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References from A bird’s white-eye view on avian sex chromosome evolution. Local targets link to admitted publications; unresolved targets remain external evidence.
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations
10.1093/nar/gkq291 · 2010 · External reference
The African coelacanth genome provides insights into tetrapod evolution
10.1038/nature12027 · 2013 · External reference
Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes
10.1186/s12864-018-4466-7 · 2018 · External reference
Sex chromosome evolution: Molecular aspects of Y-chromosome degeneration in Drosophila
10.1101/gr.3543605 · 2005 · External reference
Reduced adaptation of a non-recombining neo-Y chromosome
10.1038/416323a · 2002 · External reference
The recombination landscape of the zebra finch Taeniopygia guttata genome
10.1101/gr.101410.109 · 2010 · External reference
Unresolved reference
External reference
The recombination landscape of the zebra finch Taeniopygia guttata genome
10.1101/gr.101410.109 · 2010 · External reference
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information
10.1186/1471-2105-15-211 · 2014 · External reference
Fossil Songbirds (Passeriformes) from the Early Eocene of Australia
10.1071/mu97004 · 1997 · External reference
Trimmomatic: a flexible trimmer for Illumina sequence data
10.1093/bioinformatics/btu170 · 2014 · External reference
Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds
10.1093/molbev/msx236 · 2017 · External reference
A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird
10.1098/rsos.160805 · 2017 · External reference
Recent Secondary Contacts, Linked Selection, and Variable Recombination Rates Shape Genomic Diversity in the Model Species Anolis carolinensis
10.1093/gbe/evz110 · 2019 · External reference
Rapid neo-sex chromosome evolution and incipient speciation in a major forest pest
10.1038/s41467-017-01761-4 · 2017 · External reference
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
10.1186/2047-217x-2-10 · 2013 · External reference
Widespread Translocation from Autosomes to Sex Chromosomes Preserves Genetic Variability in an Endangered Lark
10.1007/s00239-010-9333-3 · 2010 · External reference
Near-complete phylogeny and taxonomic revision of the world’s babblers (Aves: Passeriformes)
10.1016/j.ympev.2018.10.010 · 2019 · External reference
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
10.1093/bioinformatics/btp348 · 2009 · External reference
The Evolution of Sex Chromosomes
10.1126/science.1998119 · 1991 · External reference
Rapid fixation of deleterious alleles can be caused by Muller's ratchet
10.1017/s0016672397002899 · 1997 · External reference
The degeneration of Y chromosomes
10.1098/rstb.2000.0717 · 2000 · External reference
The evolutionary dynamics of repetitive DNA in eukaryotes
10.1038/371215a0 · 1994 · External reference
The influence of gene flow and drift on genetic and phenotypic divergence in two species ofZosteropsin Vanuatu
10.1098/rstb.2009.0281 · 2010 · External reference
Chromosome evolution in eukaryotes: a multi-kingdom perspective
10.1016/j.tig.2005.09.009 · 2005 · External reference
The Genome of the “Great Speciator” Provides Insights into Bird Diversification
10.1093/gbe/evv168 · 2015 · External reference
Morphological and plumage colour variation in the Réunion grey white-eye (Aves:Zosterops borbonicus): assessing the role of selection
10.1111/bij.12428 · 2014 · External reference
A W-linked palindrome and gene conversion in New World sparrows and blackbirds
10.1007/s10577-010-9134-y · 2010 · External reference
Narrow hybrid zones in spite of very low population differentiation in neutral markers in an island bird species complex
10.1111/jeb.13177 · 2017 · External reference
Lineage diversification and morphological evolution in a large-scale continental radiation: the neotropical ovenbirds and woodcreepers (Aves: Furnariidae)
10.1111/j.1558-5646.2011.01374.x · 2011 · External reference
Species-distance relation for birds of the Solomon Archipelago, and the paradox of the great speciators
10.1073/pnas.73.6.2160 · 1976 · External reference
Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark
10.1098/rspb.2019.2613 · 2020 · External reference
Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution
10.1016/j.cell.2008.05.042 · 2008 · External reference
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
10.1093/gbe/evx069 · 2017 · External reference
10.1201/9781420064452
10.1201/9781420064452 · External reference
The Impact of Recombination on Nucleotide Substitutions in the Human Genome
10.1371/journal.pgen.1000071 · 2008 · External reference
Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes
10.1146/annurev-genom-082908-150001 · 2009 · External reference
Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs
10.1186/1471-2148-8-255 · 2008 · External reference
A new psittaciform bird from the London Clay (Lower Eocene) of England
10.1111/1475-4983.00126 · 2008 · External reference
The different levels of genetic diversity in sex chromosomes and autosomes
10.1016/j.tig.2009.04.005 · 2009 · External reference
Evolutionary stasis: the stable chromosomes of birds
10.1016/j.tree.2009.12.004 · 2010 · External reference
The Evolutionary Genomics of Birds
10.1146/annurev-ecolsys-110411-160327 · 2013 · External reference
The genomic landscape of species divergence in Ficedula flycatchers
10.1038/nature11584 · 2012 · External reference
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
10.1186/s13059-015-0721-2 · 2015 · External reference
Dating the diversification of the major lineages of Passeriformes (Aves)
10.1186/1471-2148-14-8 · 2014 · External reference
Recombination and mammalian genome evolution
10.1098/rspb.1993.0071 · 1993 · External reference
The deep conservation of the Lepidoptera Z chromosome suggests a non-canonical origin of the W
10.1038/s41467-017-01663-5 · 2017 · External reference
Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis
10.1093/oxfordjournals.molbev.a025991 · 1998 · External reference
Age of Cichlids: New Dates for Ancient Lake Fish Radiations
10.1093/molbev/msm050 · 2007 · External reference
Intra-Island Variation in the Mascarene White-Eye Zosterops borbonica
10.2307/40166689 · 1973 · External reference
The evolution of the avian genome as revealed by comparative molecular cytogenetics
10.1159/000103166 · 2007 · External reference
Circlize implements and enhances circular visualization in R
10.1093/bioinformatics/btu393 · 2014 · External reference
Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution
10.1093/molbev/mst097 · 2013 · External reference
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
10.1093/nar/gkg770 · 2003 · External reference
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
10.1038/nprot.2013.084 · 2013 · External reference
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
10.1186/gb-2008-9-1-r7 · 2008 · External reference
Approaches to Fungal Genome Annotation
10.1080/21501203.2011.606851 · 2011 · External reference
Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach
10.1093/nar/gkt371 · 2013 · External reference
Phylogenetic Comparative Methods: Learning From Trees
10.32942/osf.io/e3xnr · External reference
Dating nodes on molecular phylogenies: a critique of molecular biogeography
10.1111/j.1096-0031.2005.00052.x · 2005 · External reference
Old Taxa on Young Islands: A Critique of the Use of Island Age to Date Island-Endemic Clades and Calibrate Phylogenies
10.1093/sysbio/syq075 · 2011 · External reference
The effect of linkage on limits to artificial selection
10.1017/s0016672300010156 · 1966 · External reference
AGILE: an assembled genome mining pipeline
10.1093/bioinformatics/bty781 · 2018 · External reference
Extensive X-linked adaptive evolution in central chimpanzees
10.1073/pnas.1106877109 · 2012 · External reference
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
10.1038/nature03154 · 2004 · External reference
Whole-genome analyses resolve early branches in the tree of life of modern birds
10.1126/science.1253451 · 2014 · External reference
The global diversity of birds in space and time
10.1038/nature11631 · 2012 · External reference
Repbase Update, a database of eukaryotic repetitive elements
10.1159/000084979 · 2005 · External reference
Beanplot: A Boxplot Alternative for Visual Comparison of Distributions
10.18637/jss.v028.c01 · 2008 · External reference
Evolution of bird genomes-a transposon's-eye view
10.1111/nyas.13295 · 2017 · External reference
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
10.1093/nar/gkf436 · 2002 · External reference
A high‐density linkage map enables a second‐generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution
10.1111/mec.12810 · 2014 · External reference
HISAT: a fast spliced aligner with low memory requirements
10.1038/nmeth.3317 · 2015 · External reference
Turnover of sex chromosomes and speciation in fishes
10.1007/s10641-011-9853-8 · 2011 · External reference
A role for a neo-sex chromosome in stickleback speciation
10.1038/nature08441 · 2009 · External reference
Phylogenetically vetted and stratigraphically constrained fossil calibrations within Aves
10.26879/373 · 2015 · External reference
The abiotic and biotic drivers of rapid diversification in A ndean bellflowers (Campanulaceae)
10.1111/nph.13920 · 2016 · External reference
Population size and the rate of evolution
10.1016/j.tree.2013.09.009 · 2014 · External reference
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
10.1093/bioinformatics/btp368 · 2009 · External reference
Morphological Clocks in Paleontology, and a Mid-Cretaceous Origin of Crown Aves
10.1093/sysbio/syt110 · 2014 · External reference
NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries
10.1093/bioinformatics/btt702 · 2014 · External reference
Plotrix: A package in the red light district of R
2006 · External reference
Unresolved reference
2013 · External reference
Genetic differences between willow warbler migratory phenotypes are few and cluster in large haplotype blocks
10.1002/evl3.15 · 2017 · External reference
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
10.1186/2047-217x-1-18 · 2012 · External reference
Absolute diversification rates in angiosperm clades
10.1554/0014-3820(2001)055[1762:adriac]2.0.co;2 · 2001 · External reference
Fast-X on the Z: Rapid evolution of sex-linked genes in birds
10.1101/gr.6031907 · 2007 · External reference
Faster-Z Evolution Is Predominantly Due to Genetic Drift
10.1093/molbev/msp282 · 2010 · External reference
Evidence for Degeneration of the Y Chromosome in the Dioecious Plant Silene latifolia
10.1016/j.cub.2008.03.023 · 2008 · External reference
A Small Suboscine-Like Passeriform Bird from the Early Oligocene of France
10.1093/condor/108.3.717 · 2006 · External reference
The age of the crown group of passerine birds and its evolutionary significance – molecular calibrations versus the fossil record
10.1080/14772000.2013.765521 · 2013 · External reference
Rapid parallel evolution of aberrant traits in the diversification of the Gulf of Guinea white-eyes (Aves, Zosteropidae)
10.1111/j.1365-294x.2011.05099.x · 2011 · External reference
The geographic scale of diversification on islands: genetic and morphological divergence at a very small spatial scale in the Mascarene grey white-eye (Aves: Zosterops borbonicus)
10.1186/1471-2148-10-158 · 2010 · External reference
Explosive Pleistocene diversification and hemispheric expansion of a “great speciator”
10.1073/pnas.0809861105 · 2009 · External reference
Extensive Conservation of Sex Chromosome Organization Between Cat and Human Revealed by Parallel Radiation Hybrid Mapping
10.1101/gr.9.12.1223 · 1999 · External reference
Dynamic Evolution of Base Composition: Causes and Consequences in Avian Phylogenomics
10.1093/molbev/msr047 · 2011 · External reference
Body mass-corrected molecular rate for bird mitochondrial DNA
10.1111/mec.13780 · 2016 · External reference
Extreme selective sweeps independently targeted the X chromosomes of the great apes
10.1073/pnas.1419306112 · 2015 · External reference
Extensive gross genomic rearrangements between chicken and Old World vultures (Falconiformes: Accipitridae)
10.1159/000089883 · 2006 · External reference
Synteny conservation of the Z chromosome in 14 avian species (11 families) supports a role for Z dosage in avian sex determination
10.1159/000163092 · 2008 · External reference
Gene expression, chromosome heterogeneity and the fast-X effect in mammals
10.1098/rsbl.2015.0010 · 2015 · External reference
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
10.1093/molbev/msu300 · 2015 · External reference
Phenotypic and genotypic variation across a stable white-eye (Zosterops sp.) hybrid zone in central South Africa
10.1093/biolinnean/blx012 · 2017 · External reference
A multi-locus phylogeny reveals a complex pattern of diversification related to climate and habitat heterogeneity in southern African white-eyes
10.1016/j.ympev.2012.05.022 · 2012 · External reference
Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs
10.1038/s41467-018-04267-9 · 2018 · External reference
The Nearly Neutral Theory of Molecular Evolution
10.1146/annurev.es.23.110192.001403 · 1992 · External reference
Chromosome reshuffling in birds of prey: the karyotype of the world's largest eagle (Harpy eagle, Harpia harpyja) compared to that of the chicken (Gallus gallus)
10.1007/s00412-005-0009-5 · 2005 · External reference
Evidence of a neo-sex chromosome in birds
10.1038/hdy.2011.70 · 2012 · External reference
Patterns of Molecular Evolution of an Avian Neo-sex Chromosome
10.1093/molbev/mss177 · 2012 · External reference
Rapid Y degeneration and dosage compensation in plant sex chromosomes
10.1073/pnas.1508454112 · 2015 · External reference
APE: Analyses of Phylogenetics and Evolution in R language
10.1093/bioinformatics/btg412 · 2004 · External reference
Mosdepth: quick coverage calculation for genomes and exomes
10.1093/bioinformatics/btx699 · 2018 · External reference
How complete are “complete” genome assemblies?-An avian perspective
10.1111/1755-0998.12933 · 2018 · External reference
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
10.1038/nbt.3122 · 2015 · External reference
Evidence for Widespread GC-biased Gene Conversion in Eukaryotes
10.1093/gbe/evs052 · 2012 · External reference
Pitfalls in supermatrix phylogenomics
10.5852/ejt.2017.283 · 2017 · External reference
The genomic landscape underlying phenotypic integrity in the face of gene flow in crows
10.1126/science.1253226 · 2014 · External reference
Population size changes reshape genomic patterns of diversity
10.1111/j.1558-5646.2007.00238.x · 2007 · External reference
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
10.1038/nature15697 · 2015 · External reference
Unresolved reference
External reference
Inferring Speciation Times under an Episodic Molecular Clock
10.1080/10635150701420643 · 2007 · External reference
MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons
10.1093/molbev/msy159 · 2018 · External reference
A detailed physical map of the horse Y chromosome
10.1073/pnas.0403011101 · 2004 · External reference
phytools: an R package for phylogenetic comparative biology (and other things)
10.1111/j.2041-210x.2011.00169.x · 2012 · External reference
Hemizygosity Enhances Purifying Selection: Lack of Fast-Z Evolution in Two Satyrine Butterflies
10.1093/gbe/evw214 · 2016 · External reference
Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence
10.1371/journal.pbio.2000234 · 2016 · External reference
LoRDEC: accurate and efficient long read error correction
10.1093/bioinformatics/btu538 · 2014 · External reference
Human–Mouse Alignments with BLASTZ
10.1101/gr.809403 · 2003 · External reference
genBlastG: using BLAST searches to build homologous gene models
10.1093/bioinformatics/btr342 · 2011 · External reference
Insights into Avian Incomplete Dosage Compensation: Sex-Biased Gene Expression Coevolves with Sex Chromosome Degeneration in the Common Whitethroat
10.3390/genes9080373 · 2018 · External reference
Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes
10.1098/rspb.2019.2051 · 2019 · External reference
Evolutionary analysis of the female-specific avian W chromosome
10.1038/ncomms8330 · 2015 · External reference
Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes
10.1111/mec.14439 · 2018 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Gene prediction with a hidden markov model and a new intron submodel
10.1093/bioinformatics/btg1080 · 2003 · External reference
Should Y stay or should Y go: The evolution of non-recombining sex chromosomes
10.1002/bies.201200064 · 2012 · External reference
Evolutionary relationship of DNA sequences in finite populations
10.1093/genetics/105.2.437 · 1983 · External reference
Illumina Library Preparation for Sequencing the GC-Rich Fraction of Heterogeneous Genomic DNA
10.1093/gbe/evy022 · 2018 · External reference
Y and W Chromosome Assemblies: Approaches and Discoveries
10.1016/j.tig.2017.01.008 · 2017 · External reference
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
10.1038/nbt.1621 · 2010 · External reference
Evolution on the X chromosome: unusual patterns and processes
10.1038/nrg1914 · 2006 · External reference
Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution
10.1101/gr.103663.109 · 2010 · External reference
The genome of a songbird
10.1038/nature08819 · 2010 · External reference
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure
10.1534/g3.116.035923 · 2016 · External reference
BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics
10.1093/molbev/msx319 · 2017 · External reference
Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition
10.1186/s13059-014-0549-1 · 2014 · External reference
Neo‐sex chromosome inheritance across species in Silene hybrids?
10.1111/jeb.12371 · 2014 · External reference
Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
10.1101/gr.215095.116 · 2017 · External reference
10.1007/978-3-319-24277-4
10.1007/978-3-319-24277-4 · 2016 · External reference
Unresolved reference
External reference
Genetic Diversity on the Sex Chromosomes
10.1093/gbe/evy039 · 2018 · External reference
Nonlinear Dynamics of Nonsynonymous (dN) and Synonymous (dS) Substitution Rates Affects Inference of Selection
10.1093/gbe/evp030 · 2009 · External reference
Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution
10.1111/mec.13113 · 2015 · External reference
PAML 4: Phylogenetic Analysis by Maximum Likelihood
10.1093/molbev/msm088 · 2007 · External reference
Bayesian Estimation of Species Divergence Times Under a Molecular Clock Using Multiple Fossil Calibrations with Soft Bounds
10.1093/molbev/msj024 · 2005 · External reference
Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species
10.1371/journal.pgen.1004223 · 2014 · External reference
Comparative genomics reveals insights into avian genome evolution and adaptation
10.1126/science.1251385 · 2014 · External reference
The genome of Darwin’s Finch (Geospiza fortis)
10.5524/100040 · 2012 · External reference
Sex-Specific Adaptation Drives Early Sex Chromosome Evolution in Drosophila
10.1126/science.1225385 · 2012 · External reference
Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm
10.1101/gr.213405.116 · 2017 · External reference
