredcites →https://doi.org/10.1038/ng.3886openalex-snapshot
High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development
inferredcites →https://doi.org/10.1038/ng.654openalex-snapshot
The genome of the domesticated apple (Malus × domestica Borkh.)
inferredcites →https://doi.org/10.1038/nmeth.4285openalex-snapshot
ModelFinder: fast model selection for accurate phylogenetic estimates
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Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae
inferredcites →https://doi.org/10.1038/srep02424openalex-snapshot
Colour and odour drive fruit selection and seed dispersal by mouse lemurs
inferredcites →https://doi.org/10.1073/pnas.0900906106openalex-snapshot
Plants with double genomes might have had a better chance to survive the Cretaceous–Tertiary extinction event
inferredcites →https://doi.org/10.1073/pnas.1323926111openalex-snapshot
Phylotranscriptomic analysis of the origin and early diversification of land plants
inferredcites →https://doi.org/10.1073/pnas.2101767118openalex-snapshot
Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe
inferredcites →https://doi.org/10.1080/16546628.2017.1361779openalex-snapshot
Anthocyanidins and anthocyanins: colored pigments as food, pharmaceutical ingredients, and the potential health benefits
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Evolution of Seed Size and Biotic Seed Dispersal in Angiosperms: Paleoecological and Neoecological Evidence
inferredcites →https://doi.org/10.1089/cmb.2014.0156openalex-snapshot
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences
inferredcites →https://doi.org/10.1089/omi.2011.0118openalex-snapshot
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
inferredcites →https://doi.org/10.1093/aobpla/plz020openalex-snapshot
Rapid changes in seed dispersal traits may modify plant responses to global change
inferredcites →https://doi.org/10.1093/bioinformatics/btac669openalex-snapshot
Tree2GD: a phylogenomic method to detect large-scale gene duplication events
inferredcites →https://doi.org/10.1093/bioinformatics/btm619openalex-snapshot
Phyutility: a phyloinformatics tool for trees, alignments and molecular data
inferredcites →https://doi.org/10.1093/bioinformatics/bts199openalex-snapshot
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/bts565openalex-snapshot
CD-HIT: accelerated for clustering the next-generation sequencing 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/bioinformatics/bty560openalex-snapshot
fastp: an ultra-fast all-in-one FASTQ preprocessor
inferredcites →https://doi.org/10.1093/molbev/msaa015openalex-snapshot
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
inferredcites →https://doi.org/10.1093/molbev/msaa139openalex-snapshot
ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy
inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/mss020openalex-snapshot
PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
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/msu245openalex-snapshot
Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics
inferredcites →https://doi.org/10.1093/molbev/msw242openalex-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/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/msx268openalex-snapshot
Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)
inferredcites →https://doi.org/10.1093/nar/gkr1293openalex-snapshot
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
inferredcites →https://doi.org/10.1093/sysbio/syaa066openalex-snapshot
Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l
inferredcites →https://doi.org/10.1093/sysbio/syaa083openalex-snapshot
The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales
inferredcites →https://doi.org/10.1098/rspb.2012.1110openalex-snapshot
Evolution of leaf form correlates with tropical–temperate transitions in Viburnum (Adoxaceae)
inferredcites →https://doi.org/10.1101/gr.086827.108openalex-snapshot
Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates
inferredcites →https://doi.org/10.1101/gr.144311.112openalex-snapshot
The genome of the pear ( Pyrus bretschneideri Rehd.)
inferredcites →https://doi.org/10.1101/gr.168997.113openalex-snapshot
Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
inferredcites →https://doi.org/10.1101/gr.196469.115openalex-snapshot
TransRate: reference-free quality assessment of de novo transcriptome assemblies
inferredcites →https://doi.org/10.1105/tpc.011544openalex-snapshot
Molecular and Phylogenetic Analyses of the Complete MADS-Box Transcription Factor Family in Arabidopsis
inferredcites →https://doi.org/10.1111/2041-210x.12199openalex-snapshot
BAMM tools: an R package for the analysis of evolutionary dynamics on phylogenetic trees
inferredcites →https://doi.org/10.1111/evo.12180openalex-snapshot
FRUIT EVOLUTION AND DIVERSIFICATION IN CAMPANULID ANGIOSPERMS
inferredcites →https://doi.org/10.1111/j.1466-8238.2010.00567.xopenalex-snapshot
Are compound leaves an adaptation to seasonal drought or to rapid growth? Evidence from the Amazon rain forest
inferredcites →https://doi.org/10.1111/j.1469-8137.2012.04212.xopenalex-snapshot
Highly conserved low‐copy nuclear genes as effective markers for phylogenetic analyses in angiosperms
inferredcites →https://doi.org/10.1111/jipb.13246openalex-snapshot
Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere
inferredcites →https://doi.org/10.1111/jipb.13318openalex-snapshot
Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe)
inferredcites →https://doi.org/10.1111/jse.12542openalex-snapshot
Phylogenomic analyses of the Photinia complex support the recognition of a new genus Phippsiomeles and the resurrection of a redefined Stranvaesia in Maleae (Rosaceae)
inferredcites →https://doi.org/10.1111/nph.13491openalex-snapshot
Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications
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.14503openalex-snapshot
Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets
inferredcites →https://doi.org/10.1126/science.1193833openalex-snapshot
Effects of Rapid Global Warming at the Paleocene-Eocene Boundary on Neotropical Vegetation
inferredcites →https://doi.org/10.1126/science.289.5477.291openalex-snapshot
Timing the Radiations of Leaf Beetles: Hispines on Gingers from Latest Cretaceous to Recent
inferredcites →https://doi.org/10.1155/2014/208747openalex-snapshot
Plant Phenotypic Plasticity in Response to Environmental Factors
inferredcites →https://doi.org/10.1186/1471-2105-15-293openalex-snapshot
jvenn: an interactive Venn diagram viewer
inferredcites →https://doi.org/10.1186/1471-2148-9-99openalex-snapshot
Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies
inferredcites →https://doi.org/10.1186/1471-2229-8-16openalex-snapshot
Global gene expression analysis of apple fruit development from the floral bud to ripe fruit
inferredcites →https://doi.org/10.1186/1741-7007-12-11openalex-snapshot
Plastid phylogenomics and green plant phylogeny: almost full circle but not quite there
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/s12862-019-1546-5openalex-snapshot
Fruit syndromes in Viburnum: correlated evolution of color, nutritional content, and morphology in bird-dispersed fleshy fruits
inferredcites →https://doi.org/10.1186/s12864-018-4620-2openalex-snapshot
TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees
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/10.1186/s13742-015-0089-yopenalex-snapshot
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
inferredcites →https://doi.org/10.1242/dev.134080openalex-snapshot
MADS-domain transcription factors and the floral quartet model of flower development: linking plant development and evolution
inferredcites →https://doi.org/10.2307/2419283openalex-snapshot
Origins and Evolution of Subfam. Maloideae (Rosaceae)
inferredcites →https://doi.org/10.2307/2419287openalex-snapshot
A Synopsis of Genera in Maloideae (Rosaceae)
inferredcites →https://doi.org/10.2475/04.2015.02openalex-snapshot
Rapid change in high-elevation precipitation patterns of western North America during the Middle Eocene Climatic Optimum (MECO)
inferredcites →https://doi.org/10.3389/fpls.2021.820997openalex-snapshot
Synthesis of Nuclear and Chloroplast Data Combined With Network Analyses Supports the Polyploid Origin of the Apple Tribe and the Hybrid Origin of the Maleae—Gillenieae Clade
inferredcites →https://doi.org/10.3732/ajb.89.9.1478openalex-snapshot
The origin of the apple subfamily (Maloideae; Rosaceae) is clarified by DNA sequence data from duplicated GBSSI genes
inferredcites →https://doi.org/10.5962/p.185222openalex-snapshot
The Origin and Relationships of the Pomoideae

What points at this work

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

inferred← citeshttps://doi.org/10.3897/phytokeys.242.117481zenodo-depositor-declared
Refining the phylogeny and taxonomy of the apple tribe Maleae (Rosaceae): insights from phylogenomic analyses of 563 plastomes and a taxonomic synopsis of Photinia and its allies in the Old World
inferred← citeshttps://doi.org/10.1002/ppp3.70067openalex-snapshot
Conservation challenges and opportunities for native apple ( Malus ) species in Canada
inferred← citeshttps://doi.org/10.1007/s00468-024-02570-1openalex-snapshot
Micromorphology of the leaf structures of Aronia Medik. and Pourthiaea Decne (Rosaceae)
inferred← citeshttps://doi.org/10.1016/j.plaphy.2025.110983openalex-snapshot
Genome-wide analysis of LSH genes reveals evolutionary patterns in Rosaceae and a positive role for MdLSH10b in adventitious root formation
inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108506openalex-snapshot
Phylogenomics provides insights into the phylogeny of Liliales and the evolution of colchicine biosynthesis genes
inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108702openalex-snapshot
Introgression shapes the genomic conflict landscape of Malus, providing evidence for a reticulate backbone in a woody crop lineage
inferred← citeshttps://doi.org/10.1093/hr/uhag143openalex-snapshot
Pan-plantae aquaporin evolution: insights into PIP2 as a potential regulator of rose prickle development
inferred← citeshttps://doi.org/10.1094/phyto-10-25-0341-ropenalex-snapshot
Comprehensive Characterization of Plant Defensins in Alfalfa Reveals Conserved Evolution and Functional Specialization of MsPDF2.1
inferred← citeshttps://doi.org/10.1101/2024.09.24.614835openalex-snapshot
Unveiling allopolyploidization-driven genome duplications through progressive analysis of deep genome skimming data
inferred← citeshttps://doi.org/10.1111/jipb.13609openalex-snapshot
Nuclear phylogenomics of angiosperms and insights into their relationships and evolution
inferred← citeshttps://doi.org/10.1111/jipb.13751openalex-snapshot
The origin and morphological character evolution of the paleotropical woody bamboos
inferred← citeshttps://doi.org/10.1111/jse.70005openalex-snapshot
Advancing plant phylogenetics and evolution through genomic data bursts and methodological innovations
inferred← citeshttps://doi.org/10.1111/nph.19849openalex-snapshot
A highly resolved nuclear phylogeny uncovers strong phylogenetic conservatism and correlated evolution of fruit color and size in Solanum L.
inferred← citeshttps://doi.org/10.1111/pbi.70167openalex-snapshot
A near‐gapless genome assembly of Pseudocydonia sinensis uncovers unique phenylpropanoid pathways
inferred← citeshttps://doi.org/10.1111/tpj.16533openalex-snapshot
Origin and early divergence of tandem duplicated sorbitol transporter genes in Rosaceae: insights from evolutionary analysis of the SOT gene family in angiosperms
inferred← citeshttps://doi.org/10.1111/tpj.70320openalex-snapshot
Unraveling evolutionary pathways: allopolyploidization and introgression in polyploid Prunus (Rosaceae)
inferred← citeshttps://doi.org/10.1111/tpj.70499openalex-snapshot
Subgenomic divergence and functional innovation following whole‐genome duplication in Maleae species of Rosaceae
inferred← citeshttps://doi.org/10.1186/s12870-025-07311-1openalex-snapshot
Nuclear phylogeny of Malus with increased sampling provides new insights into biogeography and character evolution
inferred← citeshttps://doi.org/10.3389/fpls.2024.1461322openalex-snapshot
Genome-wide analysis of the WOX gene family and function exploration of RhWOX331 in rose (R. ‘The Fairy’)
inferred← citeshttps://doi.org/10.3389/fpls.2024.1480519openalex-snapshot
Evolutionary dynamics and functional characterization of proximal duplicated sorbitol-6-phosphate dehydrogenase genes in Rosaceae
inferred← citeshttps://doi.org/10.3389/fpls.2025.1619267openalex-snapshot
Complete plastome and mitogenome assembly of endangered tree Karpatiosorbus bristoliensis reveals phylogenetic architecture for Sorbus sensu lato (Rosaceae)
inferred← citeshttps://doi.org/10.3390/biology14121740openalex-snapshot
Reassessing the Evolutionary Relationships of Eriobotrya and Rhaphiolepis (Rosaceae): Evidence from Micromorphology, Complete Nuclear Ribosomal DNA and Mitochondrial Genomic Data
inferred← citeshttps://doi.org/10.3390/d17020136openalex-snapshot
Nuclear Phylogenomics of Angiosperms and Evolutionary Implications
inferred← citeshttps://doi.org/10.3390/d18030137openalex-snapshot
Pollen Morphology of Eriobotrya and Rhaphiolepis (Rosaceae): Implications for Generic Delimitation and Systematics
inferred← citeshttps://doi.org/10.3390/genes17010107openalex-snapshot
Assembly, Characterization and Comparative Analysis of the Complete Mitogenome of Small-Leaved Eriobotrya seguinii (Maleae, Rosaceae)
inferred← citeshttps://doi.org/10.35633/inmateh-78-28openalex-snapshot
DETECTION OF TREE FREEZE–THAW STATUS BASED ON THE INTEGRATION OF STEM WATER CONTENT AND STRATIFIED TEMPERATURE
inferred← citeshttps://doi.org/10.48130/tp-0025-0019openalex-snapshot
Self-incompatibility and reticulate evolution contribute to interspecific compatibility of Dendrobium, a possible mechanism for promoting species diversity
inferred← citeshttps://doi.org/10.64898/2026.04.09.717572openalex-snapshot
A coordinated regeneration–selection strategy enables genetic transformation and rapid flowering in apple × pear intergeneric hybrids
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