Molecular-clock methods for estimating evolutionary rates and timescales

Tectonic calibrations in molecular dating

(2016) Ullasa Kodandaramaiah   Current Zoology

A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models

(2014) Nahill H Matari et al.   BMC EVOLUTIONARY BIOLOGY

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

(2014) Mathieu Fourment et al.   BMC EVOLUTIONARY BIOLOGY

Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data

(2014) Sebastián Duchêne et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The impact of calibration and clock-model choice on molecular estimates of divergence times

(2014) Sebastián Duchêne et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A synchronized global sweep of the internal genes of modern avian influenza virus

(2014) Michael Worobey 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

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

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

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

ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis

(2013) Sebastián Duchêne et al.   BIOINFORMATICS

Parasitic plants have increased rates of molecular evolution across all three genomes

(2013) Lindell Bromham et al.   BMC EVOLUTIONARY BIOLOGY

A practical guide to molecular dating

(2013) Hervé Sauquet   COMPTES RENDUS PALEVOL

Stability along with Extreme Variability in Core Genome Evolution

(2013) Yuri I. Wolf et al.   Genome Biology 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

A Simple Method for Estimating Informative Node Age Priors for the Fossil Calibration of Molecular Divergence Time Analyses

(2013) Michael D. Nowak et al.   PLoS One

Dating Phylogenies with Sequentially Sampled Tips

(2013) Tanja Stadler et al.   SYSTEMATIC BIOLOGY

treePL: divergence time estimation using penalized likelihood for large phylogenies

(2012) Stephen A. Smith et al.   BIOINFORMATICS

RAxML-Light: a tool for computing terabyte phylogenies

(2012) A. Stamatakis et al.   BIOINFORMATICS

The reconstructed evolutionary process with the fossil record

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

Phylogenetic Estimation of Timescales Using Ancient DNA: The Effects of Temporal Sampling Scheme and Uncertainty in Sample Ages

(2012) M. Molak et al.   MOLECULAR BIOLOGY AND EVOLUTION

Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

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

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 Hierarchical Bayesian Model for Calibrating Estimates of Species Divergence Times

(2012) Tracy A. Heath   SYSTEMATIC BIOLOGY

From Trajectories to Averages: An Improved Description of the Heterogeneity of Substitution Rates Along Lineages

(2012) Stéphane Guindon   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

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

Universal Pacemaker of Genome Evolution

(2012) Sagi Snir et al.   PLoS Computational Biology

The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates

(2011) Brandon Gaut et al.   Annual Review of Ecology Evolution and Systematics

Exploring uncertainty in the calibration of the molecular clock

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

Rate variation and estimation of divergence times using strict and relaxed clocks

(2011) Richard P Brown et al.   BMC EVOLUTIONARY BIOLOGY

A Dirichlet Process Prior for Estimating Lineage-Specific Substitution Rates

(2011) T. A. Heath 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

Expansion Dating: Calibrating Molecular Clocks in Marine Species from Expansions onto the Sunda Shelf Following the Last Glacial Maximum

(2011) E. D. Crandall et al.   MOLECULAR BIOLOGY AND EVOLUTION

Time-dependent rates of molecular evolution

(2011) SIMON Y. W. HO et al.   MOLECULAR ECOLOGY

Skyline-plot methods for estimating demographic history from nucleotide sequences

(2011) SIMON Y. W. HO et al.   Molecular Ecology Resources

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

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

Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae

(2011) Andrew H. Thornhill et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The genome as a life-history character: why rate of molecular evolution varies between mammal species

(2011) L. Bromham   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Integrating Fossil Preservation Biases in the Selection of Calibrations for Molecular Divergence Time Estimation

(2011) Alex Dornburg et al.   SYSTEMATIC BIOLOGY

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

Testing the Impact of Calibration on Molecular Divergence Times Using a Fossil-Rich Group: The Case of Nothofagus (Fagales)

(2011) Hervé Sauquet et al.   SYSTEMATIC BIOLOGY

Best Practices for Justifying Fossil Calibrations

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

Evaluation of Bayesian Models of Substitution Rate Evolution—Parental Guidance versus Mutual Independence

(2011) Martin Linder et al.   SYSTEMATIC BIOLOGY

Evaluating Fossil Calibrations for Dating Phylogenies in Light of Rates of Molecular Evolution: A Comparison of Three Approaches

(2011) Vimoksalehi Lukoschek et al.   SYSTEMATIC BIOLOGY

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

(2010) Alexei J Drummond et al.   BMC BIOLOGY

THE LOCAL-CLOCK PERMUTATION TEST: A SIMPLE TEST TO COMPARE RATES OF MOLECULAR EVOLUTION ON PHYLOGENETIC TREES

(2010) Robert Lanfear   EVOLUTION

Sampling-through-time in birth–death trees

(2010) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks

(2010) Simon Y. W. Ho et al.   Mitochondrial DNA

Performance of Relaxed-Clock Methods in Estimating Evolutionary Divergence Times and Their Credibility Intervals

(2010) Fabia U. Battistuzzi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Estimation of Divergence Times from Large Sequence Alignments

(2010) S. Guindon   MOLECULAR BIOLOGY AND EVOLUTION

A Generation Time Effect on the Rate of Molecular Evolution in Invertebrates

(2010) Jessica A. Thomas et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages

(2010) B. Shapiro et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Universal Molecular Clock of Protein Folds and Its Power in Tracing the Early History of Aerobic Metabolism and Planet Oxygenation

(2010) Minglei Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Old Taxa on Young Islands: A Critique of the Use of Island Age to Date Island-Endemic Clades and Calibrate Phylogenies

(2010) Michael Heads   SYSTEMATIC BIOLOGY

Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection

(2010) Wangang Xie et al.   SYSTEMATIC BIOLOGY

As Time Goes by: A Simple Fool's Guide to Molecular Clock Approaches in Invertebrates*

(2009) Thomas Wilke et al.   AMERICAN MALACOLOGICAL BULLETIN

Calibrating the Tree of Life: fossils, molecules and evolutionary timescales

(2009) Félix Forest   ANNALS OF BOTANY

TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration

(2009) L. Himmelmann et al.   BIOINFORMATICS

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

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

An examination of phylogenetic models of substitution rate variation among lineages

(2009) S. Y.W. Ho   Biology Letters

Timing of morphological and ecological innovations in the cyanobacteria – a key to understanding the rise in atmospheric oxygen

(2009) C. E. BLANK et al.   Geobiology

Microsatellites Are Molecular Clocks That Support Accurate Inferences about History

(2009) J. X. Sun et al.   MOLECULAR BIOLOGY AND EVOLUTION

Accelerated Mutation Accumulation in Asexual Lineages of a Freshwater Snail

(2009) M. Neiman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quantitative Prediction of Molecular Clock and Ka/Ks at Short Timescales

(2009) G. I. Peterson et al.   MOLECULAR BIOLOGY AND EVOLUTION

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 Simple Method for Bracketing Absolute Divergence Times on Molecular Phylogenies Using Multiple Fossil Calibration Points

(2008) Charles R. Marshall   AMERICAN NATURALIST

Selection of Fossils for Calibration of Molecular Dating Models1

(2008) Maria A. Gandolfo et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics

(2008) V. N. Minin et al.   MOLECULAR BIOLOGY AND EVOLUTION