Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating

Graphical abstract

• Publication year

  2017

• Venue

  Molecular Phylogenetics and Evolution

• Publication date

  2017-09-01

• Fields of study

  Biology, Medicine, Geology

• Identifiers
  DOI 10.1016/j.ympev.2017.07.005PMID 28709986PMCID 5546266
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth–Death Process

  2019cited by this paper
• Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution

  2018cited by this paper
• Bayesian phylogenetic estimation of fossil ages

  2016cited by this paper
• Closing the gap between rocks and clocks using total-evidence dating

  2016cited by this paper
• Dating Tips for Divergence-Time Estimation.

  2015cited by this paper
• Bayesian molecular clock dating of species divergences in the genomics era

  2015cited by this paper
• Total-Evidence Dating under the Fossilized Birth–Death Process

  2015cited by this paper
• Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors

  2015cited by this paper
• The emergence of lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (decapoda: achelata, astacidea, glypheidea, polychelida).

  2014cited by this paper
• BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

  2014cited by this paper
• Characterization of the Uncertainty of Divergence Time Estimation under Relaxed Molecular Clock Models Using Multiple Loci

  2014cited by this paper
• The fossilized birth–death process for coherent calibration of divergence-time estimates

  2013cited by this paper
• Calibrated Birth–Death Phylogenetic Time-Tree Priors for Bayesian Inference

  2013influential reference
• The unbearable uncertainty of Bayesian divergence time estimation

  2012cited by this paper
• Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

  2012cited by this paper
• A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

  2012cited by this paper
• MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

  2012cited by this paper
• Establishing a time-scale for plant evolution.

  2011cited by this paper
• Inferring speciation and extinction rates under different sampling schemes.

  2011cited by this paper
• Dating primate divergences through an integrated analysis of palaeontological and molecular data.

  2011cited by this paper
• Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation

  2011influential reference
• Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times.

  2011cited by this paper
• The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times.

  2010cited by this paper
• Sampling-through-time in birth-death trees.

  2010influential reference
• Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times.

  2009cited by this paper
• Calibrating and constraining molecular clocks

  2009cited by this paper
• A Simple Method for Bracketing Absolute Divergence Times on Molecular Phylogenies Using Multiple Fossil Calibration Points

  2008cited by this paper
• Inferring speciation times under an episodic molecular clock.

  2007influential reference
• PAML 4: phylogenetic analysis by maximum likelihood.

  2007influential reference
• A general comparison of relaxed molecular clock models.

  2007cited by this paper
• Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds.

  2006influential reference
• Relaxed Phylogenetics and Dating with Confidence

  2006cited by this paper
• Molecular clocks: Closing the gap between rocks and clocks

  2005cited by this paper
• FOSSIL CALIBRATIONS AND MOLECULAR DIVERGENCE TIME ESTIMATES IN CENTRARCHID FISHES (TELEOSTEI: CENTRARCHIDAE)

  2005cited by this paper
• Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

  2005cited by this paper
• Using the fossil record to estimate the age of the last common ancestor of extant primates

  2002cited by this paper
• Performance of a divergence time estimation method under a probabilistic model of rate evolution.

  2001cited by this paper
• A likelihood approach to estimating phylogeny from discrete morphological character data.

  2001cited by this paper
• Estimating the rate of evolution of the rate of molecular evolution.

  1998cited by this paper
• Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method.

  1997influential reference
• Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods

  1994cited by this paper
• The neutral theory of molecular evolution.

  1983cited by this paper
• Ecology, Evolution and Organismal Biology Publications Ecology, Evolution and Organismal Biology Total-evidence Dating under the Fossilized Birth–death Process

  year unknowncited by this paper

• Evaluating Bayesian Morphological Clocks for Estimating a Dated Phylogeny in a Relict and Fossil‐Rich Family of Wasps (Hymenoptera, Chrysidoidea)

  2025cites this paper
• New insights on angiosperm crown age based on Bayesian node dating and skyline fossilized birth-death approaches

  2025cites this paper
• African Cichlid Lake Radiations Recapitulate Riverine Axial Morphologies Through Repeated Exploration of Morphospace

  2025cites this paper
• New fossils imply a deeper origin of modern birds in the Mesozoic

  2025cites this paper
• Systematic and taxonomic revision of emerald and tigertail dragonflies (Anisoptera: Synthemistidae and Corduliidae)

  2025cites this paper
• Fast and Accurate Node-Age Estimation Under Fossil Calibration Uncertainty Using the Adjusted Pairwise Likelihood

  2025cites this paper
• Comparative genomics provides insights into the evolutionary history of the phylum Ciliophora (Eukaryota, Alveolata) and uncovers the adaptive evolution of anaerobic ciliate classes

  2024cites this paper
• Reticulate evolution: Detection and utility in the phylogenomics era.

  2024cites this paper
• Integrating Phylogenies with Chronology to Assemble the Tree of Life

  2024cites this paper
• Comparative Analysis and Phylogeny of the Complete Chloroplast Genomes of Nine Cynanchum (Apocynaceae) Species

  2024cites this paper
• A time-calibrated ‘Tree of Life’ of aquatic insects for knitting historical patterns of evolution and measuring extant phylogenetic biodiversity across the world

  2024cites this paper
• Ediacaran origin and Ediacaran-Cambrian diversification of Metazoa

  2024cites this paper
• Major revisions in pancrustacean phylogeny and evidence of sensitivity to taxon sampling.

  2023cites this paper
• Phylogenomics reconciles molecular data with the rich fossil record on the origin of living turtles.

  2023cites this paper
• Two Notorious Nodes: A Critical Examination of Relaxed Molecular Clock Age Estimates of the Bilaterian Animals and Placental Mammals

  2023cites this paper
• Unraveling phylogenetic relationships and species boundaries in the arid adapted Gerbillus rodents (Muridae: Gerbillinae) by RAD-seq data.

  2023cites this paper
• Combining palaeontological and neontological data shows a delayed diversification burst of carcharhiniform sharks likely mediated by environmental change

  2022cites this paper
• Estimating the Divergence Times of Alphaproteobacteria Based on Mitochondrial Endosymbiosis and Eukaryotic Fossils.

  2022cites this paper
• CladeDate: Calibration information generator for divergence time estimation

  2022cites this paper
• Major revisions in pancrustacean phylogeny with recommendations for resolving challenging nodes

  2022cites this paper
• Genome survey sequence of black carp provides insights into development‐related gene duplications

  2022cites this paper
• A Multigene Phylogeny of Native American Hawkweeds (Hieracium Subgen. Chionoracium, Cichorieae, Asteraceae): Origin, Speciation Patterns, and Migration Routes

  2022cites this paper
• Genomic diversity and Demographic History of the Dromiciops genus (Marsupialia: Microbiotheriidae).

  2022cites this paper
• Two notorious nodes: a critical examination of MCMCTree relaxed molecular clock estimates of the bilaterian animals and placental mammals

  2022cites this paper
• Phylogenetics and an updated taxonomic status of the Tamarins (Callitrichinae, Cebidae).

  2022cites this paper
• Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis

  2022influential citation
• Craniodental Morphology and Phylogeny of Marsupials

  2021cites this paper
• Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies

  2021cites this paper
• Fossil-calibrated time tree of Podarcis wall lizards provides limited support for biogeographic calibration models.

  2021cites this paper
• Large-Scale Phylogenomic Analyses Reveal the Monophyly of Bryophytes and Neoproterozoic Origin of Land Plants

  2021cites this paper
• Unsupervised learning of satellite images enhances discovery of late Miocene fossil sites in the Urema Rift, Gorongosa, Mozambique

  2021cites this paper
• Principles, error sources and application suggestions of prevailing molecular dating methods

  2021cites this paper
• Checklist of fossil liverworts suitable for calibrating phylogenetic reconstructions

  2021cites this paper
• Molecular phylogenies map to biogeography better than morphological ones

  2021cites this paper
• Introduction

  2021cites this paper
• Efficient Methods for Dating Evolutionary Divergences

  2020cites this paper
• Deep mitochondrial DNA phylogeographic divergence in the threatened aoudad Ammotragus lervia (Bovidae, Caprini).

  2020cites this paper
• Insights from empirical analyses and simulations on using multiple fossil calibrations with relaxed clocks to estimate divergence times.

  2020cites this paper
• Molecular and morphological clocks for estimating evolutionary divergence times

  2020cites this paper
• Uncertainty in divergence time estimation.

  2020cites this paper
• Integrated phylogenomic and fossil evidence of stick and leaf insects (Phasmatodea) reveal a Permian–Triassic co-origination with insectivores

  2020cites this paper
• Calibrations from the Fossil Record

  2020cites this paper
• Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times

  2019cites this paper
• Survival and selection biases in early animal evolution and a source of systematic overestimation in molecular clocks

  2019cites this paper
• Best practices in justifying calibrations for dating language families

  2019cites this paper
• The impact of fossil stratigraphic ranges on tip‐calibration, and the accuracy and precision of divergence time estimates

  2019cites this paper
• A Nearly Complete Juvenile Skull of the Marsupial Sparassocynus derivatus from the Pliocene of Argentina, the Affinities of “Sparassocynids”, and the Diversification of Opossums (Marsupialia; Didelphimorphia; Didelphidae)

  2019cites this paper
• Accounting for uncertainty in the evolutionary timescale of green plants through clock-partitioning and fossil calibration strategies.

  2019cites this paper
• A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation: First evidence for extensive population admixture across South America.

  2018cites this paper
• Molecular phylogeny and diversification timing of the Nemouridae family (Insecta, Plecoptera) in the Japanese Archipelago

  2018cites this paper
• Convergent evolution of complex structures for ant–bacterial defensive symbiosis in fungus-farming ants

  2018cites this paper
• Evolutionary Associations of Endosymbiotic Ciliates Shed Light on the Timing of the Marsupial–Placental Split

  2018cites this paper
• The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates

  2017cites this paper
• RelTime Relaxes the Strict Molecular Clock throughout the Phylogeny

  2017cites this paper