(Q46240577)

20 December 2017

review article

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title

Bayesian molecular dating: opening up the black box. (English)

1 reference

20 December 2017

1

Lindell Bromham

0 references

Sebastian Duchene

2

object named as

Sebastián Duchêne

1 reference

20 December 2017

Simon Y. W. Ho

6

object named as

Simon Y W Ho

1 reference

20 December 2017

author name string

Lindell Bromham

1

1 reference

20 December 2017

Xia Hua

3

1 reference

20 December 2017

Andrew M Ritchie

4

1 reference

20 December 2017

David A Duchêne

5

1 reference

20 December 2017

publication date

15 December 2017

1 reference

20 December 2017

published in

Biological Reviews

1 reference

20 December 2017

Increased transmission of mutations by low-condition females: evidence for condition-dependent DNA repair

cites work

1 reference

Effects of Models of Rate Evolution on Estimation of Divergence Dates with Special Reference to the Metazoan 18S Ribosomal RNA Phylogeny

21 January 2018

1 reference

Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa

21 January 2018

1 reference

Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty

21 January 2018

1 reference

Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty

21 January 2018

1 reference

A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences.

21 January 2018

1 reference

A Protocol for Diagnosing the Effect of Calibration Priors on Posterior Time Estimates: A Case Study for the Cambrian Explosion of Animal Phyla

21 January 2018

1 reference

Heterogeneous Rates of Molecular Evolution and Diversification Could Explain the Triassic Age Estimate for Angiosperms

21 January 2018

1 reference

Exploring new dating approaches for parasites: the worldwide Apodanthaceae (Cucurbitales) as an example

21 January 2018

1 reference

Bayesian tests of topology hypotheses with an example from diving beetles

21 January 2018

1 reference

Did Kauri (Agathis: Araucariaceae) really survive the Oligocene drowning of New Zealand?

21 January 2018

1 reference

On statistical tests of phylogenetic tree imbalance: the Sackin and other indices revisited.

21 January 2018

1 reference

Bayesian model adequacy and choice in phylogenetics.

21 January 2018

1 reference

Inference of epidemiological dynamics based on simulated phylogenies using birth-death and coalescent models

21 January 2018

1 reference

Reconstructing phylogenies and phenotypes: a molecular view of human evolution

21 January 2018

1 reference

Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards

21 January 2018

1 reference

Accommodating heterogenous rates of evolution in molecular divergence dating methods: an example using intercontinental dispersal of Plestiodon (Eumeces) lizards

21 January 2018

1 reference

Molecular clocks and explosive radiations

21 January 2018

1 reference

Why do species vary in their rate of molecular evolution?

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Exploring the Relationships between Mutation Rates, Life History, Genome Size, Environment, and Species Richness in Flowering Plants

21 January 2018

1 reference

Can fast early rates reconcile molecular dates with the Cambrian explosion?

21 January 2018

1 reference

The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates

21 January 2018

1 reference

Bayesian dating of shallow phylogenies with a relaxed clock.

21 January 2018

1 reference

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

21 January 2018

1 reference

Molecular dating, evolutionary rates, and the age of the grasses.

21 January 2018

1 reference

Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating

21 January 2018

1 reference

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

21 January 2018

1 reference

Summarizing a posterior distribution of trees using agreement subtrees.

21 January 2018

1 reference

Clock model makes a large difference to age estimates of long-stemmed clades with no internal calibration: a test using Australian grasstrees

21 January 2018

1 reference

Gene tree discordance, phylogenetic inference and the multispecies coalescent

21 January 2018

1 reference

The structure of cytochromec and the rates of molecular evolution

21 January 2018

1 reference

The evolution of methods for establishing evolutionary timescales

21 January 2018

1 reference

Integrating fossil preservation biases in the selection of calibrations for molecular divergence time estimation

21 January 2018

1 reference

Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea).

21 January 2018

1 reference

Relaxed phylogenetics and dating with confidence

21 January 2018

1 reference

BEAST: Bayesian evolutionary analysis by sampling trees

21 January 2018

1 reference

Bayesian coalescent inference of past population dynamics from molecular sequences

21 January 2018

1 reference

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

21 January 2018

1 reference

Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations

21 January 2018

1 reference

Estimating the number and assignment of clock models in analyses of multigene datasets.

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

The Cambrian conundrum: early divergence and later ecological success in the early history of animals

21 January 2018

1 reference

Prolonging the past counteracts the pull of the present: protracted speciation can explain observed slowdowns in diversification

21 January 2018

1 reference

Choosing among partition models in Bayesian phylogenetics

21 January 2018

1 reference

Evolutionary trees from DNA sequences: A maximum likelihood approach

21 January 2018

1 reference

Taking variation of evolutionary rates between sites into account in inferring phylogenies

21 January 2018

1 reference

The influence of body size and net diversification rate on molecular evolution during the radiation of animal phyla

21 January 2018

1 reference

Strategies for Partitioning Clock Models in Phylogenomic Dating: Application to the Angiosperm Evolutionary Timescale.

21 January 2018

1 reference

Modeling compositional heterogeneity

21 January 2018

1 reference

Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA

21 January 2018

1 reference

Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration

21 January 2018

1 reference

Markov chain Monte Carlo methods in biostatistics.

21 January 2018

1 reference

The conditioned reconstructed process

21 January 2018

1 reference

Statistical tests of models of DNA substitution.

21 January 2018

1 reference

High Prevalence of Hepatitis C Virus Genotype 1b Infection in a Small Town of Argentina. Phylogenetic and Bayesian Coalescent Analysis

21 January 2018

1 reference

Sampling theory for neutral alleles in a varying environment.

21 January 2018

1 reference

Base-compositional heterogeneity in the RAG1 locus among didelphid marsupials: implications for phylogenetic inference and the evolution of GC content

21 January 2018

1 reference

From trajectories to averages: an improved description of the heterogeneity of substitution rates along lineages

21 January 2018

1 reference

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

21 January 2018

1 reference

Monte Carlo sampling methods using Markov chains and their applications

21 January 2018

1 reference

A dirichlet process prior for estimating lineage-specific substitution rates

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Bayesian inference of species trees from multilocus data

21 January 2018

1 reference

Calibrated tree priors for relaxed phylogenetics and divergence time estimation

21 January 2018

1 reference

Calibrated birth-death phylogenetic time-tree priors for bayesian inference

21 January 2018

1 reference

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

21 January 2018

1 reference

An examination of phylogenetic models of substitution rate variation among lineages

21 January 2018

1 reference

The Genome as an Evolutionary Timepiece

21 January 2018

1 reference

Molecular-clock methods for estimating evolutionary rates and timescales

21 January 2018

1 reference

Simulating and detecting autocorrelation of molecular evolutionary rates among lineages

21 January 2018

1 reference

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

21 January 2018

1 reference

Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times

21 January 2018

1 reference

Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation

21 January 2018

1 reference

Inferring speciation and extinction rates under different sampling schemes.

21 January 2018

1 reference

Bayesian analysis of amino acid substitution models

21 January 2018

1 reference

Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo.

21 January 2018

1 reference

Potential applications and pitfalls of Bayesian inference of phylogeny

21 January 2018

1 reference

Bayesian inference of phylogeny and its impact on evolutionary biology

21 January 2018

1 reference

The likelihood node density effect and consequences for evolutionary studies of molecular rates

21 January 2018

1 reference

The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times

21 January 2018

1 reference

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

21 January 2018

1 reference

The impact of modelling rate heterogeneity among sites on phylogenetic estimates of intraspecific evolutionary rates and timescales

21 January 2018

1 reference

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

21 January 2018

1 reference

Performance of a divergence time estimation method under a probabilistic model of rate evolution

21 January 2018

1 reference

Rate of de novo mutations and the importance of father's age to disease risk

21 January 2018

1 reference

Inconsistency of phylogenetic estimates from concatenated data under coalescence

21 January 2018

1 reference

Advances in Time Estimation Methods for Molecular Data

21 January 2018

1 reference

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

21 January 2018

1 reference

Taller plants have lower rates of molecular evolution

21 January 2018

1 reference

Computing Bayes factors using thermodynamic integration.

21 January 2018

1 reference

A mixed relaxed clock model

21 January 2018

1 reference

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

21 January 2018

1 reference

Rates of phenotypic and genomic evolution during the Cambrian explosion

21 January 2018

1 reference

21 January 2018

1 reference

Testing congruence in phylogenomic analysis

21 January 2018

1 reference

Bayesian phylogeography finds its roots

21 January 2018

1 reference

The importance of proper model assumption in bayesian phylogenetics.

21 January 2018

1 reference

A general comparison of relaxed molecular clock models

21 January 2018

1 reference

Continuous and tractable models for the variation of evolutionary rates.

21 January 2018

1 reference

A likelihood approach to estimating phylogeny from discrete morphological character data

21 January 2018

1 reference

Phylogenetic Tree Construction Using Markov Chain Monte Carlo

21 January 2018

1 reference

Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics

21 January 2018

1 reference

Taxon sampling effects in molecular clock dating: an example from the African Restionaceae

21 January 2018

1 reference

Evaluation of Bayesian models of substitution rate evolution--parental guidance versus mutual independence

21 January 2018

1 reference

Multiple sequence alignment: a major challenge to large-scale phylogenetics

21 January 2018

1 reference

Estimating species phylogenies using coalescence times among sequences.

21 January 2018

1 reference

Cetaceans on a molecular fast track to ultrasonic hearing

21 January 2018

1 reference

Uniting Alignments and Trees

21 January 2018

1 reference

Bayesian coestimation of phylogeny and sequence alignment

21 January 2018

1 reference

A detrimental mitochondrial-nuclear interaction causes cytoplasmic male sterility in rice

21 January 2018

1 reference

Inferring phylogeny despite incomplete lineage sorting

21 January 2018

1 reference

Using fossils to break long branches in molecular dating: a comparison of relaxed clocks applied to the origin of angiosperms

21 January 2018

1 reference

PRIMARY STRUCTURE AND EVOLUTION OF CYTOCHROME C

21 January 2018

1 reference

A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points

21 January 2018

1 reference

Inflation of Molecular Clock Rates and Dates: Molecular Phylogenetics, Biogeography, and Diversification of a Global Cicada Radiation from Australasia (Hemiptera: Cicadidae: Cicadettini).

21 January 2018

1 reference

Accurate branch length estimation in partitioned Bayesian analyses requires accommodation of among-partition rate variation and attention to branch length priors.

21 January 2018

1 reference

Diabolical survival in Death Valley: recent pupfish colonization, gene flow and genetic assimilation in the smallest species range on earth

21 January 2018

1 reference

Temperature, stress and spontaneous mutation in Caenorhabditis briggsae and Caenorhabditis elegans

21 January 2018

1 reference

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics

21 January 2018

1 reference

Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

21 January 2018

1 reference

Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA

21 January 2018

1 reference

Emile Zuckerkandl, Linus Pauling, and the molecular evolutionary clock, 1959-1965.

21 January 2018

1 reference

Incomplete lineage sorting: consistent phylogeny estimation from multiple loci.

21 January 2018

1 reference

Phylogenetic MCMC algorithms are misleading on mixtures of trees.

21 January 2018

1 reference

FOSSIL CALIBRATIONS AND MOLECULAR DIVERGENCE TIME ESTIMATES IN CENTRARCHID FISHES (TELEOSTEI: CENTRARCHIDAE)

21 January 2018

1 reference

Oscillating evolution of a mammalian locus with overlapping reading frames: an XLalphas/ALEX relay

21 January 2018

1 reference

Deflating trees: improving Bayesian branch-length estimates using informed priors

21 January 2018

1 reference

AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics

21 January 2018

1 reference

Dating Tips for Divergence-Time Estimation

21 January 2018

1 reference

Estimating divergence dates and substitution rates in the Drosophila phylogeny

21 January 2018

1 reference

Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration

21 January 2018

1 reference

Best practices for justifying fossil calibrations

21 January 2018

1 reference

An alignment confidence score capturing robustness to guide tree uncertainty

21 January 2018

1 reference

The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records

21 January 2018

1 reference

Geomolecular Dating and the Origin of Placental Mammals

21 January 2018

1 reference

The effect of recombination on the accuracy of phylogeny estimation

21 January 2018

1 reference

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

21 January 2018

1 reference

Combining multiple data sets in a likelihood analysis: which models are the best?

21 January 2018

1 reference

Evolutionary analysis of the dynamics of viral infectious disease

21 January 2018

1 reference

Conceptual issues in Bayesian divergence time estimation.

21 January 2018

1 reference

Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference

21 January 2018

1 reference

Inferring speciation times under an episodic molecular clock

21 January 2018

1 reference

Notes on the birth-death prior with fossil calibrations for Bayesian estimation of species divergence times.

21 January 2018

1 reference

Bayesian molecular clock dating of species divergences in the genomics era.

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

The impact of the rate prior on Bayesian estimation of divergence times with multiple Loci

21 January 2018

1 reference

Phylogenetic inference using whole genomes

21 January 2018

1 reference

Inferences from tip-calibrated phylogenies: a review and a practical guide

21 January 2018

1 reference

Weak convergence and optimal scaling of random walk Metropolis algorithms

21 January 2018

1 reference

Closing the gap between rocks and clocks using total-evidence dating

21 January 2018

1 reference

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

21 January 2018

1 reference

Bayesianly Justifiable and Relevant Frequency Calculations for the Applied Statistician

21 January 2018

1 reference

Failure to differentiate between divergence of species and their genes can result in over-estimation of mutation rates in recently diverged species.

21 January 2018

1 reference

Early photosynthetic eukaryotes inhabited low-salinity habitats

21 January 2018

1 reference

Evaluating molecular clock calibrations using Bayesian analyses with soft and hard bounds

21 January 2018

1 reference

Immunological Time Scale for Hominid Evolution

21 January 2018

1 reference

Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales).

21 January 2018

1 reference

Undersampling taxa will underestimate molecular divergence dates: an example from the South american lizard clade liolaemini

21 January 2018

1 reference

A Bayesian phylogenetic method to estimate unknown sequence ages

21 January 2018

1 reference

Evidence for elevated mutation rates in low-quality genotypes

21 January 2018

1 reference

Bayesian hypothesis testing of four-taxon topologies using molecular sequence data

21 January 2018

1 reference

On the number of genomic pacemakers: a geometric approach

21 January 2018

1 reference

The influence of taxon sampling and tree shape on molecular dating: an empirical example from Mammalian mitochondrial genomes

21 January 2018

1 reference

The influence of taxon sampling on Bayesian divergence time inference under scenarios of rate heterogeneity among lineages

21 January 2018

1 reference

The influence of rate heterogeneity among sites on the time dependence of molecular rates

21 January 2018

1 reference

Technical comment on "The placental mammal ancestor and the post-K-Pg radiation of placentals".

21 January 2018

1 reference

Placental mammal diversification and the Cretaceous-Tertiary boundary

21 January 2018

1 reference

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

21 January 2018

1 reference

Dating phylogenies with sequentially sampled tips

21 January 2018

1 reference

Bayesian selection of continuous-time Markov chain evolutionary models

21 January 2018

1 reference

Model Selection in Phylogenetics

21 January 2018

1 reference

The inference of gene trees with species trees

21 January 2018

1 reference

Estimating the rate of evolution of the rate of molecular evolution

21 January 2018

1 reference

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

21 January 2018

1 reference

Inferring Ancestral Recombination Graphs from Bacterial Genomic Data.

21 January 2018

1 reference

Speciation as an active force in promoting genetic evolution

21 January 2018

1 reference

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

21 January 2018

1 reference

Exploring uncertainty in the calibration of the molecular clock

21 January 2018

1 reference

Correlates of substitution rate variation in mammalian protein-coding sequences

21 January 2018

1 reference

Molecular dating when rates vary

21 January 2018

1 reference

Molecular dates for the "cambrian explosion": the influence of prior assumptions.

21 January 2018

1 reference

Small genome of Candidatus Blochmannia, the bacterial endosymbiont of Camponotus, implies irreversible specialization to an intracellular lifestyle.

21 January 2018

1 reference

Relaxed molecular clocks, the bias-variance trade-off, and the quality of phylogenetic inference

21 January 2018

1 reference

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

21 January 2018

1 reference

Dating primate divergences through an integrated analysis of palaeontological and molecular data

21 January 2018

1 reference

A molecular time scale for human evolution

21 January 2018

1 reference

Alignment uncertainty and genomic analysis

21 January 2018

1 reference

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

21 January 2018

1 reference

Bayesian selection of nucleotide substitution models and their site assignments

21 January 2018

1 reference

Accounting for alignment uncertainty in phylogenomics

21 January 2018

1 reference

Improving marginal likelihood estimation for Bayesian phylogenetic model selection

21 January 2018

1 reference

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods

21 January 2018

1 reference

Models of amino acid substitution and applications to mitochondrial protein evolution.

21 January 2018

1 reference

Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method

21 January 2018

1 reference

Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds

21 January 2018

1 reference

Estimation of primate speciation dates using local molecular clocks

21 January 2018

1 reference

Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function

21 January 2018

1 reference

A Mathematical Theory of Evolution, Based on the Conclusions of Dr. J. C. Willis, F.R.S

21 January 2018

1 reference

Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci

21 January 2018

1 reference

Evolutionary Divergence and Convergence in Proteins

21 January 2018

1 reference

Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics.

21 January 2018

1 reference

A divergence dating analysis of turtles using fossil calibrations: an example of best practices

21 January 2018

1 reference

Amino-Acid Sequence Investigations of Fibrinopeptides from Various Mammals: Evolutionary Implications

21 January 2018

1 reference

Biogeochemistry: Food for early animal evolution

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1111/BRV.12390

1 reference

20 December 2017

PubMed ID

29243391

1 reference

20 December 2017