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Convergent regulatory evolution and loss of flight in paleognathous birds

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What this work says

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

inferredcites →https://doi.org/10.1007/978-1-4612-4318-2_13openalex-snapshot

Mitochondrial DNA from Ancient Bones

inferredcites →https://doi.org/10.1007/978-1-4939-7216-6_2openalex-snapshot

Comparative Genomics as a Foundation for Evo-Devo Studies in Birds

inferredcites →https://doi.org/10.1007/978-1-62703-646-7_10openalex-snapshot

Phylogeny-aware alignment with PRANK

inferredcites →https://doi.org/10.1007/bf00411355openalex-snapshot

Unique amanitin resistance of RNA synthesis in isolated nuclei from Amanita species accumulating amanitins

inferredcites →https://doi.org/10.1016/j.aanat.2011.03.008openalex-snapshot

Setting the stage – Building and working in an ancient DNA laboratory

inferredcites →https://doi.org/10.1016/j.cell.2017.12.017openalex-snapshot

Ultraconserved Enhancers Are Required for Normal Development

inferredcites →https://doi.org/10.1016/j.celrep.2012.08.032openalex-snapshot

A “Forward Genomics” Approach Links Genotype to Phenotype using Independent Phenotypic Losses among Related Species

inferredcites →https://doi.org/10.1016/j.cub.2016.10.029openalex-snapshot

Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites

inferredcites →https://doi.org/10.1016/j.devcel.2014.03.001openalex-snapshot

Formation of Proximal and Anterior Limb Skeleton Requires Early Function of Irx3 and Irx5 and Is Negatively Regulated by Shh Signaling

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Modification of Enhancer Chromatin: What, How, and Why?

inferredcites →https://doi.org/10.1016/j.ympev.2017.01.005openalex-snapshot

Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell

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Ostrich ancestors found in the Northern Hemisphere suggest new hypothesis of ratite origins

inferredcites →https://doi.org/10.1038/nature00814openalex-snapshot

T-box gene tbx5 is essential for formation of the pectoral limb bud

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In vivo enhancer analysis of human conserved non-coding sequences

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Digit loss in archosaur evolution and the interplay between selection and constraints

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Patterning and post-patterning modes of evolutionary digit loss in mammals

inferredcites →https://doi.org/10.1038/nbt.1621openalex-snapshot

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

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Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features

inferredcites →https://doi.org/10.1038/ncomms1851openalex-snapshot

Evolution of a tissue-specific silencer underlies divergence in the expression of pax2 and pax8 paralogues

inferredcites →https://doi.org/10.1038/ng.2007.55openalex-snapshot

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

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Convergent evolution of the genomes of marine mammals

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Enzymatic assembly of DNA molecules up to several hundred kilobases

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Fast gapped-read alignment with Bowtie 2

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Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

inferredcites →https://doi.org/10.1038/nprot.2013.084openalex-snapshot

De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity

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Causes of molecular convergence and parallelism in protein evolution

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The genetic causes of convergent evolution

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Co-option of the cardiac transcription factor Nkx2.5 during development of the emu wing

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A genomics approach reveals insights into the importance of gene losses for mammalian adaptations

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The Unquiet Ice

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Regulating Evolution

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Phylogenomic evidence for multiple losses of flight in ratite birds

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Evidence for an ancient adaptive episode of convergent molecular evolution

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Sex-biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution

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Regulatory modulation of the T-box gene Tbx5 links development, evolution, and adaptation of the sternum

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Deep conservation of wrist and digit enhancers in fish

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TEAD Transcription Factors Mediate the Function of TAZ in Cell Growth and Epithelial-Mesenchymal Transition

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clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

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PHAST and RPHAST: phylogenetic analysis with space/time models

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HyPhy: hypothesis testing using phylogenies

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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

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BEDTools: a flexible suite of utilities for comparing genomic features

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HAL: a hierarchical format for storing and analyzing multiple genome alignments

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mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

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GAT: a simulation framework for testing the association of genomic intervals

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PEAR: a fast and accurate Illumina Paired-End reAd mergeR

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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

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Trimmomatic: a flexible trimmer for Illumina sequence data

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ExaML version 3: a tool for phylogenomic analyses on supercomputers

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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

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Multiple roles for neurofibromin in skeletal development and growth

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PAML 4: Phylogenetic Analysis by Maximum Likelihood

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inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

inferredcites →https://doi.org/10.1093/molbev/mst160openalex-snapshot

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inferredcites →https://doi.org/10.1093/molbev/msu153openalex-snapshot

Genomic Support for a Moa–Tinamou Clade and Adaptive Morphological Convergence in Flightless Ratites

inferredcites →https://doi.org/10.1093/molbev/msu309openalex-snapshot

Feather Development Genes and Associated Regulatory Innovation Predate the Origin of Dinosauria

inferredcites →https://doi.org/10.1093/molbev/msu400openalex-snapshot

RELAX: Detecting Relaxed Selection in a Phylogenetic Framework

inferredcites →https://doi.org/10.1093/molbev/msv013openalex-snapshot

Determining the Null Model for Detecting Adaptive Convergence from Genomic Data: A Case Study using Echolocating Mammals

inferredcites →https://doi.org/10.1093/molbev/msv022openalex-snapshot

Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection

inferredcites →https://doi.org/10.1093/molbev/msv091openalex-snapshot

Are Convergent and Parallel Amino Acid Substitutions in Protein Evolution More Prevalent Than Neutral Expectations?

inferredcites →https://doi.org/10.1093/molbev/msw001openalex-snapshot

“Reverse Genomics” Predicts Function of Human Conserved Noncoding Elements

inferredcites →https://doi.org/10.1093/molbev/msw046openalex-snapshot

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

inferredcites →https://doi.org/10.1093/molbev/msw112openalex-snapshot

Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals

inferredcites →https://doi.org/10.1093/molbev/msw277openalex-snapshot

Genome-Wide Convergence during Evolution of Mangroves from Woody Plants

inferredcites →https://doi.org/10.1093/molbev/msy109openalex-snapshot

Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages

inferredcites →https://doi.org/10.1093/molbev/msz049openalex-snapshot

Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees

inferredcites →https://doi.org/10.1093/molbev/msz107openalex-snapshot

Robust Method for Detecting Convergent Shifts in Evolutionary Rates

inferredcites →https://doi.org/10.1093/nar/gkr1060openalex-snapshot

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

inferredcites →https://doi.org/10.1093/nar/gky741openalex-snapshot

Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals

inferredcites →https://doi.org/10.1093/sysbio/syp079openalex-snapshot

Tinamous and Moa Flock Together: Mitochondrial Genome Sequence Analysis Reveals Independent Losses of Flight among Ratites

inferredcites →https://doi.org/10.1093/sysbio/syw001openalex-snapshot

Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).

inferredcites →https://doi.org/10.1093/sysbio/syw018openalex-snapshot

Gene Tree Discordance Causes Apparent Substitution Rate Variation

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Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction

inferredcites →https://doi.org/10.1093/sysbio/syx058openalex-snapshot

Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics

inferredcites →https://doi.org/10.1098/rstb.2013.0025openalex-snapshot

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inferredcites →https://doi.org/10.1101/181826openalex-snapshot

Comment on “A genetic signature of the evolution of loss of flight in the Galapagos cormorant”

inferredcites →https://doi.org/10.1101/260745openalex-snapshot

Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees

inferredcites →https://doi.org/10.1101/262816openalex-snapshot

First nuclear genome assembly of an extinct moa species, the little bush moa ( Anomalopteryx didiformis )

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/10.1101/574756openalex-snapshot

Integrating natural history-derived phenomics with comparative genomics to study the genetic architecture of convergent evolution

inferredcites →https://doi.org/10.1101/gad.12.17.2735openalex-snapshot

Pax9 -deficient mice lack pharyngeal pouch derivatives and teeth and exhibit craniofacial and limb abnormalities

inferredcites →https://doi.org/10.1101/gad.1664408openalex-snapshot

TEAD mediates YAP-dependent gene induction and growth control

inferredcites →https://doi.org/10.1101/gr.097857.109openalex-snapshot

Detection of nonneutral substitution rates on mammalian phylogenies

inferredcites →https://doi.org/10.1101/gr.123356.111openalex-snapshot

Cactus: Algorithms for genome multiple sequence alignment

inferredcites →https://doi.org/10.1101/gr.125864.111openalex-snapshot

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

inferredcites →https://doi.org/10.1101/gr.3715005openalex-snapshot

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

inferredcites →https://doi.org/10.1101/gr.7337908openalex-snapshot

ALLPATHS: De novo assembly of whole-genome shotgun microreads

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THE LOCI OF REPEATED EVOLUTION: A CATALOG OF GENETIC HOTSPOTS OF PHENOTYPIC VARIATION

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Congenic method in the chick limb buds by electroporation

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PHYLOGENY AND EVOLUTION OF THE RATITE BIRDS

inferredcites →https://doi.org/10.1111/j.1558-5646.2011.01289.xopenalex-snapshot

CONVERGENCE, ADAPTATION, AND CONSTRAINT

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Evolution at Two Levels in Humans and Chimpanzees

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Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

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Parallel Molecular Evolution in an Herbivore Community

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Comparative genomics reveals insights into avian genome evolution and adaptation

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Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution

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Whole-genome analyses resolve early branches in the tree of life of modern birds

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Evidence for a single loss of mineralized teeth in the common avian ancestor

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Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

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The Status and Future of the American Agronomist

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Convergent local adaptation to climate in distantly related conifers

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Predictable convergence in hemoglobin function has unpredictable molecular underpinnings

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A genetic signature of the evolution of loss of flight in the Galapagos cormorant

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DNA fragility in the parallel evolution of pelvic reduction in stickleback fish

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GEISHA: an in situ hybridization gene expression resource for the chicken embryo

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MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

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A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

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Transcriptomic analyses of regenerating adult feathers in chicken

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Tbx5 is required for forelimb bud formation and continued outgrowth

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Chick Dach1 interacts with the Smad complex and Sin3a to control AER formation and limb development along the proximodistal axis

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Accelerated Profile HMM Searches

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Discordance of Species Trees with Their Most Likely Gene Trees

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Forces Shaping the Fastest Evolving Regions in the Human Genome

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REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

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A shift in anterior–posterior positional information underlies the fin-to-limb evolution

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What points at this work

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

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inferred← citeshttps://doi.org/10.1016/j.cub.2024.08.045openalex-snapshot

Evolution: Sea robins get a leg up

inferred← citeshttps://doi.org/10.1016/j.jgg.2021.06.013openalex-snapshot

Phylogeny and sex chromosome evolution of Palaeognathae

inferred← citeshttps://doi.org/10.1016/j.jgg.2025.04.022openalex-snapshot

Unveiling cell-type-specific mode of evolution in comparative single-cell expression data

inferred← citeshttps://doi.org/10.1016/j.micpath.2020.104361openalex-snapshot

Adaptive evolution of peptidoglycan recognition protein family regulates the innate signaling against microbial pathogens in vertebrates

inferred← citeshttps://doi.org/10.1016/j.psj.2025.105503openalex-snapshot

Cytoskeletal signaling as a shared pathway for convergent genetic mechanisms underlying loss of flight in birds

inferred← citeshttps://doi.org/10.1016/j.tem.2021.07.007openalex-snapshot

Bird evolution by insulin resistance

inferred← citeshttps://doi.org/10.1016/j.tree.2019.07.013openalex-snapshot

Dissecting Trait Variation across Species Barriers

inferred← citeshttps://doi.org/10.1016/j.tree.2020.01.005openalex-snapshot

Phylogenetics is the New Genetics (for Most of Biodiversity)

inferred← citeshttps://doi.org/10.1016/j.tree.2020.01.012openalex-snapshot

Dispersal Reduction: Causes, Genomic Mechanisms, and Evolutionary Consequences

inferred← citeshttps://doi.org/10.1016/j.tree.2020.10.005openalex-snapshot

Examining Natural History through the Lens of Palaeogenomics

inferred← citeshttps://doi.org/10.1016/j.tree.2023.11.007openalex-snapshot

Divergence time shapes gene reuse during repeated adaptation

inferred← citeshttps://doi.org/10.1016/j.xinn.2025.100798openalex-snapshot

Multi-level genomic convergence of secondary aquatic adaptation in marine mammals

inferred← citeshttps://doi.org/10.1016/j.xplc.2023.100671openalex-snapshot

Comparative phylogenomics and phylotranscriptomics provide insights into the genetic complexity of nitrogen-fixing root-nodule symbiosis

inferred← citeshttps://doi.org/10.1016/j.ydbio.2025.08.007openalex-snapshot

Nkx2.5 triggers vascular remodeling in chicken but not in emu wing mesoderm

inferred← citeshttps://doi.org/10.1016/j.ydbio.2026.02.007openalex-snapshot

Did the evolution of multiple microchromosomes help save bird and other dinosaurs from extinction?

inferred← citeshttps://doi.org/10.1016/j.ygeno.2022.110518openalex-snapshot

Chromosome-level genome assembly of the Muscovy duck provides insight into fatty liver susceptibility

inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107291openalex-snapshot

Sequential colonization of oceanic archipelagos led to a species-level radiation in the common chaffinch complex (Aves: Fringilla coelebs)

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.2025.108475openalex-snapshot

Phylogenomics insights into the evolution of pronotal leaf mimicry in Hierodulinae (Mantodea: Mantidae)

inferred← citeshttps://doi.org/10.1038/d41586-019-02234-yopenalex-snapshot

Genomic mechanisms for the evolution of flightlessness in steamer ducks

inferred← citeshttps://doi.org/10.1038/s41467-019-10682-3openalex-snapshot

Convergent genomic signatures of flight loss in birds suggest a switch of main fuel

inferred← citeshttps://doi.org/10.1038/s41467-020-17190-9openalex-snapshot

Megaevolutionary dynamics and the timing of evolutionary innovation in reptiles

inferred← citeshttps://doi.org/10.1038/s41467-021-22100-8openalex-snapshot

Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research

inferred← citeshttps://doi.org/10.1038/s41467-023-36421-3openalex-snapshot

Transcription factor binding sites are frequently under accelerated evolution in primates

inferred← citeshttps://doi.org/10.1038/s41467-023-41412-5openalex-snapshot

Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies

inferred← citeshttps://doi.org/10.1038/s41467-024-48303-3openalex-snapshot

Conserved regulatory switches for the transition from natal down to juvenile feather in birds

inferred← citeshttps://doi.org/10.1038/s41467-024-52203-xopenalex-snapshot

Immobilization secondary to cell death of muscle precursors with a dual transcriptional signature contributes to the emu wing skeletal pattern

inferred← citeshttps://doi.org/10.1038/s41467-024-53141-4openalex-snapshot

The macroevolutionary dynamics of pharyngognathy in fishes fail to support the key innovation hypothesis

inferred← citeshttps://doi.org/10.1038/s41467-025-64134-2openalex-snapshot

Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution

inferred← citeshttps://doi.org/10.1038/s41467-026-72602-6openalex-snapshot

Heterochronic activation of TGF-β signaling drives the diversity of the avian sterna

inferred← citeshttps://doi.org/10.1038/s41477-023-01384-2openalex-snapshot

An efficient CRISPR–Cas12a promoter editing system for crop improvement

inferred← citeshttps://doi.org/10.1038/s41559-020-1209-3openalex-snapshot

Convergent molecular evolution among ash species resistant to the emerald ash borer

inferred← citeshttps://doi.org/10.1038/s41559-023-02001-3openalex-snapshot

Convergent and complementary selection shaped gains and losses of eusociality in sweat bees

inferred← citeshttps://doi.org/10.1038/s41559-026-03003-7openalex-snapshot

The molecular evolution of vertebrate organs

inferred← citeshttps://doi.org/10.1038/s41576-026-00933-7openalex-snapshot

The genetic foundations of convergent traits

inferred← citeshttps://doi.org/10.1038/s41586-024-07305-3openalex-snapshot

Emx2 underlies the development and evolution of marsupial gliding membranes

inferred← citeshttps://doi.org/10.1038/s41586-025-08777-7openalex-snapshot

Drivers of avian genomic change revealed by evolutionary rate decomposition

inferred← citeshttps://doi.org/10.1038/s41598-021-04077-yopenalex-snapshot

Recurrent erosion of COA1/MITRAC15 exemplifies conditional gene dispensability in oxidative phosphorylation

inferred← citeshttps://doi.org/10.1038/s41598-024-62455-8openalex-snapshot

Convergent accelerated evolution of mammal-specific conserved non-coding elements in hibernators

inferred← citeshttps://doi.org/10.1038/s41598-025-88217-8openalex-snapshot

Palaeognath birds innovate to solve a novel foraging problem

inferred← citeshttps://doi.org/10.1038/s42003-023-05359-zopenalex-snapshot

Genomic signatures of convergent shifts to plunge-diving behavior in birds

inferred← citeshttps://doi.org/10.1073/pnas.1818532116openalex-snapshot

A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales

inferred← citeshttps://doi.org/10.1073/pnas.1819657116openalex-snapshot

Comparative transcriptomics of 3 high-altitude passerine birds and their low-altitude relatives

inferred← citeshttps://doi.org/10.1073/pnas.1922873117openalex-snapshot

Water lily ( Nymphaea thermarum ) genome reveals variable genomic signatures of ancient vascular cambium losses

inferred← citeshttps://doi.org/10.1073/pnas.2014634118openalex-snapshot

The Tiger Rattlesnake genome reveals a complex genotype underlying a simple venom phenotype

inferred← citeshttps://doi.org/10.1073/pnas.2106799118openalex-snapshot

Profile of Scott Edwards

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.2110218118openalex-snapshot

Ancient DNA from the koala lemur puts Madagascar on the paleogenomic map

inferred← citeshttps://doi.org/10.1073/pnas.2313440121openalex-snapshot

The genetic regulatory architecture and epigenomic basis for age-related changes in rattlesnake venom

inferred← citeshttps://doi.org/10.1073/pnas.2418254122openalex-snapshot

Language models reveal a complex sequence basis for adaptive convergent evolution of protein functions

inferred← citeshttps://doi.org/10.1073/pnas.2500165122openalex-snapshot

Convergent expansions of keystone gene families drive metabolic innovation in Saccharomycotina yeasts

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/10.1073/pnas.2616248123openalex-snapshot

Adaptive molecular convergence is pervasive across deep time and largely decoupled from phenotypic convergence

inferred← citeshttps://doi.org/10.1080/03014223.2020.1766520openalex-snapshot

Complete mitochondrial genomes offer insights into the evolutionary relationships and comparative genetic diversity of New Zealand’s iconic kiwi ( Apteryx spp.)

inferred← citeshttps://doi.org/10.1086/732200openalex-snapshot

Effects of Testosterone on Gene Expression Are Concordant between Sexes but Divergent across Species of Sceloporus Lizards

inferred← citeshttps://doi.org/10.1088/1748-3190/ae0aa2openalex-snapshot

Biology for biomimetics: II. A tutorial on how to diversify a list of biological models

inferred← citeshttps://doi.org/10.1093/bib/bbae614openalex-snapshot

A versatile pipeline to identify convergently lost ancestral conserved fragments associated with convergent evolution of vocal learning

inferred← citeshttps://doi.org/10.1093/biolre/ioaa028openalex-snapshot

Sequence comparisons of cytochrome P450 aromatases from Australian animals predict differences in enzymatic activity and/or efficiency†

inferred← citeshttps://doi.org/10.1093/cz/zoab075openalex-snapshot

Inter-glacial isolation caused divergence of cold-adapted species: the case of the snow partridge

inferred← citeshttps://doi.org/10.1093/cz/zoz057openalex-snapshot

Prospects for sociogenomics in avian cooperative breeding and parental care

inferred← citeshttps://doi.org/10.1093/evolut/qpac069openalex-snapshot

Widespread convergent morphological evolution within the largest family of songbirds

inferred← citeshttps://doi.org/10.1093/g3journal/jkab139openalex-snapshot

Population and comparative genetics of thermotolerance divergence between yeast species

inferred← citeshttps://doi.org/10.1093/g3journal/jkac135openalex-snapshot

Genomic signatures of the evolution of a diurnal lifestyle in Strigiformes

inferred← citeshttps://doi.org/10.1093/gbe/evab242openalex-snapshot

Analysis of Sex Chromosome Evolution in the Clade Palaeognathae from Phased Genome Assembly

inferred← citeshttps://doi.org/10.1093/gbe/evac155openalex-snapshot

Shared Patterns of Gene Expression and Protein Evolution Associated with Adaptation to Desert Environments in Rodents

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/evae073openalex-snapshot

Parthenogenetic Stick Insects Exhibit Signatures of Preservation in the Molecular Architecture of Male Reproduction

inferred← citeshttps://doi.org/10.1093/gbe/evae087openalex-snapshot

Evolutionary Rate Shifts in Coding and Regulatory Regions Underpin Repeated Adaptation to Sulfidic Streams in Poeciliid Fishes

inferred← citeshttps://doi.org/10.1093/gbe/evae095openalex-snapshot

Genome-Wide Gene Birth–Death Dynamics Are Associated with Diet Breadth Variation in Lepidoptera

inferred← citeshttps://doi.org/10.1093/gbe/evaf150openalex-snapshot

From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions

inferred← citeshttps://doi.org/10.1093/gbe/evag131openalex-snapshot

Truncated Life History Underlies Rapid Local Adaptation in Island Rattlesnake Venom Expression

inferred← citeshttps://doi.org/10.1093/gbe/evz154openalex-snapshot

Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds

inferred← citeshttps://doi.org/10.1093/genetics/iyab077openalex-snapshot

Parallel and population-specific gene regulatory evolution in cold-adapted fly populations

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/icae056openalex-snapshot

Practical Guidance and Workflows for Identifying Fast Evolving Non-Coding Genomic Elements Using PhyloAcc

inferred← citeshttps://doi.org/10.1093/icb/icaf037openalex-snapshot

Integrating Intermediate Traits in Phylogenetic Genotype-to-Phenotype Studies

inferred← citeshttps://doi.org/10.1093/jeb/voag057openalex-snapshot

Back on the ground: genome analysis of convergent flight loss in rails

inferred← citeshttps://doi.org/10.1093/jhered/esad046openalex-snapshot

Species differences in hormonally mediated gene expression underlie the evolutionary loss of sexually dimorphic coloration inSceloporuslizards

inferred← citeshttps://doi.org/10.1093/jhered/esaf087openalex-snapshot

Genomic resources for comparative analyses of avian obligate brood parasitism

inferred← citeshttps://doi.org/10.1093/jhered/esz076openalex-snapshot

ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets

inferred← citeshttps://doi.org/10.1093/molbev/msaa028openalex-snapshot

Phenotypic Convergence Is Not Mirrored at the Protein Level in a Lizard Adaptive Radiation

inferred← citeshttps://doi.org/10.1093/molbev/msaa068openalex-snapshot

Multiple Genetic Trajectories to Extreme Abiotic Stress Adaptation in Arctic Brassicaceae

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/msaa213openalex-snapshot

Genomic Consequences of Long-Term Population Decline in Brown Eared Pheasant

inferred← citeshttps://doi.org/10.1093/molbev/msaa297openalex-snapshot

Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps

inferred← citeshttps://doi.org/10.1093/molbev/msab057openalex-snapshot

Parallel Genomic Changes Drive Repeated Evolution of Placentas in Live-Bearing Fish

inferred← citeshttps://doi.org/10.1093/molbev/msac082openalex-snapshot

Venom Gene Sequence Diversity and Expression Jointly Shape Diet Adaptation in Pitvipers

inferred← citeshttps://doi.org/10.1093/molbev/msac172openalex-snapshot

Evolutionary Changes in the Chromatin Landscape Contribute to Reorganization of a Developmental Gene Network During Rapid Life History Evolution in Sea Urchins

inferred← citeshttps://doi.org/10.1093/molbev/msad188openalex-snapshot

Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages

inferred← citeshttps://doi.org/10.1093/molbev/msad195openalex-snapshot

PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance

inferred← citeshttps://doi.org/10.1093/molbev/msad208openalex-snapshot

Genomic Signatures Associated with Transitions to Viviparity in Cyprinodontiformes

inferred← citeshttps://doi.org/10.1093/molbev/msae157openalex-snapshot

Parallel Evolution at the Regulatory Base-Pair Level Contributes to Mammalian Interspecific Differences in Polygenic Traits

inferred← citeshttps://doi.org/10.1093/molbev/msae165openalex-snapshot

Distinct Genes with Similar Functions Underlie Convergent Evolution in Myotis Bat Ecomorphs

inferred← citeshttps://doi.org/10.1093/molbev/msaf179openalex-snapshot

Convergent Molecular Evolution Associated With Repeated Transitions to Gregarious Larval Behavior in Heliconiini

inferred← citeshttps://doi.org/10.1093/molbev/msag073openalex-snapshot

WASTER: Practical de novo Phylogenomics from Low-coverage Short Reads

inferred← citeshttps://doi.org/10.1093/molbev/msy217openalex-snapshot

Repeated Evolution of Asexuality Involves Convergent Gene Expression Changes

inferred← citeshttps://doi.org/10.1093/molbev/msz049openalex-snapshot

Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees

inferred← citeshttps://doi.org/10.1093/nsr/nwz138openalex-snapshot

Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows

inferred← citeshttps://doi.org/10.1093/nsr/nwz213openalex-snapshot

Convergent genomic signatures of high-altitude adaptation among domestic mammals

inferred← citeshttps://doi.org/10.1093/sysbio/syab086openalex-snapshot

Theoretical and Practical Considerations when using Retroelement Insertions to Estimate Species Trees in the Anomaly Zone

inferred← citeshttps://doi.org/10.1093/sysbio/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/syag002openalex-snapshot

An Evolving View of Species Tree Inference

inferred← citeshttps://doi.org/10.1093/sysbio/syz019openalex-snapshot

Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone

inferred← citeshttps://doi.org/10.1093/zoolinnean/zlab080openalex-snapshot

The evolution of tinamous (Palaeognathae: Tinamidae) in light of molecular and combined analyses

inferred← citeshttps://doi.org/10.1098/rsbl.2025.0320openalex-snapshot

Quantitative analysis of stem-palaeognath flight capabilities sheds light on ratite dispersal and flight loss

inferred← citeshttps://doi.org/10.1098/rspb.2022.0841openalex-snapshot

What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda

inferred← citeshttps://doi.org/10.1098/rspb.2024.0818openalex-snapshot

Comparative genomics sheds new light on the convergent evolution of infrared vision in snakes

inferred← citeshttps://doi.org/10.1098/rstb.2018.0248openalex-snapshot

Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution

inferred← citeshttps://doi.org/10.1098/rstb.2019.0102openalex-snapshot

Convergent evolution in the genomics era: new insights and directions

inferred← citeshttps://doi.org/10.1098/rstb.2020.0186openalex-snapshot

The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

inferred← citeshttps://doi.org/10.1101/2020.02.03.933069openalex-snapshot

Genomic analyses reveal the origin of domestic ducks and identify different genetic underpinnings of wild ducks

inferred← citeshttps://doi.org/10.1101/2020.03.31.017939openalex-snapshot

Convergence and novelty in adaptation to whole genome duplication in three independent polyploids

inferred← citeshttps://doi.org/10.1101/2020.08.03.232421openalex-snapshot

Genomics of a killifish from the Seychelles islands supports transoceanic island colonization and reveals relaxed selection of developmental genes

inferred← citeshttps://doi.org/10.1101/2021.09.10.459863openalex-snapshot

Convergent patterns of gene expression and protein evolution associated with adaptation to desert environments in rodents

inferred← citeshttps://doi.org/10.1101/2021.12.04.471218openalex-snapshot

What can cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance?

inferred← citeshttps://doi.org/10.1101/2022.05.22.492970openalex-snapshot

Patterns of lineage-specific genome evolution in the brood parasitic black-headed duck ( Heteronetta atricapilla )

inferred← citeshttps://doi.org/10.1101/2022.07.12.499761openalex-snapshot

Microstructural and crystallographic evolution of palaeognath (Aves) eggshells

inferred← citeshttps://doi.org/10.1101/2022.08.12.503723openalex-snapshot

Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies

inferred← citeshttps://doi.org/10.1101/2022.10.12.511720openalex-snapshot

Genetic analysis of a phenotypic loss in the mechanosensory entrainment of a circalunar clock

inferred← citeshttps://doi.org/10.1101/2022.10.20.508685openalex-snapshot

Genomic underpinnings of convergent adaptation to high altitudes for alpine plants

inferred← citeshttps://doi.org/10.1101/2022.11.23.516993openalex-snapshot

Heterotopic reduction of forelimb progenitors underpins development of the vestigial emu wing; implications for vertebrate limb evolution

inferred← citeshttps://doi.org/10.1101/2022.12.23.521765openalex-snapshot

PhyloAcc-GT: A Bayesian method for inferring patterns of substitution rate shifts and associations with binary traits under gene tree discordance

inferred← citeshttps://doi.org/10.1101/2023.10.31.564698openalex-snapshot

The molecular groundplan of male reproduction is partially preserved in parthenogenetic stick insects

inferred← citeshttps://doi.org/10.1101/2024.07.22.604484openalex-snapshot

Convergent expansions of keystone gene families drive metabolic innovation in a major eukaryotic clade

inferred← citeshttps://doi.org/10.1101/2024.09.18.613604openalex-snapshot

Species-specific evolution of conserved noncoding elements associated with distinctive traits of Caenorhabditis inopinata

inferred← citeshttps://doi.org/10.1101/2024.10.02.616319openalex-snapshot

Convergent transcriptomic and genomic adaptation in xeric rodents

inferred← citeshttps://doi.org/10.1101/2024.11.15.623873openalex-snapshot

GWAC: A machine learning method to identify functional variants in data-constrained species

inferred← citeshttps://doi.org/10.1101/2025.02.08.637240openalex-snapshot

Convergent molecular changes are associated with the evolution of low susceptibility to the ash dieback pathogen

inferred← citeshttps://doi.org/10.1101/2025.02.12.637905openalex-snapshot

Decay of the CTCF paralog BORIS in neognathous birds

inferred← citeshttps://doi.org/10.1101/2025.02.19.638997openalex-snapshot

Drivers of avian genomic change revealed by evolutionary rate decomposition

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/10.1101/2025.09.26.678543openalex-snapshot

Convergent molecular evolution of viviparity across squamate reptiles

inferred← citeshttps://doi.org/10.1101/260745openalex-snapshot

Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees

inferred← citeshttps://doi.org/10.1101/262816openalex-snapshot

First nuclear genome assembly of an extinct moa species, the little bush moa ( Anomalopteryx didiformis )

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/10.1101/574756openalex-snapshot

Integrating natural history-derived phenomics with comparative genomics to study the genetic architecture of convergent evolution

inferred← citeshttps://doi.org/10.1101/643296openalex-snapshot

Retroposon Insertions within a Multispecies Coalescent Framework Suggest that Ratite Phylogeny is not in the ‘Anomaly Zone’

inferred← citeshttps://doi.org/10.1101/679456openalex-snapshot

Variation in protein coding genes identifies information flow as a contributor to animal complexity

inferred← citeshttps://doi.org/10.1101/709477openalex-snapshot

An ABBA-BABA Test for Introgression Using Retroposon Insertion Data

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/10.1101/844951openalex-snapshot

Noncoding regions underpin avian bill shape diversification at macroevolutionary scales

inferred← citeshttps://doi.org/10.1101/cshperspect.a041451openalex-snapshot

Avian Island Radiations Shed Light on the Dynamics of Adaptive and Nonadaptive Radiation

inferred← citeshttps://doi.org/10.1101/gr.248641.119openalex-snapshot

Regional epigenetic differentiation of the Z Chromosome between sexes in a female heterogametic system

inferred← citeshttps://doi.org/10.1101/gr.255752.119openalex-snapshot

Noncoding regions underpin avian bill shape diversification at macroevolutionary scales

inferred← citeshttps://doi.org/10.1101/gr.268516.120openalex-snapshot

Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals

inferred← citeshttps://doi.org/10.1101/gr.271569.120openalex-snapshot

A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes

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/10.1101/gr.277784.123openalex-snapshot

GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes

inferred← citeshttps://doi.org/10.1101/gr.280089.124openalex-snapshot

Degrees of convergent evolution in rodent adaptations to arid environments

inferred← citeshttps://doi.org/10.1111/1365-2656.14157openalex-snapshot

Alternative splicing in parallel evolution and the evolutionary potential in sticklebacks

inferred← citeshttps://doi.org/10.1111/1749-4877.12851openalex-snapshot

Genomic signatures associated with recurrent scale loss in cyprinid fish

inferred← citeshttps://doi.org/10.1111/1749-4877.13018openalex-snapshot

Comparative Genomic Screening Identifies Developmental Constraint Loci Underscoring the Phenotypic Evolution of Syngnathids

inferred← citeshttps://doi.org/10.1111/1749-4877.70043openalex-snapshot

The Genetic Basis of Elongated Tails in Birds: Evidence for Sexual Selection as a Driver of Convergent Evolution

inferred← citeshttps://doi.org/10.1111/1755-0998.13457openalex-snapshot

Evaluating the role of reference‐genome phylogenetic distance on evolutionary inference

inferred← citeshttps://doi.org/10.1111/brv.12918openalex-snapshot

Feather function and the evolution of birds

inferred← citeshttps://doi.org/10.1111/evo.13758openalex-snapshot

Gradual evolution towards flightlessness in steamer ducks*

inferred← citeshttps://doi.org/10.1111/evo.13827openalex-snapshot

Digest: A single genetic origin and a role for bone development pathways in repeated losses of flight in steamer ducks*

inferred← citeshttps://doi.org/10.1111/evo.14213openalex-snapshot

How should functional relationships be evaluated using phylogenetic comparative methods? A case study using metabolic rate and body temperature

inferred← citeshttps://doi.org/10.1111/evo.14245openalex-snapshot

Shifts in eggshell thickness are related to changes in locomotor ecology in dinosaurs

inferred← citeshttps://doi.org/10.1111/ibi.12951openalex-snapshot

Gaps in genetic knowledge affect conservation management of kiwi (Apteryx) species

inferred← citeshttps://doi.org/10.1111/jeb.14222openalex-snapshot

Candidate gene polymorphisms are linked to dispersive and migratory behaviour: Searching for a mechanism behind the “paradox of the great speciators”

inferred← citeshttps://doi.org/10.1111/jipb.13485openalex-snapshot

Genomic convergence underlying high‐altitude adaptation in alpine plants

inferred← citeshttps://doi.org/10.1111/joa.13072openalex-snapshot

How to walk carrying a huge egg? Trade‐offs between locomotion and reproduction explain the special pelvis and leg anatomy in kiwi (Aves;Apteryxspp.)

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/joa.13936openalex-snapshot

Description of natal down of the ostrich (Struthio camelus) and comparison with common quail (Coturnix coturnix): Developmental and evolutionary implications

inferred← citeshttps://doi.org/10.1111/joa.13992openalex-snapshot

Ostrich (Struthio camelus) syrinx morphology and vocal repertoire across postnatal ontogeny and sex: Implications for understanding vocal evolution in birds

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