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Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization
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Patterns of microchromosome organization remain highly conserved throughout avian evolution
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Genetic Mapping and Biochemical Basis of Yellow Feather Pigmentation in Budgerigars
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Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
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The Origin and Diversification of Birds
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Embracing Uncertainty in Reconstructing Early Animal Evolution
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Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes
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Phylogenomics: the beginning of incongruence?
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Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model
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Towards the global monitoring of biodiversity change
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Model use in phylogenetics: nine key questions
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Deciphering ancient rapid radiations
inferredcites →https://doi.org/10.1016/j.tree.2009.12.004openalex-snapshot
Evolutionary stasis: the stable chromosomes of birds
inferredcites →https://doi.org/10.1016/j.tree.2011.09.004openalex-snapshot
From snout to beak: the loss of teeth in birds
inferredcites →https://doi.org/10.1016/j.tree.2013.09.004openalex-snapshot
Computational approaches to species phylogeny inference and gene tree reconciliation
inferredcites →https://doi.org/10.1016/j.tree.2015.12.007openalex-snapshot
An Integrated Perspective on Phylogenetic Workflows
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Hi–C: A comprehensive technique to capture the conformation of genomes
inferredcites →https://doi.org/10.1016/j.ymeth.2018.04.033openalex-snapshot
Iteratively improving Hi-C experiments one step at a time
inferredcites →https://doi.org/10.1016/j.ympev.2017.08.002openalex-snapshot
The development of scientific consensus: Analyzing conflict and concordance among avian phylogenies
inferredcites →https://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?
inferredcites →https://doi.org/10.1016/s0169-5347(03)00017-xopenalex-snapshot
‘Big bang’ for tertiary birds?
inferredcites →https://doi.org/10.1038/hdy.2011.70openalex-snapshot
Evidence of a neo-sex chromosome in birds
inferredcites →https://doi.org/10.1038/nature03154openalex-snapshot
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
inferredcites →https://doi.org/10.1038/nature08696openalex-snapshot
The sequence and de novo assembly of the giant panda genome
inferredcites →https://doi.org/10.1038/nature14181openalex-snapshot
Evolution of Darwin’s finches and their beaks revealed by genome sequencing
inferredcites →https://doi.org/10.1038/nature15697openalex-snapshot
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
inferredcites →https://doi.org/10.1038/nature19417openalex-snapshot
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
inferredcites →https://doi.org/10.1038/ncomms12709openalex-snapshot
Tectonic collision and uplift of Wallacea triggered the global songbird radiation
inferredcites →https://doi.org/10.1038/ncomms1448openalex-snapshot
Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds
inferredcites →https://doi.org/10.1038/ncomms8330openalex-snapshot
Evolutionary analysis of the female-specific avian W chromosome
inferredcites →https://doi.org/10.1038/nmeth.4285openalex-snapshot
ModelFinder: fast model selection for accurate phylogenetic estimates
inferredcites →https://doi.org/10.1038/s41559-019-0850-1openalex-snapshot
Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds
inferredcites →https://doi.org/10.1038/s41576-018-0003-4openalex-snapshot
Piercing the dark matter: bioinformatics of long-range sequencing and mapping
inferredcites →https://doi.org/10.1073/pnas.0904103106openalex-snapshot
Natural selection and phylogenetic analysis
inferredcites →https://doi.org/10.1073/pnas.1315456110openalex-snapshot
Repeated elevational transitions in hemoglobin function during the evolution of Andean hummingbirds
inferredcites →https://doi.org/10.1073/pnas.1616702114openalex-snapshot
Dynamics of genome size evolution in birds and mammals
inferredcites →https://doi.org/10.1073/pnas.1700188114openalex-snapshot
Early Paleocene landbird supports rapid phylogenetic and morphological diversification of crown birds after the K–Pg mass extinction
inferredcites →https://doi.org/10.1073/pnas.1707515115openalex-snapshot
Pairwise comparisons across species are problematic when analyzing functional genomic data
inferredcites →https://doi.org/10.1073/pnas.1813206116openalex-snapshot
Earth history and the passerine superradiation
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/10.1080/10635150500234609openalex-snapshot
An Empirical Assessment of Long-Branch Attraction Artefacts in Deep Eukaryotic Phylogenomics
inferredcites →https://doi.org/10.1080/10635150500354928openalex-snapshot
Inferring Phylogeny Despite Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1080/10635150701397643openalex-snapshot
Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies
inferredcites →https://doi.org/10.1080/10635150701884640openalex-snapshot
Taxon Sampling Affects Inferences of Macroevolutionary Processes from Phylogenetic Trees
inferredcites →https://doi.org/10.1093/bib/bbr014openalex-snapshot
The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy
inferredcites →https://doi.org/10.1093/bioinformatics/btn025openalex-snapshot
SOAP: short oligonucleotide alignment program
inferredcites →https://doi.org/10.1093/bioinformatics/btv184openalex-snapshot
ExaML version 3: a tool for phylogenomic analyses on supercomputers
inferredcites →https://doi.org/10.1093/bioinformatics/bty839openalex-snapshot
ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes
inferredcites →https://doi.org/10.1093/bioinformatics/btz305openalex-snapshot
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
inferredcites →https://doi.org/10.1093/gbe/evr080openalex-snapshot
Genome-Wide Heterogeneity of Nucleotide Substitution Model Fit
inferredcites →https://doi.org/10.1093/gbe/evv261openalex-snapshot
The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference
inferredcites →https://doi.org/10.1093/gbe/evw264openalex-snapshot
Evolution and Diversity of Transposable Elements in Vertebrate Genomes
inferredcites →https://doi.org/10.1093/gbe/evy180openalex-snapshot
Genetic and Molecular Basis of Feather Diversity in Birds
inferredcites →https://doi.org/10.1093/jhered/esp086openalex-snapshot
Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species
inferredcites →https://doi.org/10.1093/molbev/msh112openalex-snapshot
A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
inferredcites →https://doi.org/10.1093/molbev/msr014openalex-snapshot
Evolution of Modern Birds Revealed by Mitogenomics: Timing the Radiation and Origin of Major Orders
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/molbev/msx236openalex-snapshot
Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds
inferredcites →https://doi.org/10.1093/sysbio/syp008openalex-snapshot
Properties of Consensus Methods for Inferring Species Trees from Gene Trees
inferredcites →https://doi.org/10.1093/sysbio/syv059openalex-snapshot
Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny
inferredcites →https://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
inferredcites →https://doi.org/10.1093/sysbio/syx058openalex-snapshot
Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics
inferredcites →https://doi.org/10.1093/sysbio/syy061openalex-snapshot
Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary Methods
inferredcites →https://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
inferredcites →https://doi.org/10.1098/rspb.2009.1004openalex-snapshot
The smallest avian genomes are found in hummingbirds
inferredcites →https://doi.org/10.1101/262949openalex-snapshot
Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone
inferredcites →https://doi.org/10.1101/447110openalex-snapshot
RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference
inferredcites →https://doi.org/10.1101/460121openalex-snapshot
The Prevalence and Impact of Model Violations in Phylogenetics Analysis
inferredcites →https://doi.org/10.1101/gr.097261.109openalex-snapshot
De novo assembly of human genomes with massively parallel short read sequencing
inferredcites →https://doi.org/10.1101/gr.123356.111openalex-snapshot
Cactus: Algorithms for genome multiple sequence alignment
inferredcites →https://doi.org/10.1101/gr.245126.118openalex-snapshot
Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly
inferredcites →https://doi.org/10.1111/1755-0998.12933openalex-snapshot
How complete are “complete” genome assemblies?—An avian perspective
inferredcites →https://doi.org/10.1111/evo.12047openalex-snapshot
MICROEVOLUTIONARY PROCESSES GENERATE PHYLOGENOMIC DISCORDANCE AT ANCIENT DIVERGENCES
inferredcites →https://doi.org/10.1111/evo.13649openalex-snapshot
Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes*
inferredcites →https://doi.org/10.1111/ibi.12285openalex-snapshot
The Avian Hybrids Project: gathering the scientific literature on avian hybridization
inferredcites →https://doi.org/10.1111/j.0014-3820.2002.tb00854.xopenalex-snapshot
A BIRD'S-EYE VIEW OF THE C-VALUE ENIGMA: GENOME SIZE, CELL SIZE, AND METABOLIC RATE IN THE CLASS AVES
inferredcites →https://doi.org/10.1111/j.0014-3820.2004.tb01655.xopenalex-snapshot
BIRDS IN A BUSH: FIVE GENES INDICATE EXPLOSIVE EVOLUTION OF AVIAN ORDERS
inferredcites →https://doi.org/10.1111/j.1096-0031.2005.00059.xopenalex-snapshot
A review of long‐branch attraction
inferredcites →https://doi.org/10.1111/nyas.13295openalex-snapshot
Evolution of bird genomes—a transposon's‐eye view
inferredcites →https://doi.org/10.1111/zsc.12213openalex-snapshot
The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves
inferredcites →https://doi.org/10.1126/sciadv.1501005openalex-snapshot
A new time tree reveals Earth history’s imprint on the evolution of modern birds
inferredcites →https://doi.org/10.1126/science.1157704openalex-snapshot
A Phylogenomic Study of Birds Reveals Their Evolutionary History
inferredcites →https://doi.org/10.1126/science.1187512openalex-snapshot
Global Biodiversity: Indicators of Recent Declines
inferredcites →https://doi.org/10.1126/science.1230422openalex-snapshot
Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon
inferredcites →https://doi.org/10.1126/science.1246338openalex-snapshot
Complex evolutionary trajectories of sex chromosomes across bird taxa
inferredcites →https://doi.org/10.1126/science.1250463openalex-snapshot
Statistical binning enables an accurate coalescent-based estimation of the avian tree
inferredcites →https://doi.org/10.1126/science.1251385openalex-snapshot
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/10.1126/science.1254390openalex-snapshot
Evidence for a single loss of mineralized teeth in the common avian ancestor
inferredcites →https://doi.org/10.1126/science.1254449openalex-snapshot
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
inferredcites →https://doi.org/10.1126/science.1256846openalex-snapshot
Convergent transcriptional specializations in the brains of humans and song-learning birds
inferredcites →https://doi.org/10.1126/science.2014.346.6215.346_1308openalex-snapshot
A flock of genomes
inferredcites →https://doi.org/10.1126/science.267.5198.637openalex-snapshot
Explosive Evolution in Tertiary Birds and Mammals
inferredcites →https://doi.org/10.1126/science.aad8786openalex-snapshot
A beak size locus in Darwin’s finches facilitated character displacement during a drought
inferredcites →https://doi.org/10.1126/science.aaf9070openalex-snapshot
Predictable convergence in hemoglobin function has unpredictable molecular underpinnings
inferredcites →https://doi.org/10.1126/science.aal3327openalex-snapshot
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
inferredcites →https://doi.org/10.1126/science.aal3345openalex-snapshot
A genetic signature of the evolution of loss of flight in the Galapagos cormorant
inferredcites →https://doi.org/10.1126/science.aao4593openalex-snapshot
Rapid hybrid speciation in Darwin’s finches
inferredcites →https://doi.org/10.1126/science.aar6343openalex-snapshot
High-resolution comparative analysis of great ape genomes
inferredcites →https://doi.org/10.1126/science.aat7244openalex-snapshot
Convergent regulatory evolution and loss of flight in paleognathous birds
inferredcites →https://doi.org/10.1146/annurev-animal-090414-014900openalex-snapshot
The Genome 10K Project: A Way Forward
inferredcites →https://doi.org/10.1146/annurev-genet-120213-092532openalex-snapshot
Lineage Sorting in Apes
inferredcites →https://doi.org/10.1146/annurev.ecolsys.35.112202.130205openalex-snapshot
Phylogenomics
inferredcites →https://doi.org/10.1159/000063018openalex-snapshot
Origin and evolution of avian microchromosomes
inferredcites →https://doi.org/10.1186/1471-2148-7-s1-s4openalex-snapshot
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
inferredcites →https://doi.org/10.1186/2047-217x-3-26openalex-snapshot
Comparative genomic data of the Avian Phylogenomics Project
inferredcites →https://doi.org/10.1186/2047-217x-3-27openalex-snapshot
Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment
inferredcites →https://doi.org/10.1186/preaccept-4747137171262766openalex-snapshot
Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition
inferredcites →https://doi.org/10.1186/s12862-014-0249-1openalex-snapshot
Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles
inferredcites →https://doi.org/10.1186/s12862-014-0250-8openalex-snapshot
Temporal genomic evolution of bird sex chromosomes
inferredcites →https://doi.org/10.1186/s12864-015-1924-3openalex-snapshot
Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds
inferredcites →https://doi.org/10.1186/s12864-017-3879-zopenalex-snapshot
Scaffolding of long read assemblies using long range contact information
inferredcites →https://doi.org/10.1186/s13059-015-0588-2openalex-snapshot
Avianbase: a community resource for bird genomics
inferredcites →https://doi.org/10.1186/s13059-015-0711-4openalex-snapshot
Kiwi genome provides insights into evolution of a nocturnal lifestyle
inferredcites →https://doi.org/10.1186/s13059-018-1585-zopenalex-snapshot
The bird’s-eye view on chromosome evolution
inferredcites →https://doi.org/10.1186/s13742-015-0062-9openalex-snapshot
Improving the ostrich genome assembly using optical mapping data
inferredcites →https://doi.org/10.1186/s40657-017-0088-zopenalex-snapshot
Avian introgression in the genomic era
inferredcites →https://doi.org/10.1196/annals.1439.003openalex-snapshot
Ecosystem Services Provided by Birds
inferredcites →https://doi.org/10.1371/journal.pbio.0040352openalex-snapshot
Bushes in the Tree of Life
inferredcites →https://doi.org/10.1371/journal.pbio.1000475openalex-snapshot
Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis
inferredcites →https://doi.org/10.1371/journal.pbio.1002224openalex-snapshot
The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds
inferredcites →https://doi.org/10.1371/journal.pgen.0020068openalex-snapshot
Discordance of Species Trees with Their Most Likely Gene Trees
inferredcites →https://doi.org/10.1371/journal.pgen.1002660openalex-snapshot
The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection
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.0129183openalex-snapshot
Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
inferredcites →https://doi.org/10.3390/genes9030132openalex-snapshot
Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies
inferredcites →https://doi.org/10.3390/genes9040181openalex-snapshot
Karyotype Evolution in Birds: From Conventional Staining to Chromosome Painting
inferredcites →https://doi.org/10.3791/1869openalex-snapshot
Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
inferredcites →https://doi.org/10.3791/1869-vopenalex-snapshot
Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
inferredcites →https://doi.org/10.48550/arxiv.1605.04619openalex-snapshot
An end-to-end assembly of the Aedes aegypti genome
inferredcites →https://doi.org/10.7717/peerj.6399openalex-snapshot
Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Phylogenetic relationships within the genus Garrulus Brisson, 1760 (Corvidae, Aves) with special emphasis on the Garrulus glandarius complex based on mitochondrial marker sequences
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Common patterns in the molecular phylogeography of western palearctic birds: a comprehensive review
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Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree
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A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta)
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The relationship between diet, plasma glucose, and cancer prevalence across vertebrates
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A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics
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A bird’s eye view of the fossil record: perspectives on avian systematics
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A Chromosome-Level Genome of the Agile Gracile Mouse Opossum (Gracilinanus agilis)
inferred← citeshttps://doi.org/10.1093/gigascience/giz117openalex-snapshot
High-coverage genomes to elucidate the evolution of penguins
inferred← citeshttps://doi.org/10.1093/icb/icab158openalex-snapshot
Integrative Studies of Sexual Selection in Manakins, a Clade of Charismatic Tropical Birds
inferred← citeshttps://doi.org/10.1111/1755-0998.13124openalex-snapshot
Genome of an iconic Australian bird: High‐quality assembly and linkage map of the superb fairy‐wren ( Malurus cyaneus )
inferred← citeshttps://doi.org/10.1111/1755-0998.13524openalex-snapshot
Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs
inferred← citeshttps://doi.org/10.1111/ele.13898openalex-snapshot
AVONET: morphological, ecological and geographical data for all birds
inferred← citeshttps://doi.org/10.1111/ele.13960openalex-snapshot
A bird in the hand: Global‐scale morphological trait datasets open new frontiers of ecology, evolution and ecosystem science
inferred← citeshttps://doi.org/10.1126/science.adw1931openalex-snapshot
Multispecies pangenomes reveal a pervasive influence of population size on structural variation
inferred← citeshttps://doi.org/10.1146/annurev-ecolsys-012121-085928openalex-snapshot
What Have We Learned from the First 500 Avian Genomes?
inferred← citeshttps://doi.org/10.1146/annurev-ecolsys-110218-025023openalex-snapshot
Avian Diversity: Speciation, Macroevolution, and Ecological Function
inferred← citeshttps://doi.org/10.1371/journal.pone.0241098openalex-snapshot
Complete mitogenome of endemic plum-headed parakeet Psittacula cyanocephala – characterization and phylogenetic analysis
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Utilization of Large-Scale Genomic Data and Phylogenetic Methods in Studying Evolutionary Radiations
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KEANEKARAGAMAN JENIS BURUNG DI LAHAN AGROFORESTRI (Studi Kasus : Lahan Pengembangan Agroforestri Universitas Lancang Kuning)
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Genomic Insights Into the Molecular Basis of Sexual Selection in Birds
inferred← citeshttps://doi.org/10.3390/ani12152004openalex-snapshot
De Novo Whole-Genome Sequencing and Assembly of the Yellow-Throated Bunting (Emberiza elegans) Provides Insights into Its Evolutionary Adaptation
inferred← citeshttps://doi.org/10.3390/birds2010001openalex-snapshot
Data Types and the Phylogeny of Neoaves
inferred← citeshttps://doi.org/10.3390/cells10020362openalex-snapshot
Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution
inferred← citeshttps://doi.org/10.3390/d11100178openalex-snapshot
Special Issue: Genomic Analyses of Avian Evolution
inferred← citeshttps://doi.org/10.3390/d12040164openalex-snapshot
Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation
inferred← citeshttps://doi.org/10.3390/d14030216openalex-snapshot
Red-Backed Shrike Lanius collurio Whole-Genome Sequencing Reveals Population Genetic Admixture
inferred← citeshttps://doi.org/10.3390/v13020212openalex-snapshot
Highly Pathogenic Avian Influenza Viruses at the Wild–Domestic Bird Interface in Europe: Future Directions for Research and Surveillance
inferred← citeshttps://doi.org/10.38001/ijlsb.1297886openalex-snapshot
Phylogenetic Analysis of Some Wild Birds in Şanlıurfa (Türkiye)
inferred← citeshttps://doi.org/10.7818/ecos.1969openalex-snapshot
Relevance of genomics for a better understanding of the host-parasite interaction in birds
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