Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling

Phylogenetics: Tertiary protein structures needed

(2017) David Penny   Nature Ecology & Evolution

Ancestral range reconstruction of Galliformes: the effects of topology and taxon sampling

(2016) Ning Wang et al.   JOURNAL OF BIOGEOGRAPHY

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

(2016) Scott V. Edwards et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The gene tree delusion

(2016) Mark S. Springer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Causes of evolutionary rate variation among protein sites

(2016) Julian Echave et al.   NATURE REVIEWS GENETICS

Selection on protein structure, interaction, and sequence

(2016) Peter B. Chi et al.   PROTEIN SCIENCE

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

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

(2016) Alexander Suh   ZOOLOGICA SCRIPTA

Irrational exuberance for resolved species trees

(2015) Matthew W. Hahn et al.   EVOLUTION

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)

(2015) Peter A. Hosner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Building the avian tree of life using a large-scale, sparse supermatrix

(2015) J. Gordon Burleigh et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2015) Richard O. Prum et al.   NATURE

Error, signal, and the placement of Ctenophora sister to all other animals

(2015) Nathan V. Whelan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny

(2015) Meng-Yun Chen et al.   SYSTEMATIC BIOLOGY

Can We Identify Genes with Increased Phylogenetic Reliability?

(2015) Vinson P. Doyle 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

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

(2014) Andre J. Aberer et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Incongruence among different mitochondrial regions: A case study using complete mitogenomes

(2014) Kelly A. Meiklejohn et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

(2014) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Two Low Coverage Bird Genomes and a Comparison of Reference-Guided versus De Novo Genome Assemblies

(2014) Daren C. Card et al.   PLoS One

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

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

The Phylogenetic Likelihood Library

(2014) T. Flouri et al.   SYSTEMATIC BIOLOGY

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

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

(2013) N. A. Rosenberg   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

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh 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

Deep metazoan phylogeny: When different genes tell different stories

(2013) Tetyana Nosenko et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

Assessing Parameter Identifiability in Phylogenetic Models Using Data Cloning

(2012) José Miguel Ponciano et al.   SYSTEMATIC BIOLOGY

Ratite Nonmonophyly: Independent Evidence from 40 Novel Loci

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

Low-Parameter Phylogenetic Inference Under the General Markov Model

(2012) Barbara R. Holland et al.   SYSTEMATIC BIOLOGY

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Phylogeny and Biogeography of the Core Babblers (Aves: Timaliidae)

(2012) Robert G. Moyle et al.   SYSTEMATIC BIOLOGY

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Homoplastic microinversions and the avian tree of life

(2011) Edward L Braun et al.   BMC EVOLUTIONARY 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

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

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

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

(2011) Daniel L. Ayres 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

From Reptilian Phylogenomics to Reptilian Genomes: Analyses of c-Jun and DJ-1 Proto-Oncogenes

(2010) Y. Katsu et al.   CYTOGENETIC AND GENOME RESEARCH

Comparative molecular evolution and phylogenetic utility of 3′-UTRs and introns in Galliformes

(2010) Amber J. Bonilla et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

DIVERGENCE ACROSS AUSTRALIA'S CARPENTARIAN BARRIER: STATISTICAL PHYLOGEOGRAPHY OF THE RED-BACKED FAIRY WREN (MALURUS MELANOCEPHALUS)

(2008) June Y. Lee et al.   EVOLUTION

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

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

(2008) Jena L. Chojnowski et al.   GENE

A well-tested set of primers to amplify regions spread across the avian genome

(2008) Rebecca T. Kimball et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The genetic code can cause systematic bias in simple phylogenetic models

(2008) S. Whelan   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenomic evidence for multiple losses of flight in ratite birds

(2008) J. Harshman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Phylogenomic Study of Birds Reveals Their Evolutionary History

(2008) S. J. Hackett et al.   SCIENCE

On the Distributions of Bootstrap Support and Posterior Distributions for a Star Tree

(2008) Edward Susko   SYSTEMATIC BIOLOGY

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY