Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins

The space of ultrametric phylogenetic trees

(2016) Alex Gavryushkin et al.   JOURNAL OF THEORETICAL BIOLOGY

The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record

(2015) Allison Y Hsiang et al.   BMC EVOLUTIONARY BIOLOGY

An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae)

(2015) Dahiana Arcila et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Bayesian analysis of a morphological supermatrix sheds light on controversial fossil hominin relationships

(2015) Mana Dembo et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Quantifying Age-dependent Extinction from Species Phylogenies

(2015) Helen K. Alexander et al.   SYSTEMATIC BIOLOGY

Total-Evidence Dating under the Fossilized Birth–Death Process

(2015) Chi Zhang et al.   SYSTEMATIC BIOLOGY

Age-Dependent Speciation Can Explain the Shape of Empirical Phylogenies

(2015) Oskar Hagen et al.   SYSTEMATIC BIOLOGY

Climate warming during Antarctic ice sheet expansion at the Middle Miocene transition

(2014) Gregor Knorr et al.   Nature Geoscience

The Evolution of Seabirds in the Humboldt Current: New Clues from the Pliocene of Central Chile

(2014) Martín Chávez Hoffmeister et al.   PLoS One

Bayesian Analysis Using a Simple Likelihood Model Outperforms Parsimony for Estimation of Phylogeny from Discrete Morphological Data

(2014) April M. Wright et al.   PLoS One

The fossilized birth-death process for coherent calibration of divergence-time estimates

(2014) T. A. Heath et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors

(2014) R. C. M. Warnock et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals

(2014) R. M. D. Beck et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds

(2014) M. S. Y. Lee et al.   SCIENCE

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

(2014) E. D. Jarvis et al.   SCIENCE

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

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

Predictive Approaches to Assessing the Fit of Evolutionary Models

(2014) Jeremy M. Brown   SYSTEMATIC BIOLOGY

Calibrated Birth–Death Phylogenetic Time-Tree Priors for Bayesian Inference

(2014) Joseph Heled et al.   SYSTEMATIC BIOLOGY

Methods for the Quantitative Comparison of Molecular Estimates of Clade Age and the Fossil Record

(2014) Julia A. Clarke et al.   SYSTEMATIC BIOLOGY

Characterization of the Uncertainty of Divergence Time Estimation under Relaxed Molecular Clock Models Using Multiple Loci

(2014) Tianqi Zhu et al.   SYSTEMATIC BIOLOGY

Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data

(2014) Daniele Silvestro et al.   SYSTEMATIC BIOLOGY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration

(2014) Alexandra Gavryushkina et al.   PLoS Computational Biology

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

(2014) Cai Li et al.   GigaScience

Recursive algorithms for phylogenetic tree counting

(2013) Alexandra Gavryushkina et al.   Algorithms for Molecular Biology

Evidence for a recent origin of penguins

(2013) S. Subramanian et al.   Biology Letters

Looking for trees in the forest: summary tree from posterior samples

(2013) Joseph Heled et al.   BMC EVOLUTIONARY BIOLOGY

Efficacy or convenience? Model-based approaches to phylogeny estimation using morphological data

(2013) Marc R. Spencer et al.   CLADISTICS

ANCESTRAL CHARACTER ESTIMATION UNDER THE THRESHOLD MODEL FROM QUANTITATIVE GENETICS

(2013) Liam J. Revell   EVOLUTION

Climate sensitivity, sea level and atmospheric carbon dioxide

(2013) J. Hansen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Posterior Predictive Bayesian Phylogenetic Model Selection

(2013) Paul O. Lewis et al.   SYSTEMATIC BIOLOGY

Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Palaeogene boundary

(2013) Graham J. Slater   Methods in Ecology and Evolution

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

(2012) Joseph W Brown et al.   BMC BIOLOGY

Bayesian transmogrification of clade divergence dates: a critique

(2012) Michael Heads   JOURNAL OF BIOGEOGRAPHY

The reconstructed evolutionary process with the fossil record

(2012) Gilles Didier et al.   JOURNAL OF THEORETICAL BIOLOGY

New fossil penguins (Aves, Sphenisciformes) from the Oligocene of New Zealand reveal the skeletal plan of stem penguins

(2012) Daniel T. Ksepka et al.   JOURNAL OF VERTEBRATE PALEONTOLOGY

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele 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

The global diversity of birds in space and time

(2012) W. Jetz et al.   NATURE

Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)

(2012) T. Stadler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Hierarchical Bayesian Model for Calibrating Estimates of Species Divergence Times

(2012) Tracy A. Heath   SYSTEMATIC BIOLOGY

A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Treating Fossils as Terminal Taxa in Divergence Time Estimation Reveals Ancient Vicariance Patterns in the Palpimanoid Spiders

(2012) Hannah Marie Wood 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

The unbearable uncertainty of Bayesian divergence time estimation

(2012) Mario DOS REIS et al.   Journal of Systematics and Evolution

Exploring uncertainty in the calibration of the molecular clock

(2011) R. C. M. Warnock et al.   Biology Letters

A Dirichlet Process Prior for Estimating Lineage-Specific Substitution Rates

(2011) T. A. Heath et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring Speciation and Extinction Rates under Different Sampling Schemes

(2011) S. Hohna et al.   MOLECULAR BIOLOGY AND EVOLUTION

Model Averaging and Bayes Factor Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics

(2011) W. L. S. Li 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

Phylogenetic and Biogeographic Analysis of Sphaerexochine Trilobites

(2011) Curtis R. Congreve et al.   PLoS One

Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation

(2011) Joseph Heled et al.   SYSTEMATIC BIOLOGY

Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of Lissamphibia

(2011) R. Alexander Pyron   SYSTEMATIC BIOLOGY

Best Practices for Justifying Fossil Calibrations

(2011) James F. Parham et al.   SYSTEMATIC BIOLOGY

The contour of splitting trees is a Lévy process

(2010) Amaury Lambert   ANNALS OF PROBABILITY

Bayesian random local clocks, or one rate to rule them all

(2010) Alexei J Drummond et al.   BMC BIOLOGY

The Basal Penguin (Aves: Sphenisciformes) Perudyptes devriesi and a Phylogenetic Evaluation of the Penguin Fossil Record

(2010) Daniel T. Ksepka et al.   BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY

A Fast Algorithm for Computing Geodesic Distances in Tree Space

(2010) Megan Owen et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Sampling-through-time in birth–death trees

(2010) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

On incomplete sampling under birth–death models and connections to the sampling-based coalescent

(2009) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

Computational Methods for Evaluating Phylogenetic Models of Coding Sequence Evolution with Dependence between Codons

(2009) N. Rodrigue et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates

(2009) M. E. Alfaro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times

(2009) Simon Y. W. Ho et al.   SYSTEMATIC BIOLOGY

W(h)ither Fossils? Studying Morphological Character Evolution in the Age of Molecular Sequences1

(2008) Elizabeth J. Hermsen et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

Dinucleotide repeat polymorphism in Fms-like tyrosine kinase-1 (Flt-1) gene is not associated with preeclampsia

(2008) Shin-Young Kim et al.   BMC Medical Genetics

The conditioned reconstructed process

(2008) Tanja Gernhard   JOURNAL OF THEORETICAL BIOLOGY

Phylogenetic uncertainty and molecular clock calibrations: A case study of legless lizards (Pygopodidae, Gekkota)

(2008) M.S.Y. Lee et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION