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

Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals

(2014) M. dos Reis et al.   Biology Letters

Phylogenetic Position of Avian Nocturnal and Diurnal Raptors

(2014) M. T. Mahmood et al.   Genome Biology and Evolution

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY AND EVOLUTION

Statistical binning enables an accurate coalescent-based estimation of the avian tree

(2014) S. Mirarab et al.   SCIENCE

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

(2014) R. E. Green et al.   SCIENCE

Complex evolutionary trajectories of sex chromosomes across bird taxa

(2014) Q. Zhou et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

Morphological Clocks in Paleontology, and a Mid-Cretaceous Origin of Crown Aves

(2014) M. S. Y. Lee et al.   SYSTEMATIC BIOLOGY

The changing face of the molecular evolutionary clock

(2014) Simon Y.W. Ho   TRENDS IN ECOLOGY & EVOLUTION

Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment

(2014) Cai Li et al.   GigaScience

High-coverage sequencing and annotated assemblies of the budgerigar genome

(2014) Ganeshkumar Ganapathy et al.   GigaScience

Comparative genomic data of the Avian Phylogenomics Project

(2014) Guojie Zhang et al.   GigaScience

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

Naive binning improves phylogenomic analyses

(2013) Md Shamsuzzoha Bayzid et al.   BIOINFORMATICS

Comparative genomics as a tool to understand evolution and disease

(2013) J. Alfoldi et al.   GENOME RESEARCH

Discordance of Species Trees with Their Most Likely Gene Trees: A Unifying Principle

(2013) N. A. Rosenberg   MOLECULAR BIOLOGY AND EVOLUTION

Twisted Signatures of GC-Biased Gene Conversion Embedded in an Evolutionary Stable Karyotype

(2013) Carina F. Mugal et al.   MOLECULAR BIOLOGY AND EVOLUTION

CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models

(2013) Manuel Gil et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identifying localized biases in large datasets: A case study using the avian tree of life

(2013) Rebecca T. Kimball et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome-wide signatures of convergent evolution in echolocating mammals

(2013) Joe Parker et al.   NATURE

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

(2013) Zhuo Wang et al.   NATURE GENETICS

Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle

(2013) Xiangjiang Zhan et al.   NATURE GENETICS

The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

(2013) Yinhua Huang et al.   NATURE GENETICS

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

(2013) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing

(2013) John E. McCormack et al.   PLoS One

The Placental Mammal Ancestor and the Post-K-Pg Radiation of Placentals

(2013) M. A. O'Leary et al.   SCIENCE

Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon

(2013) M. D. Shapiro et al.   SCIENCE

The age of the crown group of passerine birds and its evolutionary significance – molecular calibrations versus the fossil record

(2013) Gerald Mayr   SYSTEMATICS AND BIODIVERSITY

Behavioral Evidence for Song Learning in the Suboscine Bellbirds (Procniasspp.; Cotingidae)

(2013) Donald Kroodsma et al.   Wilson Journal of Ornithology

RAxML-Light: a tool for computing terabyte phylogenies

(2012) A. Stamatakis et al.   BIOINFORMATICS

Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages

(2012) Joseph W Brown et al.   BMC BIOLOGY

A Universal Method for the Study of CR1 Retroposons in Nonmodel Bird Genomes

(2012) A. Suh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Retroposon Insertion Patterns of Neoavian Birds: Strong Evidence for an Extensive Incomplete Lineage Sorting Era

(2012) A. Matzke et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

The global diversity of birds in space and time

(2012) W. Jetz et al.   NATURE

UCNEbase—a database of ultraconserved non-coding elements and genomic regulatory blocks

(2012) Slavica Dimitrieva et al.   NUCLEIC ACIDS RESEARCH

Australia's oldest Anseriform fossil: a quadrate from the Early Eocene Tingamarra Fauna

(2012) ANDRZEJ ELZANOWSKI et al.   PALAEONTOLOGY

Quantifying historical trends in the completeness of the fossil record and the contributing factors: an example using Aves

(2012) Daniel T. Ksepka et al.   PALEOBIOLOGY

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

(2012) S. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds

(2012) O. Haddrath et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Going to Extremes: Contrasting Rates of Diversification in a Recent Radiation of New World Passerine Birds

(2012) F. Keith Barker et al.   SYSTEMATIC BIOLOGY

Ratite Nonmonophyly: Independent Evidence from 40 Novel Loci

(2012) Jordan V. Smith et al.   SYSTEMATIC BIOLOGY

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

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

(2011) J. E. McCormack et al.   GENOME RESEARCH

Next-generation hybridization and introgression

(2011) A D Twyford et al.   HEREDITY

Evolution of terrestrial birds in three continents: biogeography and parallel radiations

(2011) Per G. P. Ericson   JOURNAL OF BIOGEOGRAPHY

Dynamic Evolution of Base Composition: Causes and Consequences in Avian Phylogenomics

(2011) B. Nabholz et al.   MOLECULAR BIOLOGY AND EVOLUTION

Retroposon Insertions and the Chronology of Avian Sex Chromosome Evolution

(2011) Alexander Suh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times

(2011) M. d. Reis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Testing Hypotheses about the Sister Group of the Passeriformes Using an Independent 30-Locus Data Set

(2011) N. Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of Modern Birds Revealed by Mitogenomics: Timing the Radiation and Origin of Major Orders

(2011) M. A. Pacheco et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome of the green anole lizard and a comparative analysis with birds and mammals

(2011) Jessica Alföldi et al.   NATURE

Out of Africa: Fossils shed light on the origin of the hoatzin, an iconic Neotropic bird

(2011) Gerald Mayr et al.   NATURWISSENSCHAFTEN

TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees

(2011) Marina Marcet-Houben et al.   NUCLEIC ACIDS RESEARCH

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Mass extinction of birds at the Cretaceous-Paleogene (K-Pg) boundary

(2011) N. R. Longrich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

Are Transposable Element Insertions Homoplasy Free?: An Examination Using the Avian Tree of Life

(2011) Kin-Lan Han et al.   SYSTEMATIC BIOLOGY

SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees

(2011) Kevin Liu et al.   SYSTEMATIC BIOLOGY

Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds

(2011) Alexander Suh et al.   Nature Communications

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes

(2010) J. Romiguier et al.   GENOME RESEARCH

How Many Bootstrap Replicates Are Necessary?

(2010) Nicholas D. Pattengale et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Ecological opportunity and the origin of adaptive radiations

(2010) J. B. YODER et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Biogeographical and phylogenetic implications of an early Miocene wren (Aves: Passeriformes: Acanthisittidae) from New Zealand

(2010) Trevor H. Worthy et al.   JOURNAL OF VERTEBRATE PALEONTOLOGY

Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species

(2010) AXEL KÜNSTNER et al.   MOLECULAR ECOLOGY

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score

(2010) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

(2010) J. Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

The origins of modern biodiversity on land

(2010) M. J. Benton   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Chicxulub Asteroid Impact and Mass Extinction at the Cretaceous-Paleogene Boundary

(2010) P. Schulte et al.   SCIENCE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

(2010) Rami A. Dalloul et al.   PLOS BIOLOGY

Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions

(2010) Maria A. Nilsson et al.   PLOS BIOLOGY

Reappraisal of Eocypselus—a stem group apodiform from the early Eocene of Northern Europe

(2010) Gerald Mayr   Palaeobiodiversity and Palaeoenvironments

The Madagascan “Cuckoo-Roller” (Aves: Leptosomidae) is Not a Roller — Notes on the Phylogenetic Affinities and Evolutionary History of a “Living Fossil”

(2009) Gerald Mayr   ACTA ORNITHOLOGICA

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

(2009) Laurent Duret et al.   Annual Review of Genomics and Human Genetics

A Large Fruit Pigeon (Columbidae) from the Early Miocene of New Zealand

(2009) Trevor H. Worthy et al.   AUK

Affinities ofPalaeospiza bellaand the Phylogeny and Biogeography of Mousebirds (Coliiformes)

(2009) Daniel T. Ksepka et al.   AUK

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

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Integrating Genomes, Brain and Behavior in the Study of Songbirds

(2009) David F. Clayton et al.   CURRENT BIOLOGY

Statistical Methods for Evolutionary Trees

(2009) A. W. F. Edwards   GENETICS

Mosaic retroposon insertion patterns in placental mammals

(2009) G. Churakov et al.   GENOME RESEARCH

Phylogenies reveal new interpretation of speciation and the Red Queen

(2009) Chris Venditti et al.   NATURE

Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals

(2009) H. Nishihara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

(2009) K. Liu et al.   SCIENCE

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

(2008) Julien Dutheil et al.   BMC EVOLUTIONARY BIOLOGY

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS

Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes

(2008) Jena L. Chojnowski et al.   GENE

New specimens ofLithoptila abdounensis(Aves, Prophaethontidae) from the lower Paleogene of Morocco

(2008) Estelle Bourdon et al.   JOURNAL OF VERTEBRATE PALEONTOLOGY

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

(2008) T.-K. Seo   MOLECULAR BIOLOGY AND EVOLUTION

Toward Resolving Deep Neoaves Phylogeny: Data, Signal Enhancement, and Priors

(2008) R. C. Pratt et al.   MOLECULAR BIOLOGY AND EVOLUTION

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

(2008) Timo Lassmann et al.   NUCLEIC ACIDS RESEARCH

A Phylogenomic Study of Birds Reveals Their Evolutionary History

(2008) S. J. Hackett et al.   SCIENCE

Hemiplasy: A New Term in the Lexicon of Phylogenetics

(2008) John C. Avise et al.   SYSTEMATIC BIOLOGY

Large-Scale Appearance of Ultraconserved Elements in Tetrapod Genomes and Slowdown of the Molecular Clock

(2007) S. Stephen et al.   MOLECULAR BIOLOGY AND EVOLUTION