The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

(2016) James E. Tarver et al.   Genome Biology and Evolution

LS³: A Method for Improving Phylogenomic Inferences When Evolutionary Rates Are Heterogeneous among Taxa

(2016) Carlos J. Rivera-Rivera et al.   MOLECULAR BIOLOGY AND EVOLUTION

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-whiteFicedulaflycatchers

(2016) Krystyna Nadachowska-Brzyska et al.   MOLECULAR ECOLOGY

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

(2016) Charles W. Linkem et al.   SYSTEMATIC BIOLOGY

Gene Tree Discordance Causes Apparent Substitution Rate Variation

(2016) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods

(2016) Kelly A. Meiklejohn et al.   SYSTEMATIC BIOLOGY

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

(2016) James B. Pease et al.   PLOS BIOLOGY

Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data

(2016) Andrej Kuritzin et al.   PLoS Computational Biology

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

(2016) Claudia Solís-Lemus et al.   PLoS Genetics

Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class

(2016) Erich D. Jarvis   Annual Review of Animal Biosciences

The unexpected survival of an ancient lineage of anseriform birds into the Neogene of Australia: the youngest record of Presbyornithidae

(2016) Vanesa L. De Pietri et al.   Royal Society Open Science

New Antarctic findings of Upper Cretaceous and lower Eocene loons (Aves: Gaviiformes)

(2015) Carolina Acosta Hospitaleche et al.   ANNALES DE PALEONTOLOGIE

Avian Diversification Patterns across the K-Pg Boundary: Influence of Calibrations, Datasets, and Model Misspecification1

(2015) Daniel T. Ksepka et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

Estimating phylogenetic trees from genome-scale data

(2015) Liang Liu et al.   Annals of the New York Academy of Sciences

Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences

(2015) Krystyna Nadachowska-Brzyska et al.   CURRENT BIOLOGY

Irrational exuberance for resolved species trees

(2015) Matthew W. Hahn et al.   EVOLUTION

Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach

(2015) K. R. Veeramah et al.   GENETICS

Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis

(2015) Roy N. Platt et al.   Genome Biology and Evolution

A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach

(2015) Britta S. Meyer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

(2015) James B. Pease et al.   SYSTEMATIC BIOLOGY

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

(2015) Alexander Nater et al.   SYSTEMATIC BIOLOGY

The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

(2015) Alexander Suh et al.   PLOS BIOLOGY

Phylogenomic analyses data of the avian phylogenomics project

(2015) Erich D Jarvis et al.   GigaScience

A new time tree reveals Earth historys imprint on the evolution of modern birds

(2015) S. Claramunt et al.   Science Advances

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

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

Hybridization, Introgression, and the Nature of Species Boundaries

(2014) Richard G. Harrison et al.   JOURNAL OF HEREDITY

Bears in a Forest of Gene Trees: Phylogenetic Inference Is Complicated by Incomplete Lineage Sorting and Gene Flow

(2014) Verena E. Kutschera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Maximum likelihood inference of reticulate evolutionary histories

(2014) Yun Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) E. D. Jarvis et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

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

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

Heterogeneous Models Place the Root of the Placental Mammal Phylogeny

(2013) Claire C. Morgan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals

(2013) Jonathan Romiguier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

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

Technical Comment on "The Placental Mammal Ancestor and the Post-K-Pg Radiation of Placentals"

(2013) M. S. Springer et al.   SCIENCE

Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting

(2013) Yun Yu et al.   SYSTEMATIC BIOLOGY

Networks: expanding evolutionary thinking

(2013) Eric Bapteste et al.   TRENDS IN GENETICS

New insights into family relationships within the avian superfamily Sylvioidea (Passeriformes) based on seven molecular markers

(2012) Silke Fregin et al.   BMC EVOLUTIONARY BIOLOGY

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

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

T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks

(2012) A. Boc et al.   NUCLEIC ACIDS RESEARCH

Multilocus Resolution of Phylogeny and Timescale in the Extant Adaptive Radiation of Hawaiian Honeycreepers

(2011) Heather R.L. Lerner et al.   CURRENT BIOLOGY

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

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

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

(2011) Alexander Suh et al.   Nature Communications

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Metaves, Mirandornithes, Strisores and other novelties - a critical review of the higher-level phylogeny of neornithine birds

(2010) Gerald Mayr   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Mammalian Evolution May not Be Strictly Bifurcating

(2010) B. M. Hallstrom et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mosaic retroposon insertion patterns in placental mammals

(2009) G. Churakov et al.   GENOME RESEARCH

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

Explosive Pleistocene diversification and hemispheric expansion of a “great speciator”

(2009) Robert G. Moyle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

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

(2008) Jena L. Chojnowski et al.   GENE

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

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

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

Accounting for Phylogenetic Uncertainty in Biogeography: A Bayesian Approach to Dispersal-Vicariance Analysis of the Thrushes (Aves: Turdus)

(2008) Johan A. A. Nylander et al.   SYSTEMATIC BIOLOGY