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Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Selection on protein structure, interaction, and sequence
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Basal Divergences in Birds and the Phylogenetic Utility of the Nuclear RAG-1 Gene
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Comparison of phylogenetic trees
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Phylogenetic inference based on matrix representation of trees
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Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes
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Should phylogenetic models be trying to ‘fit an elephant’?
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Phylogenomics: the beginning of incongruence?
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Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
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Genome-scale data, angiosperm relationships, and ‘ending incongruence’: a cautionary tale in phylogenetics
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A well-tested set of primers to amplify regions spread across the avian genome
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Comparative molecular evolution and phylogenetic utility of 3′-UTRs and introns in Galliformes
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Deep metazoan phylogeny: When different genes tell different stories
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Identifying localized biases in large datasets: A case study using the avian tree of life
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Incongruence among different mitochondrial regions: A case study using complete mitogenomes
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Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
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Building the avian tree of life using a large-scale, sparse supermatrix
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Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics
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Translational control by the 3′-UTR: the ends specify the means
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Applications of Interval Methods to Phylogenetics
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The effect of linkage on limits to artificial selection
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The effect of linkage on limits to artificial selection
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The global diversity of birds in space and time
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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
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Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds
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Causes of evolutionary rate variation among protein sites
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Phylogenomics and the reconstruction of the tree of life
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Phylogenetics: Tertiary protein structures needed
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The Hill–Robertson effect: evolutionary consequences of weak selection and linkage in finite populations
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Phylogenomic evidence for multiple losses of flight in ratite birds
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Phylotranscriptomic analysis of the origin and early diversification of land plants
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Error, signal, and the placement of Ctenophora sister to all other animals
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Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
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Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents
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Reconstructing evolutionary trees from DNA and proteinsequences: paralinear distances.
inferredcites →https://doi.org/10.1080/106351500750049761openalex-snapshot
Improved Bootstrap Confidence Limits in Large-Scale Phylogenies, with an Example from Neo-Astragalus (Leguminosae)
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Bias in Phylogenetic Estimation and Its Relevance to the Choice between Parsimony and Likelihood Methods
inferredcites →https://doi.org/10.1080/10635150290069922openalex-snapshot
Model Misspecification and Probabilistic Tests of Topology: Evidence from Empirical Data Sets
inferredcites →https://doi.org/10.1080/10635150290102294openalex-snapshot
Examining Basal Avian Divergences with Mitochondrial Sequences: Model Complexity, Taxon Sampling, and Sequence Length
inferredcites →https://doi.org/10.1080/10635150290102339openalex-snapshot
Increased Taxon Sampling Greatly Reduces Phylogenetic Error
inferredcites →https://doi.org/10.1080/10635150290102357openalex-snapshot
Increased Taxon Sampling Is Advantageous for Phylogenetic Inference
inferredcites →https://doi.org/10.1080/10635150390132911openalex-snapshot
Is Sparse Taxon Sampling a Problem for Phylogenetic Inference?
inferredcites →https://doi.org/10.1080/10635150490445779openalex-snapshot
Modeling Compositional Heterogeneity
inferredcites →https://doi.org/10.1080/10635150590924208openalex-snapshot
Polytomies and Bayesian Phylogenetic Inference
inferredcites →https://doi.org/10.1080/10635150590945313openalex-snapshot
Branch-Length Prior Influences Bayesian Posterior Probability of Phylogeny
inferredcites →https://doi.org/10.1080/10635150590947339openalex-snapshot
Choosing the Best Genes for the Job: The Case for Stationary Genes in Genome-Scale Phylogenetics
inferredcites →https://doi.org/10.1080/10635150601146041openalex-snapshot
Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence
inferredcites →https://doi.org/10.1080/10635150701627304openalex-snapshot
Phylogenetic Mixtures on a Single Tree Can Mimic a Tree of Another Topology
inferredcites →https://doi.org/10.1080/10635150802302468openalex-snapshot
On the Distributions of Bootstrap Support and Posterior Distributions for a Star Tree
inferredcites →https://doi.org/10.1080/10635150802422274openalex-snapshot
Penalized Likelihood Phylogenetic Inference: Bridging the Parsimony-Likelihood Gap
inferredcites →https://doi.org/10.1080/10635150802429642openalex-snapshot
A Rapid Bootstrap Algorithm for the RAxML Web Servers
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Clann: investigating phylogenetic information through supertree analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btq228openalex-snapshot
DendroPy: a Python library for phylogenetic computing
inferredcites →https://doi.org/10.1093/bioinformatics/btt403openalex-snapshot
nhmmer: DNA homology search with profile HMMs
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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ASTRAL: genome-scale coalescent-based species tree estimation
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A space-time process model for the evolution of DNA sequences.
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Bayes or Bootstrap? A Simulation Study Comparing the Performance of Bayesian Markov Chain Monte Carlo Sampling and Bootstrapping in Assessing Phylogenetic Confidence
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How Meaningful Are Bayesian Support Values?
inferredcites →https://doi.org/10.1093/molbev/msm028openalex-snapshot
The Bayesian "Star Paradox" Persists for Long Finite Sequences
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Testing Hypotheses about the Sister Group of the Passeriformes Using an Independent 30-Locus Data Set
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PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
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Ultrafast Approximation for Phylogenetic Bootstrap
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Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals
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Discordance of Species Trees with Their Most Likely Gene Trees: A Unifying Principle
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ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era
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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
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Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)
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Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
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The State of Software for Evolutionary Biology
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
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Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis
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Recovering evolutionary trees under a more realistic model of sequence evolution.
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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
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Cases in which Parsimony or Compatibility Methods will be Positively Misleading
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Are Transposable Element Insertions Homoplasy Free?: An Examination Using the Avian Tree of Life
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BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics
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Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales
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Phylogeny and Biogeography of the Core Babblers (Aves: Timaliidae)
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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
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Assessing Parameter Identifiability in Phylogenetic Models Using Data Cloning
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Ratite Nonmonophyly: Independent Evidence from 40 Novel Loci
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Low-Parameter Phylogenetic Inference Under the General Markov Model
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The Phylogenetic Likelihood Library
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Can We Identify Genes with Increased Phylogenetic Reliability?
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Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny
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Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods
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Incomplete Lineage Sorting in Mammalian Phylogenomics
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Diversification of Neoaves: integration of molecular sequence data and fossils
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The genetic code can cause systematic bias in simple phylogenetic models
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Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes
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Creating the CIPRES Science Gateway for inference of large phylogenetic trees
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Irrational exuberance for resolved species trees
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POLYTOMIES, THE POWER OF PHYLOGENETIC INFERENCE, AND THE STOCHASTIC NATURE OF MOLECULAR EVOLUTION: A COMMENT ON WALSH ET AL. (1999)
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PARALLEL RADIATIONS IN THE PRIMARY CLADES OF BIRDS
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BIRDS IN A BUSH: FIVE GENES INDICATE EXPLOSIVE EVOLUTION OF AVIAN ORDERS
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Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species
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DIVERGENCE ACROSS AUSTRALIA'S CARPENTARIAN BARRIER: STATISTICAL PHYLOGEOGRAPHY OF THE RED-BACKED FAIRY WREN (MALURUS MELANOCEPHALUS)
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IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
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Ancestral range reconstruction of Galliformes: the effects of topology and taxon sampling
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The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves
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Human Genome Ultraconserved Elements Are Ultraselected
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A Phylogenomic Study of Birds Reveals Their Evolutionary History
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Comparative genomics reveals insights into avian genome evolution and adaptation
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Whole-genome analyses resolve early branches in the tree of life of modern birds
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Phylogenomics resolves the timing and pattern of insect evolution
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From Reptilian Phylogenomics to Reptilian Genomes: Analyses of c-Jun and DJ-1 Proto-Oncogenes
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BLAST+: architecture and applications
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Homoplastic microinversions and the avian tree of life
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Phylogenomic analyses data of the avian phylogenomics project
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Bushes in the Tree of Life
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The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds
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Discordance of Species Trees with Their Most Likely Gene Trees
inferredcites →https://doi.org/10.1371/journal.pone.0054848openalex-snapshot
A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0106649openalex-snapshot
Two Low Coverage Bird Genomes and a Comparison of Reference-Guided versus De Novo Genome Assemblies
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The Howard and Moore Complete Checklist of the Birds of the World
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Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees
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Cases in which Parsimony or Compatibility Methods Will be Positively Misleading
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A Framework for the Quantitative Study of Evolutionary Trees
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The Status of Avian Systematics and Its Unsolved Problems
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Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals
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Taxon sampling and the accuracy of phylogenetic analyses
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Species limits in Wiedomys (Cricetidae: Sigmodontinae) reinforce the South American São Francisco River as a biogeographic barrier
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Evolution of the syrinx of Apodiformes, including the vocal-learning Trochilidae (Aves: Strisores)
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Poor taxonomic sampling undermines nomenclatural stability: A reply to Roxo et al. (2019)
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Quill mites of the family Syringophilidae (Acariformes: Prostigmata) parasitizing coraciiform birds (Aves: Coraciiformes)
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Resolving the conflictive phylogenetic relationships of Oceanites (Oceanitidae: Procellariiformes) with the description of a new species
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A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales
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Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum
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Cervical anatomy and its relation to foraging habits in aquatic birds (Aves: Neornithes: Neoaves)
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Brain surface morphology and ecological and macroevolutionary inferences of avian New World suboscines (Aves, Passeriformes , Tyrannides)
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Paleoneurology of stem palaeognaths clarifies the plesiomorphic condition of the crown bird central nervous system
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Population Genomics of Birds: Evolutionary History and Conservation
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Resolving the Avian Tree of Life from Top to Bottom: The Promise and Potential Boundaries of the Phylogenomic Era
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Origin and Evolution of Birds
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Detecting Outlier Subtrees of Gene Trees Using SPR Moves and Machine Learning
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Concatenation, Conflict, and Complexity: Genealogical Heterogeneity Mimics Substitutional Heterogeneity for Nucleotide Model Selection
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Interfamilial relationships in order Fabales: new insights from the nuclear regions sqd1 and 26S rDNA
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Phylogenetic definitions for 25 higher-level clade names of birds
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Differential Splicing of ANP32A in Birds Alters Its Ability to Stimulate RNA Synthesis by Restricted Influenza Polymerase
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Early Evolution of Modern Birds Structured by Global Forest Collapse at the End-Cretaceous Mass Extinction
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Synergistic innovations enabled the radiation of anglerfishes in the deep open ocean
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Evolution across the adaptive landscape in a hyperdiverse beetle radiation
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A new time tree of birds reveals the interplay between dispersal, geographic range size, and diversification
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Hemiplasy helps explain high rates of apparent morphological convergence in neoavian birds
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Diversity favours the old: Metrics of avian diversity increase in aging regrowth Acacia woodlands of semi-arid eastern Australia
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Patterns and effects of GC3 heterogeneity and parsimony informative sites on the phylogenetic tree of genes
inferred← citeshttps://doi.org/10.1016/j.geobios.2024.03.003openalex-snapshot
Taphonomic damage obfuscates interpretation of the retroarticular region of the Asteriornis mandible
inferred← citeshttps://doi.org/10.1016/j.jcz.2021.10.003openalex-snapshot
Systematics of the rare Amazonian genus Eutrachelophis (Serpentes: Dipsadidae), with an emended diagnosis for Eutrachelophis papilio
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.08.002openalex-snapshot
The development of scientific consensus: Analyzing conflict and concordance among avian phylogenies
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.09.005openalex-snapshot
Tapping the woodpecker tree for evolutionary insight
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.08.007openalex-snapshot
Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.09.001openalex-snapshot
Phylogenetic analysis of Antarctic notothenioids illuminates the utility of RADseq for resolving Cenozoic adaptive radiations
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.09.005openalex-snapshot
A simple strategy for recovering ultraconserved elements, exons, and introns from low coverage shotgun sequencing of museum specimens: Placement of the partridge genus Tropicoperdix within the galliformes
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.10.008openalex-snapshot
What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data?
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.01.025openalex-snapshot
Assessing phylogenetic information to reveal uncertainty in historical data: An example using Goodeinae (Teleostei: Cyprinodontiformes: Goodeidae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.02.022openalex-snapshot
Phylogenomics of the superfamily Dytiscoidea (Coleoptera: Adephaga) with an evaluation of phylogenetic conflict and systematic error
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.106611openalex-snapshot
Extracting phylogenetic signal from phylogenomic data: Higher-level relationships of the nightbirds (Strisores)
inferred← citeshttps://doi.org/10.1016/j.ympev.2020.106899openalex-snapshot
Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana)
inferred← citeshttps://doi.org/10.1016/j.ympev.2020.106923openalex-snapshot
Resolving the phylogenetic position of Hygrobiidae (Coleoptera: Adephaga) requires objective statistical tests and exhaustive phylogenetic methodology: a response to Cai et al. (2020)
inferred← citeshttps://doi.org/10.1016/j.ympev.2020.107013openalex-snapshot
Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness
inferred← citeshttps://doi.org/10.1016/j.ympev.2020.107065openalex-snapshot
Diverse phylogenomic datasets uncover a concordant scenario of laurasiatherian interordinal relationships
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107086openalex-snapshot
Assessing topological congruence among concatenation-based phylogenomic approaches in empirical datasets
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107242openalex-snapshot
Autosomal, sex-linked and mitochondrial loci resolve evolutionary relationships among wrens in the genus Campylorhynchus
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107339openalex-snapshot
Phylogenomics resolves ambiguous relationships within Aciculata (Errantia, Annelida)
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107344openalex-snapshot
Gene-tree misrooting drives conflicts in phylogenomic coalescent analyses of palaeognath birds
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107482openalex-snapshot
Investigating the utility of Anchored Hybrid Enrichment data to investigate the relationships among the Killifishes (Actinopterygii: Cyprinodontiformes), a globally distributed group of fishes
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107543openalex-snapshot
Interpreting phylogenetic conflict: Hybridization in the most speciose genus of lichen-forming fungi
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107550openalex-snapshot
Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107559openalex-snapshot
Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107620openalex-snapshot
Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes)
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107700openalex-snapshot
Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107806openalex-snapshot
Multiple outgroups can cause random rooting in phylogenomics
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107869openalex-snapshot
Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107892openalex-snapshot
Interspecific gene flow obscures phylogenetic relationships in an important insect pest species complex
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107935openalex-snapshot
Interrelationships and biogeography of the New World pufferfish genus Sphoeroides (Tetraodontiformes: Tetraodontidae) inferred using ultra-conserved DNA elements
inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108212openalex-snapshot
Imperiled wanderlust lichens in steppe habitats of western North America comprise geographically structured mycobiont lineages and a reversal to sexual reproduction within this asexual clade
inferred← citeshttps://doi.org/10.1038/s41467-023-40308-8openalex-snapshot
Rapid gene content turnover on the germline-restricted chromosome in songbirds
inferred← citeshttps://doi.org/10.1038/s41586-020-2096-0openalex-snapshot
Late Cretaceous neornithine from Europe illuminates the origins of crown birds
inferred← citeshttps://doi.org/10.1038/s41586-024-07323-1openalex-snapshot
Complexity of avian evolution revealed by family-level genomes
inferred← citeshttps://doi.org/10.1038/s41597-022-01680-0openalex-snapshot
Draft genome assemblies of four manakins
inferred← citeshttps://doi.org/10.1038/s41598-018-35328-0openalex-snapshot
Genome sequences identify three families of Coleoptera as morphologically derived click beetles (Elateridae)
inferred← citeshttps://doi.org/10.1038/s41598-019-45455-xopenalex-snapshot
Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota)
inferred← citeshttps://doi.org/10.1038/s41598-022-18904-3openalex-snapshot
Unveiling new perspective of phylogeography, genetic diversity, and population dynamics of Southeast Asian and Pacific chickens
inferred← citeshttps://doi.org/10.1038/s41598-023-35784-3openalex-snapshot
Statistical evaluation of character support reveals the instability of higher-level dinosaur phylogeny
inferred← citeshttps://doi.org/10.1038/s44358-025-00062-9openalex-snapshot
Phylogenomics and comparative genomic perspective on the avian radiation
inferred← citeshttps://doi.org/10.1073/pnas.1817373116openalex-snapshot
Germline-restricted chromosome (GRC) is widespread among songbirds
inferred← citeshttps://doi.org/10.1073/pnas.2109326119openalex-snapshot
Ancient proteins resolve controversy over the identity of Genyornis eggshell
inferred← citeshttps://doi.org/10.1073/pnas.2319506121openalex-snapshot
A region of suppressed recombination misleads neoavian phylogenomics
inferred← citeshttps://doi.org/10.1073/pnas.2319696121openalex-snapshot
Genomes, fossils, and the concurrent rise of modern birds and flowering plants in the Late Cretaceous
inferred← citeshttps://doi.org/10.1073/pnas.2409658122openalex-snapshot
A complete and dynamic tree of birds
inferred← citeshttps://doi.org/10.1073/pnas.2500553122openalex-snapshot
Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES
inferred← citeshttps://doi.org/10.1080/01584197.2017.1387030openalex-snapshot
Resolving a phylogenetic hypothesis for parrots: implications from systematics to conservation
inferred← citeshttps://doi.org/10.1080/02724634.2025.2514121openalex-snapshot
A new species of Morsoravidae sheds light on beak and limb morphology in stem passerines
inferred← citeshttps://doi.org/10.1080/08912963.2025.2473546openalex-snapshot
The phylogenetic relationships of the Dodo ( Raphus cucullatus ) and the Solitaire ( Pezophaps solitaria ) within Columbidae (Aves: Columbiformes), including other large extinct taxa, based on morphological data
inferred← citeshttps://doi.org/10.1080/14772000.2017.1401016openalex-snapshot
On the importance of homology in the age of phylogenomics
inferred← citeshttps://doi.org/10.1080/24750263.2024.2371843openalex-snapshot
New insights into the relationship of parasitic quill mites and birds: Picobia species in Asian and New World Barbets
inferred← citeshttps://doi.org/10.1086/722100openalex-snapshot
Loss of Avian Intromittent Organs as a Sperm Competition Strategy: A Race to Be Last
inferred← citeshttps://doi.org/10.1088/1751-8121/ab305bopenalex-snapshot
Systematics and symmetry in molecular phylogenetic modelling: perspectives from physics
inferred← citeshttps://doi.org/10.1089/cmb.2021.0543openalex-snapshot
Scalable Species Tree Inference with External Constraints
inferred← citeshttps://doi.org/10.1093/aob/mcae170openalex-snapshot
Inferring complex evolutionary history of the closely related East Asian wild roses in Rosa sect. Synstylae (Rosaceae) based on genomic evidence from conserved orthologues
inferred← citeshttps://doi.org/10.1093/aob/mcaf002openalex-snapshot
Ancient reticulation, incomplete lineage sorting and the evolution of the pyrenoid at the dawn of hornwort diversification
inferred← citeshttps://doi.org/10.1093/aob/mcaf128openalex-snapshot
Resolving relationships in the radiation of Australia’s largest pea clade (Fabaceae tribe Mirbelieae) with target-capture sequencing
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa884openalex-snapshot
PhyloWGA: chromosome-aware phylogenetic interrogation of whole genome alignments
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab093openalex-snapshot
FASTRAL: improving scalability of phylogenomic analysis
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab428openalex-snapshot
wQFM: highly accurate genome-scale species tree estimation from weighted quartets
inferred← citeshttps://doi.org/10.1093/bioinformatics/btad332openalex-snapshot
Quartet Fiduccia–Mattheyses revisited for larger phylogenetic studies
inferred← citeshttps://doi.org/10.1093/bioinformatics/btag273openalex-snapshot
Phlag: scalable detection of genomics regions with unexplained phylogenetic heterogeneity
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty261openalex-snapshot
An evolutionary model motivated by physicochemical properties of amino acids reveals variation among proteins
inferred← citeshttps://doi.org/10.1093/biolinnean/blad003openalex-snapshot
Oligo-Miocene radiation within South-west Pacific arc terranes underpinned repeated upstream continental dispersals in pigeons (Columbiformes)
inferred← citeshttps://doi.org/10.1093/evolut/qpaf020openalex-snapshot
Feather evolution following flight loss in crown group birds: relaxed selection and developmental constraints
inferred← citeshttps://doi.org/10.1093/gbe/evab099openalex-snapshot
Rampant Genome-Wide Admixture across theHeliconiusRadiation
inferred← citeshttps://doi.org/10.1093/gbe/evab161openalex-snapshot
Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree
inferred← citeshttps://doi.org/10.1093/gbe/evab200openalex-snapshot
Taxonomic Uncertainty and the Anomaly Zone: Phylogenomics Disentangle a Rapid Radiation to Resolve Contentious Species ( Gila robusta Complex) in the Colorado River
inferred← citeshttps://doi.org/10.1093/gbe/evac129openalex-snapshot
A Practical Guide to Design and Assess a Phylogenomic Study
inferred← citeshttps://doi.org/10.1093/gbe/evad070openalex-snapshot
Filtration of Gene Trees From 9,000 Exons, Introns, and UCEs Disentangles Conflicting Phylogenomic Relationships in Tree Frogs (Hylidae)
inferred← citeshttps://doi.org/10.1093/gbe/evad092openalex-snapshot
Effect of Different Types of Sequence Data on Palaeognath Phylogeny
inferred← citeshttps://doi.org/10.1093/gbe/evx147openalex-snapshot
Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences
inferred← citeshttps://doi.org/10.1093/gbe/evy094openalex-snapshot
Differences in Performance among Test Statistics for Assessing Phylogenomic Model Adequacy
inferred← citeshttps://doi.org/10.1093/gbe/evz120openalex-snapshot
Phylogenomic Analysis of a Putative Missing Link Sparks Reinterpretation of Leech Evolution
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/iob/obag038openalex-snapshot
Anatomical Atlas and Three-Dimensional Musculoskeletal Model of the Flight Apparatus in the Southern Screamer (Anseriformes: Chauna torquata )
inferred← citeshttps://doi.org/10.1093/isd/ixae024openalex-snapshot
Dissecting the Pandora’s box: preliminary phylogenomic insights into the internal and external relationships of stink bugs (Hemiptera: Pentatomidae)
inferred← citeshttps://doi.org/10.1093/isd/ixaf019openalex-snapshot
Exploring species delimitation of high-altitude flower bugs (Heteroptera: Anthocoridae) in the presence of complex reticulate evolution: the case of a biodiversity hotspot in the Qinghai–Tibet Plateau and surrounding mountains
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/msab026openalex-snapshot
Genome-Scale Profiling Reveals Noncoding Loci Carry Higher Proportions of Concordant Data
inferred← citeshttps://doi.org/10.1093/molbev/msac215openalex-snapshot
Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees
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/msy112openalex-snapshot
Comparative Genomics Reveals a Burst of Homoplasy-Free Numt Insertions
inferred← citeshttps://doi.org/10.1093/molbev/msz263openalex-snapshot
Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements
inferred← citeshttps://doi.org/10.1093/obo/9780199941728-0146openalex-snapshot
Diversification of Amniotes
inferred← citeshttps://doi.org/10.1093/ornithology/ukad025openalex-snapshot
Ultraconserved elements support the elevation of a new avian family, Eurocephalidae, the white-crowned shrikes
inferred← citeshttps://doi.org/10.1093/ornithology/ukag014openalex-snapshot
Phylogenomic analysis of pigeons and doves (Columbiformes) informs molecular evolution of a potential magnetoreceptor
inferred← citeshttps://doi.org/10.1093/sysbio/syaa038openalex-snapshot
Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets
inferred← citeshttps://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
inferred← citeshttps://doi.org/10.1093/sysbio/syaa101openalex-snapshot
Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to Resolve Recent Radiations of Pelagic Seabirds
inferred← citeshttps://doi.org/10.1093/sysbio/syab009openalex-snapshot
Of Traits and Trees: Probabilistic Distances under Continuous Trait Models for Dissecting the Interplay among Phylogeny, Model, and Data
inferred← citeshttps://doi.org/10.1093/sysbio/syab051openalex-snapshot
Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference
inferred← citeshttps://doi.org/10.1093/sysbio/syab072openalex-snapshot
Phylogenetic Signal and Bias in Paleontology
inferred← citeshttps://doi.org/10.1093/sysbio/syab075openalex-snapshot
Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data
inferred← citeshttps://doi.org/10.1093/sysbio/syac002openalex-snapshot
On the Need for New Measures of Phylogenomic Support
inferred← citeshttps://doi.org/10.1093/sysbio/syac062openalex-snapshot
Exploring Conflicts in Whole Genome Phylogenetics: A Case Study Within Manakins (Aves: Pipridae)
inferred← citeshttps://doi.org/10.1093/sysbio/syad011openalex-snapshot
Impacts of Taxon-Sampling Schemes on Bayesian Tip Dating Under the Fossilized Birth-Death Process
inferred← citeshttps://doi.org/10.1093/sysbio/syae036openalex-snapshot
Whole Genomes Reveal Evolutionary Relationships and Mechanisms Underlying Gene-Tree Discordance in Neodiprion Sawflies
inferred← citeshttps://doi.org/10.1093/sysbio/syaf068openalex-snapshot
No Consistent Effect of Migration on Speciation Rates in Two Avian Superfamilies: A Check on the Robustness of Trait-Dependent Diversification Methods
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/syaf077openalex-snapshot
Whole Genomes Illuminate the Drivers of Gene Tree Discordance and the Tempo of Tinamou Diversification (Aves: Tinamidae)
inferred← citeshttps://doi.org/10.1093/sysbio/syaf080openalex-snapshot
Efficient Inference of Macrophylogenies: Insights from the Avian Tree of Life
inferred← citeshttps://doi.org/10.1093/sysbio/syag055openalex-snapshot
The Y Chromosome Is a Reliable Marker for Deep-Time Phylogenetic Inference
inferred← citeshttps://doi.org/10.1093/sysbio/syx058openalex-snapshot
Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics
inferred← citeshttps://doi.org/10.1093/sysbio/syy047openalex-snapshot
Optimal Rates for Phylogenetic Inference and Experimental Design in the Era of Genome-Scale Data Sets
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/sysbio/syz027openalex-snapshot
Dense Geographic and Genomic Sampling Reveals Paraphyly and a Cryptic Lineage in a Classic Sibling Species Complex
inferred← citeshttps://doi.org/10.1093/zoolinnean/zlaa136openalex-snapshot
Osteological characters of birds and reptiles show greater congruence with molecular phylogenies than soft characters: homoplasy of morphological partitions
inferred← citeshttps://doi.org/10.1093/zoolinnean/zlab080openalex-snapshot
The evolution of tinamous (Palaeognathae: Tinamidae) in light of molecular and combined analyses
inferred← citeshttps://doi.org/10.1093/zoolinnean/zlae098openalex-snapshot
Discordance between mitochondrial, nuclear, and symbiont genomes in aphid phylogenetics: who is telling the truth?
inferred← citeshttps://doi.org/10.1098/rspb.2019.0672openalex-snapshot
A phylogenomic rodent tree reveals the repeated evolution of masseter architectures
inferred← citeshttps://doi.org/10.1098/rspb.2019.1745openalex-snapshot
Mass estimation of extinct taxa and phylogenetic hypotheses both influence analyses of character evolution in a large clade of birds (Telluraves)
inferred← citeshttps://doi.org/10.1098/rspb.2019.2025openalex-snapshot
Sex biases in bird and mammal natural history collections
inferred← citeshttps://doi.org/10.1098/rspb.2020.2102openalex-snapshot
Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae)
inferred← citeshttps://doi.org/10.1098/rspb.2023.0988openalex-snapshot
Confusion will be my epitaph: genome-scale discordance stifles phylogenetic resolution of Holothuroidea
inferred← citeshttps://doi.org/10.1098/rstb.2020.0249openalex-snapshot
Re-evaluating vocal production learning in non-oscine birds
inferred← citeshttps://doi.org/10.1101/2020.01.28.923458openalex-snapshot
Protein evolution is structure dependent and non-homogeneous across the tree of life
inferred← citeshttps://doi.org/10.1101/2020.01.28.923805openalex-snapshot
Phylogenetic signal is associated with the degree of variation in root-to-tip distances
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/10.1101/2020.05.12.092197openalex-snapshot
Evolution of body size and wing shape trade-offs in arsenurine silkmoths
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/10.1101/2021.09.22.461455openalex-snapshot
The Influence of Model Violation on Phylogenetic Inference: A Simulation Study
inferred← citeshttps://doi.org/10.1101/2021.11.16.468757openalex-snapshot
Impacts of Taxon-Sampling Schemes on Bayesian Molecular Dating under the Unresolved Fossilized Birth-Death Process
inferred← citeshttps://doi.org/10.1101/2021.11.18.468700openalex-snapshot
Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)
inferred← citeshttps://doi.org/10.1101/2021.11.18.469131openalex-snapshot
Interrogating Genomic Data in the Phylogenetic Placement of Treeshrews Reveals Potential Sources of Conflict
inferred← citeshttps://doi.org/10.1101/2022.09.11.507458openalex-snapshot
The Chalcidoidea bush of life – a massive radiation blurred by mutational saturation
inferred← citeshttps://doi.org/10.1101/2022.12.06.519392openalex-snapshot
The Inherited Rate Matrix algorithm for phylogenetic model selection for non-stationary Markov processes
inferred← citeshttps://doi.org/10.1101/2024.01.12.575380openalex-snapshot
Reproductive innovation enabled radiation in the deep sea during an ecological crisis
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/10.1101/2024.05.29.596376openalex-snapshot
The genus Cortinarius should not (yet) be split
inferred← citeshttps://doi.org/10.1101/2024.07.05.602039openalex-snapshot
Evolutionary new centromeres in the snowy owl genome putatively seeded from a transposable element
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/10.1101/2025.06.02.657453openalex-snapshot
The phylogenetic position of the extinct Hawaiian honeyeaters: Overcoming the limitations of antique DNA
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/10.1101/262949openalex-snapshot
Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone
inferred← citeshttps://doi.org/10.1101/400465openalex-snapshot
Why do phylogenomic analyses of early animal evolution continue to disagree? Sites in different structural environments yield different answers
inferred← citeshttps://doi.org/10.1101/414201openalex-snapshot
Genome-wide admixture is common across the Heliconius radiation
inferred← citeshttps://doi.org/10.1101/601237openalex-snapshot
Phylogenetic Synecdoche Demonstrates Optimality of Subsampling and Improves Recovery of the Blaberoidea Phylogeny
inferred← citeshttps://doi.org/10.1101/692509openalex-snapshot
Taxonomic Uncertainty and the Anomaly Zone: Phylogenomics Disentangle a Rapid Radiation to Resolve Contentious Species ( Gila robusta complex) in the Colorado River
inferred← citeshttps://doi.org/10.1101/750109openalex-snapshot
Phylogeny, transposable element and sex chromosome evolution of the basal lineage of birds
inferred← citeshttps://doi.org/10.1101/765610openalex-snapshot
Exons, Introns, and UCEs Reveal Conflicting Phylogenomic Signals in a Rapid Radiation of Frogs (Ranidae: Hylarana )
inferred← citeshttps://doi.org/10.1101/816967openalex-snapshot
A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales
inferred← citeshttps://doi.org/10.1101/832683openalex-snapshot
Species delimitation in the grey zone: introgression obfuscates phylogenetic inference and species boundaries in a cryptic frog complex (Ranidae: Pulchrana picturata )
inferred← citeshttps://doi.org/10.1101/gr.275989.121openalex-snapshot
Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans
inferred← citeshttps://doi.org/10.1111/1749-4877.12853openalex-snapshot
“Isolation by Gentes with Asymmetric Migration” shapes the genetic structure of the common cuckoo in China
inferred← citeshttps://doi.org/10.1111/1755-0998.13496openalex-snapshot
A novel exome probe set captures phototransduction genes across birds (Aves) enabling efficient analysis of vision evolution
inferred← citeshttps://doi.org/10.1111/1755-0998.13517openalex-snapshot
FrogCap: A modular sequence capture probe‐set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales
inferred← citeshttps://doi.org/10.1111/1755-0998.13735openalex-snapshot
Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non‐model organisms
inferred← citeshttps://doi.org/10.1111/cla.12476openalex-snapshot
Parsimony analysis of phylogenomic datasets (II): evaluation of PAUP*, MEGA and MPBoot
inferred← citeshttps://doi.org/10.1111/cla.12477openalex-snapshot
Parsimony analysis of phylogenomic datasets (I): scripts and guidelines for using TNT (Tree Analysis using New Technology)
inferred← citeshttps://doi.org/10.1111/cla.12561openalex-snapshot
The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps
inferred← citeshttps://doi.org/10.1111/cla.70010openalex-snapshot
Phylogenomic reconstruction reveals deep reticulate evolutionary history and polyphyletic genus ( Boeica ) in the subtribe Leptoboeinae (Gesneriaceae), with description of a novel genus
inferred← citeshttps://doi.org/10.1111/evo.13649openalex-snapshot
Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes*
inferred← citeshttps://doi.org/10.1111/ibi.12707openalex-snapshot
Rapid Laurasian diversification of a pantropical bird family during the Oligocene–Miocene transition
inferred← citeshttps://doi.org/10.1111/ibi.13097openalex-snapshot
Re‐assessing the phylogenetic status and evolutionary relationship of Forest Owlet ( Athene blewitti (Hume 1873)) using genomic data
inferred← citeshttps://doi.org/10.1111/jbi.13392openalex-snapshot
Isolation by marine barriers and climate explain areas of endemism in an island rodent
inferred← citeshttps://doi.org/10.1111/jfb.14686openalex-snapshot
Brown trout phylogenetics: A persistent mirage towards (too) many species
inferred← citeshttps://doi.org/10.1111/joa.13919openalex-snapshot
3D atlas of tinamou (Neornithes: Tinamidae) pectoral morphology: Implications for reconstructing the ancestral neornithine flight apparatus
inferred← citeshttps://doi.org/10.1111/jse.13053openalex-snapshot
Assembling an illustrated family‐level tree of life for exploration in mobile devices
inferred← citeshttps://doi.org/10.1111/syen.12333openalex-snapshot
Hybrid capture data unravel a rapid radiation of pimpliform parasitoid wasps (Hymenoptera: Ichneumonidae: Pimpliformes)
inferred← citeshttps://doi.org/10.1111/syen.12363openalex-snapshot
Phylogenomic analysis resolves the relationships among net‐winged beetles (Coleoptera: Lycidae) and reveals the parallel evolution of morphological traits
inferred← citeshttps://doi.org/10.1111/syen.12427openalex-snapshot
Conflicting signal in transcriptomic markers leads to a poorly resolved backbone phylogeny of chalcidoid wasps
inferred← citeshttps://doi.org/10.1111/syen.12454openalex-snapshot
Assessing support for Blaberoidea phylogeny suggests optimal locus quality
inferred← citeshttps://doi.org/10.1111/syen.12514openalex-snapshot
Opening Pandora's box: molecular phylogeny of the stink bugs (Hemiptera: Heteroptera: Pentatomidae) reveals great incongruences in the current classification
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