Bayesian molecular clock dating of species divergences in the genomics era

Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales

(2015) Mario dos Reis et al.   CURRENT BIOLOGY

The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times

(2015) Konstantinos Angelis et al.   Current Zoology

Comparative and population mitogenomic analyses of Madagascar's extinct, giant ‘subfossil’ lemurs

(2015) Logan Kistler et al.   JOURNAL OF HUMAN EVOLUTION

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

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

Reconstructing ancient genomes and epigenomes

(2015) Ludovic Orlando et al.   NATURE REVIEWS GENETICS

The Fossil Calibration Database—A New Resource for Divergence Dating

(2015) Daniel T. Ksepka et al.   SYSTEMATIC BIOLOGY

Dating Tips for Divergence-Time Estimation

(2015) Joseph E. O’Reilly et al.   TRENDS IN GENETICS

The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times

(2015) Konstantinos Angelis et al.   Current Zoology

Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data

(2014) Mathieu Fourment et al.   BMC EVOLUTIONARY BIOLOGY

Molecular-clock methods for estimating evolutionary rates and timescales

(2014) Simon Y. W. Ho et al.   MOLECULAR ECOLOGY

Gibbon genome and the fast karyotype evolution of small apes

(2014) Lucia Carbone et al.   NATURE

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

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

The early spread and epidemic ignition of HIV-1 in human populations

(2014) N. R. Faria et al.   SCIENCE

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

(2014) S. K. Gire et al.   SCIENCE

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

(2014) E. D. Jarvis et al.   SCIENCE

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

(2014) Tianqi Zhu et al.   SYSTEMATIC BIOLOGY

The Emergence of Lobsters: Phylogenetic Relationships, Morphological Evolution and Divergence Time Comparisons of an Ancient Group (Decapoda: Achelata, Astacidea, Glypheidea, Polychelida)

(2014) Heather D. Bracken-Grissom et al.   SYSTEMATIC BIOLOGY

The Impact of the Rate Prior on Bayesian Estimation of Divergence Times with Multiple Loci

(2014) Mario Dos Reis et al.   SYSTEMATIC BIOLOGY

The changing face of the molecular evolutionary clock

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

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology

(2014) Christy A. Hipsley et al.   Frontiers in Genetics

Combining fossil and molecular data to date the diversification of New World Primates

(2013) C. G. Schrago et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae

(2013) Markos A. Alexandrou et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Molecular dating of phylogenies by likelihood methods: A comparison of models and a new information criterion

(2013) Emmanuel Paradis   MOLECULAR PHYLOGENETICS AND EVOLUTION

Three keys to the radiation of angiosperms into freezing environments

(2013) Amy E. Zanne et al.   NATURE

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

(2013) Ludovic Orlando et al.   NATURE

Himalayan fossils of the oldest known pantherine establish ancient origin of big cats

(2013) Z. J. Tseng et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Dating Phylogenies with Sequentially Sampled Tips

(2013) Tanja Stadler et al.   SYSTEMATIC BIOLOGY

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Mid-Pliocene warm-period deposits in the High Arctic yield insight into camel evolution

(2013) Natalia Rybczynski et al.   Nature Communications

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

Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees

(2013) Robert S. Sansom et al.   Scientific Reports

treePL: divergence time estimation using penalized likelihood for large phylogenies

(2012) Stephen A. Smith et al.   BIOINFORMATICS

Revising the human mutation rate: implications for understanding human evolution

(2012) Aylwyn Scally et al.   NATURE REVIEWS GENETICS

Estimating divergence times in large molecular phylogenies

(2012) K. Tamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

(2012) M. dos Reis et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

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

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

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

A distance-based least-square method for dating speciation events

(2011) Xuhua Xia et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

How Many Species Are There on Earth and in the Ocean?

(2011) Camilo Mora et al.   PLOS BIOLOGY

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

(2010) Alexei J Drummond et al.   BMC BIOLOGY

Bayesian Estimation of Divergence Times from Large Sequence Alignments

(2010) S. Guindon   MOLECULAR BIOLOGY AND EVOLUTION

Charting the Host Adaptation of Influenza Viruses

(2010) M. dos Reis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient human genome sequence of an extinct Palaeo-Eskimo

(2010) Morten Rasmussen et al.   NATURE

Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity

(2010) C. Hoorn et al.   SCIENCE

Dating Primate Divergences through an Integrated Analysis of Palaeontological and Molecular Data

(2010) Richard D. Wilkinson et al.   SYSTEMATIC BIOLOGY

The dating game: a reply to Heads (2010)

(2010) Anjali Goswami et al.   ZOOLOGICA SCRIPTA

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

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Using Non-Homogeneous Models of Nucleotide Substitution to Identify Host Shift Events: Application to the Origin of the 1918 ‘Spanish’ Influenza Pandemic Virus

(2009) Mario dos Reis et al.   JOURNAL OF MOLECULAR EVOLUTION

10,000 genomes to come

(2009) Erika Check Hayden   NATURE

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Dating the emergence of pandemic influenza viruses

(2009) Gavin J. D. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. canadensis

(2009) M. H. Schweitzer et al.   SCIENCE

Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times

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

The Impact of the Representation of Fossil Calibrations on Bayesian Estimation of Species Divergence Times

(2009) Jun Inoue et al.   SYSTEMATIC BIOLOGY

A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

(2008) Richard E. Green et al.   CELL

Cladistic analysis of continuous modularized traits provides phylogenetic signals in Homo evolution

(2008) Rolando González-José et al.   NATURE

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960

(2008) Michael Worobey et al.   NATURE