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The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Evolving Perceptions on the Antiquity of the Modern Avian Tree
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Patterns of speciation and limits to phylogenetic resolution
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Deciphering ancient rapid radiations
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Gene tree discordance, phylogenetic inference and the multispecies coalescent
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Evolutionary stasis: the stable chromosomes of birds
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Identifying localized biases in large datasets: A case study using the avian tree of life
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Basic Local Alignment Search Tool
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Genome trees and the tree of life
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Insights into hominid evolution from the gorilla genome sequence
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The global diversity of birds in space and time
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Inferring ancient divergences requires genes with strong phylogenetic signals
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Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds
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Darwin's abominable mystery: Insights from a supertree of the angiosperms
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Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals
inferredcites →https://doi.org/10.1073/pnas.0811087106openalex-snapshot
Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates
inferredcites →https://doi.org/10.1073/pnas.1110395108openalex-snapshot
Mass extinction of birds at the Cretaceous–Paleogene (K–Pg) boundary
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Rates and patterns of great ape retrotransposition
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SINEs of a Nearly Perfect Character
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Hemiplasy: A New Term in the Lexicon of Phylogenetics
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PHYLIP: Phylogeny Inference Package. Version 3.2. Joel Felsenstein
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Recent developments in the MAFFT multiple sequence alignment program
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Retroposon Insertion Patterns of Neoavian Birds: Strong Evidence for an Extensive Incomplete Lineage Sorting Era
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A Universal Method for the Study of CR1 Retroposons in Nonmodel Bird Genomes
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Advanced birds (Neoaves)
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Phylogenetic Relationships and Ancient Incomplete Lineage Sorting Among Cichlid Fishes in Lake Tanganyika as Revealed by Analysis of the Insertion of Retroposons
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Are Transposable Element Insertions Homoplasy Free?: An Examination Using the Avian Tree of Life
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WebLogo: A Sequence Logo Generator: Figure 1
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MICROEVOLUTIONARY PROCESSES GENERATE PHYLOGENOMIC DISCORDANCE AT ANCIENT DIVERGENCES
inferredcites →https://doi.org/10.1111/evo.12118openalex-snapshot
MORE ACCURATE PHYLOGENIES INFERRED FROM LOW-RECOMBINATION REGIONS IN THE PRESENCE OF INCOMPLETE LINEAGE SORTING
inferredcites →https://doi.org/10.1111/j.1365-2699.2011.02650.xopenalex-snapshot
Evolution of terrestrial birds in three continents: biogeography and parallel radiations
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The origins of crown group birds: molecules and fossils
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A Phylogenomic Study of Birds Reveals Their Evolutionary History
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The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals
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Comparative genomics reveals insights into avian genome evolution and adaptation
inferredcites →https://doi.org/10.1126/science.1253451openalex-snapshot
Whole-genome analyses resolve early branches in the tree of life of modern birds
inferredcites →https://doi.org/10.1146/annurev-ecolsys-110411-160327openalex-snapshot
The Evolutionary Genomics of Birds
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Repbase Update, a database of eukaryotic repetitive elements
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inferredcites →https://doi.org/10.1186/s13742-014-0038-1openalex-snapshot
Phylogenomic analyses data of the avian phylogenomics project
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Genetic structure and common ancestry expose the dingo-dog hybrid myth
inferred← citeshttps://doi.org/10.1093/evolinnean/kzaf021openalex-snapshot
Rapid divergence with gene flow creates intractable nodes in the tree of life: an empirical demonstration in the buzzing flowerpecker ( Dicaeum hypoleucum )
inferred← citeshttps://doi.org/10.1093/evolinnean/kzag003openalex-snapshot
Revisiting the determinants of molecular evolutionary rate variation
inferred← citeshttps://doi.org/10.1093/gbe/evab259openalex-snapshot
Genome Stability Is in the Eye of the Beholder: CR1 Retrotransposon Activity Varies Significantly across Avian Diversity
inferred← citeshttps://doi.org/10.1093/gbe/evad094openalex-snapshot
“Correcting” Gene Trees to be More Like Species Trees Frequently Increases Topological Error
inferred← citeshttps://doi.org/10.1093/gbe/evae017openalex-snapshot
Ancient and Modern Genomes Reveal Microsatellites Maintain a Dynamic Equilibrium Through Deep Time
inferred← citeshttps://doi.org/10.1093/gbe/evae236openalex-snapshot
Expansion of MHC-IIB Has Constrained the Evolution of MHC-IIA in Passerines
inferred← citeshttps://doi.org/10.1093/gbe/evv213openalex-snapshot
Determining the Position of Storks on the Phylogenetic Tree of Waterbirds by Retroposon Insertion Analysis
inferred← citeshttps://doi.org/10.1093/gbe/evv235openalex-snapshot
A Genome-Scale Investigation of Incongruence in Culicidae Mosquitoes
inferred← citeshttps://doi.org/10.1093/gbe/evw264openalex-snapshot
Evolution and Diversity of Transposable Elements in Vertebrate Genomes
inferred← citeshttps://doi.org/10.1093/gbe/evx170openalex-snapshot
Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes
inferred← citeshttps://doi.org/10.1093/gbe/evy274openalex-snapshot
Genome Sequence of Jaltomata Addresses Rapid Reproductive Trait Evolution and Enhances Comparative Genomics in the Hyper-Diverse Solanaceae
inferred← citeshttps://doi.org/10.1093/gbe/evz246openalex-snapshot
Reprogramming of retrotransposon activity during speciation of the genus Citrus
inferred← citeshttps://doi.org/10.1093/gigascience/giae124openalex-snapshot
Genomic evidence for hybridization and introgression between blue peafowl and endangered green peafowl and molecular foundation of leucistic plumage of blue peafowl
inferred← citeshttps://doi.org/10.1093/gigascience/giz003openalex-snapshot
Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise
inferred← citeshttps://doi.org/10.1093/iob/obaf029openalex-snapshot
Toward a Comprehensive Anatomical Matrix for Crown Birds: Phylogenetic Insights from the Pectoral Girdle and Forelimb Skeleton
inferred← citeshttps://doi.org/10.1093/jhered/esag018openalex-snapshot
Sex-biased dispersal drives mito-nuclear discordance in simulated populations
inferred← citeshttps://doi.org/10.1093/jhered/esz076openalex-snapshot
ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets
inferred← citeshttps://doi.org/10.1093/jmammal/gyy186openalex-snapshot
Illuminating the obscured phylogenetic radiation of South AmericanSylvilagusGray, 1867 (Lagomorpha: Leporidae)
inferred← citeshttps://doi.org/10.1093/molbev/msaa191openalex-snapshot
An Unbiased Molecular Approach Using 3′-UTRs Resolves the Avian Family-Level Tree of Life
inferred← citeshttps://doi.org/10.1093/molbev/msab063openalex-snapshot
Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus
inferred← citeshttps://doi.org/10.1093/molbev/msac278openalex-snapshot
A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats
inferred← citeshttps://doi.org/10.1093/molbev/msag018openalex-snapshot
Phylogeny of waterfowl (Anseriformes) constructed using genome sequences provides insights into topological incongruences
inferred← citeshttps://doi.org/10.1093/molbev/msag250openalex-snapshot
kamino: fast proteome-wide variant calling for amino acid phylogenomics
inferred← citeshttps://doi.org/10.1093/molbev/msv188openalex-snapshot
Exploring Massive Incomplete Lineage Sorting in Arctoids (Laurasiatheria, Carnivora)
inferred← citeshttps://doi.org/10.1093/molbev/msw197openalex-snapshot
Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time
inferred← citeshttps://doi.org/10.1093/molbev/msy112openalex-snapshot
Comparative Genomics Reveals a Burst of Homoplasy-Free Numt Insertions
inferred← citeshttps://doi.org/10.1093/nargab/lqac064openalex-snapshot
Pitfalls of the site-concordance factor (sCF) as measure of phylogenetic branch support
inferred← citeshttps://doi.org/10.1093/oso/9780198838944.003.0005openalex-snapshot
Genealogy in evolution
inferred← citeshttps://doi.org/10.1093/sysbio/syaa034openalex-snapshot
Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
inferred← citeshttps://doi.org/10.1093/sysbio/syaa041openalex-snapshot
The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous–Paleogene (K–Pg) Mass Extinction Event
inferred← citeshttps://doi.org/10.1093/sysbio/syaa099openalex-snapshot
Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere
inferred← citeshttps://doi.org/10.1093/sysbio/syab013openalex-snapshot
Interrogating Phylogenetic Discordance Resolves Deep Splits in the Rapid Radiation of Old World Fruit Bats (Chiroptera: Pteropodidae)
inferred← citeshttps://doi.org/10.1093/sysbio/syab018openalex-snapshot
Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria)
inferred← citeshttps://doi.org/10.1093/sysbio/syab023openalex-snapshot
Ultraconserved Elements Improve the Resolution of Difficult Nodes within the Rapid Radiation of Neotropical Sigmodontine Rodents (Cricetidae: Sigmodontinae)
inferred← citeshttps://doi.org/10.1093/sysbio/syab086openalex-snapshot
Theoretical and Practical Considerations when using Retroelement Insertions to Estimate Species Trees in the Anomaly Zone
inferred← citeshttps://doi.org/10.1093/sysbio/syac017openalex-snapshot
Origin and Diversification of the Saguaro Cactus (Carnegiea gigantea): A Within-Species Phylogenomic Analysis
inferred← citeshttps://doi.org/10.1093/sysbio/syac025openalex-snapshot
Reunion of Australasian Possums by Shared SINE Insertions
inferred← citeshttps://doi.org/10.1093/sysbio/syac051openalex-snapshot
Exon-based Phylogenomics and the Relationships of African Cichlid Fishes: Tackling the Challenges of Reconstructing Phylogenies with Repeated Rapid Radiations
inferred← citeshttps://doi.org/10.1093/sysbio/syad038openalex-snapshot
Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance
inferred← citeshttps://doi.org/10.1093/sysbio/syae018openalex-snapshot
Phylogenomic Discordance is Driven by Wide-Spread Introgression and Incomplete Lineage Sorting During Rapid Species Diversification Within Rattlesnakes (Viperidae: Crotalus and Sistrurus )
inferred← citeshttps://doi.org/10.1093/sysbio/syaf057openalex-snapshot
Phylogenetic Resolution and Conflict in the Species-Rich Flowering Plant Family Leguminosae
inferred← citeshttps://doi.org/10.1093/sysbio/syaf075openalex-snapshot
Phylogenomics of a Genus of “Great Speciators” Reveals Rampant Incomplete Lineage Sorting, Gene Flow, and Mitochondrial Discordance in Island Systems
inferred← citeshttps://doi.org/10.1093/sysbio/syag039openalex-snapshot
The Effects of Hemiplasy and Maintained Polymorphisms in Fossil Clades
inferred← citeshttps://doi.org/10.1093/sysbio/syw001openalex-snapshot
Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).
inferred← citeshttps://doi.org/10.1093/sysbio/syw018openalex-snapshot
Gene Tree Discordance Causes Apparent Substitution Rate Variation
inferred← citeshttps://doi.org/10.1093/sysbio/syw069openalex-snapshot
Disentangling Incomplete Lineage Sorting and Introgression to Refine Species-Tree Estimates for Lake Tanganyika Cichlid Fishes
inferred← citeshttps://doi.org/10.1093/sysbio/syx041openalex-snapshot
Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling
inferred← citeshttps://doi.org/10.1093/sysbio/syx063openalex-snapshot
Why Concatenation Fails Near the Anomaly Zone
inferred← citeshttps://doi.org/10.1093/sysbio/syx078openalex-snapshot
Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo Clade (Caryophyllales)
inferred← citeshttps://doi.org/10.1093/sysbio/syy006openalex-snapshot
Bayesian Divergence-Time Estimation with Genome-Wide Single-Nucleotide Polymorphism Data of Sea Catfishes (Ariidae) Supports Miocene Closure of the Panamanian Isthmus
inferred← citeshttps://doi.org/10.1093/sysbio/syy076openalex-snapshot
True Homoplasy of Retrotransposon Insertions in Primates
inferred← citeshttps://doi.org/10.1093/sysbio/syy085openalex-snapshot
Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting
inferred← citeshttps://doi.org/10.1093/sysbio/syz019openalex-snapshot
Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone
inferred← citeshttps://doi.org/10.1093/zoolinnean/zly085openalex-snapshot
A stem anseriform from the early Palaeocene of Antarctica provides new key evidence in the early evolution of waterfowl
inferred← citeshttps://doi.org/10.1093/zoolinnean/zlz015openalex-snapshot
Exploring the effects of character construction and choice, outgroups and analytical method on phylogenetic inference from discrete characters in extant crocodilians
inferred← citeshttps://doi.org/10.1098/rspb.2026.0102openalex-snapshot
An early burst of skeletal evolution at the origin of dinosaurs
inferred← citeshttps://doi.org/10.1101/2020.03.27.012237openalex-snapshot
When species trees disagree: an approach consistent with the coalescent that quantifies phylogenomic support for contentious relationships
inferred← citeshttps://doi.org/10.1101/2020.06.17.157768openalex-snapshot
A new (old) approach to genotype-based phylogenomic inference within species, with an example from the saguaro cactus ( Carnegiea gigantea )
inferred← citeshttps://doi.org/10.1101/2020.08.11.246108openalex-snapshot
Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere
inferred← citeshttps://doi.org/10.1101/2021.07.27.453752openalex-snapshot
Substitution Rate Variation in a Robust Procellariiform Seabird Phylogeny is not Solely Explained by Body Mass, Flight Efficiency, Population Size or Life History Traits
inferred← citeshttps://doi.org/10.1101/2022.06.21.496980openalex-snapshot
A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats
inferred← citeshttps://doi.org/10.1101/2022.08.12.503770openalex-snapshot
Resolving marine–freshwater transitions by diatoms through a fog of discordant gene trees
inferred← citeshttps://doi.org/10.1101/2022.08.21.504711openalex-snapshot
“Correcting” gene trees to be more like species trees increases topological error when incomplete lineage sorting is high
inferred← citeshttps://doi.org/10.1101/2023.12.27.573425openalex-snapshot
Genomic evidence for hybridization and introgression between blue peafowl and green peafowl and selection for white plumage
inferred← citeshttps://doi.org/10.1101/2024.02.28.582627openalex-snapshot
Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny
inferred← citeshttps://doi.org/10.1101/2024.04.16.589693openalex-snapshot
Balancing selection and the functional effects of shared polymorphism in cryptic Daphnia species
inferred← citeshttps://doi.org/10.1101/2024.08.28.610082openalex-snapshot
Phylogenomics of a genus of ‘Great Speciators’ reveals rampant incomplete lineage sorting, gene flow, and mitochondrial capture in island systems
inferred← citeshttps://doi.org/10.1101/2025.07.10.664098openalex-snapshot
A Maximum-Likelihood Method to Construct Phylogenetic Trees Using Low-Homoplasy Markers: New Insights into Neoaves Phylogeny
inferred← citeshttps://doi.org/10.1101/249755openalex-snapshot
Shallow evolutionary divergence between two Andean hummingbirds: Speciation with gene flow?
inferred← citeshttps://doi.org/10.1101/262949openalex-snapshot
Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone
inferred← citeshttps://doi.org/10.1101/276642openalex-snapshot
Evolutionary inferences about quantitative traits are affected by underlying genealogical discordance
inferred← citeshttps://doi.org/10.1101/287086openalex-snapshot
Comparative Genomics and Genome Evolution in birds-of-paradise
inferred← citeshttps://doi.org/10.1101/593699openalex-snapshot
Whole genome duplication potentiates inter-specific hybridisation and niche shifts in Australian burrowing frogs Neobatrachus
inferred← citeshttps://doi.org/10.1101/643296openalex-snapshot
Retroposon Insertions within a Multispecies Coalescent Framework Suggest that Ratite Phylogeny is not in the ‘Anomaly Zone’
inferred← citeshttps://doi.org/10.1101/709477openalex-snapshot
An ABBA-BABA Test for Introgression Using Retroposon Insertion Data
inferred← citeshttps://doi.org/10.1101/829887openalex-snapshot
Genomics of a complete butterfly continent
inferred← citeshttps://doi.org/10.1101/860114openalex-snapshot
Infection risk and extensive parental care govern the molecular evolution of Toll-like receptors in birds
inferred← citeshttps://doi.org/10.1101/gr.210948.116openalex-snapshot
Speciation network in Laurasiatheria: retrophylogenomic signals
inferred← citeshttps://doi.org/10.1111/1755-0998.12514openalex-snapshot
Identification of CR 1 retroposons in Arborophila rufipectus and their application to P hasianidae phylogeny
inferred← citeshttps://doi.org/10.1111/brv.12274openalex-snapshot
The early E ocene birds of the M essel fossil site: a 48 million‐year‐old bird community adds a temporal perspective to the evolution of tropical avifaunas
inferred← citeshttps://doi.org/10.1111/cla.12559openalex-snapshot
Large‐scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea)
inferred← citeshttps://doi.org/10.1111/evo.12832openalex-snapshot
Irrational exuberance for resolved species trees
inferred← citeshttps://doi.org/10.1111/evo.13490openalex-snapshot
A global analysis of selection at the avian MHC
inferred← citeshttps://doi.org/10.1111/jbi.14360openalex-snapshot
Rapid radiation of Southern Ocean shags in response to receding sea ice
inferred← citeshttps://doi.org/10.1111/jeb.13401openalex-snapshot
Parallel plumage colour evolution and introgressive hybridization in wheatears
inferred← citeshttps://doi.org/10.1111/jse.12479openalex-snapshot
Plastomes of Betulaceae and phylogenetic implications
inferred← citeshttps://doi.org/10.1111/mec.14439openalex-snapshot
Abundant recent activity of retrovirus‐like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes
inferred← citeshttps://doi.org/10.1111/mec.14462openalex-snapshot
Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis)
inferred← citeshttps://doi.org/10.1111/mec.14795openalex-snapshot
Detecting introgression despite phylogenetic uncertainty: The case of the South American siskins
inferred← citeshttps://doi.org/10.1111/mec.15683openalex-snapshot
Phylogenomics and species delimitation for effective conservation of manta and devil rays
inferred← citeshttps://doi.org/10.1111/mec.17080openalex-snapshot
Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers
inferred← citeshttps://doi.org/10.1111/mec.17082openalex-snapshot
Multiple paths toward repeated phenotypic evolution in the spiny‐leg adaptive radiation ( Tetragnatha ; Hawai'i)
inferred← citeshttps://doi.org/10.1111/mec.17632openalex-snapshot
Trans‐Specific Polymorphisms Between Cryptic Daphnia Species Affect Fitness and Behavior
inferred← citeshttps://doi.org/10.1111/mec.17763openalex-snapshot
Exploring Mitonuclear Discordance: Ghost Introgression From an Ancient Extinction Lineage in the Odorrana swinhoana Complex
inferred← citeshttps://doi.org/10.1111/mec.70050openalex-snapshot
Revealing Speciation Mechanisms Across Endemic Southern Andean Lilies (Phycella, Hippeastreae, Amaryllidaceae) in the Chilean Biodiversity Hotspot
inferred← citeshttps://doi.org/10.1111/mec.70306openalex-snapshot
Phylogeomics Reveals Ancestral Introgression and Paleogeoclimate Co‐Facilitated Speciation and Diversification of Chinese Endemic Cavefishes
inferred← citeshttps://doi.org/10.1111/njb.04413openalex-snapshot
Analysis of chloroplast genomes of ten central Asian Fritillaria species and their phylogenetic relationships
inferred← citeshttps://doi.org/10.1111/nph.16290openalex-snapshot
Large‐scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near‐simultaneous evolutionary origin of all six subfamilies
inferred← citeshttps://doi.org/10.1111/nyas.13295openalex-snapshot
Evolution of bird genomes—a transposon's‐eye view
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