Advances in Time Estimation Methods for Molecular Data (Q31046422)

10 July 2018

title

Advances in Time Estimation Methods for Molecular Data (English)

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10 July 2018

2

S Blair Hedges

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10 July 2018

Sudhir Kumar

series ordinal

1

object named as

Sudhir Kumar

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10 July 2018

publication date

16 February 2016

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10 July 2018

Molecular Biology and Evolution

published in

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10 July 2018

volume

33

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10 July 2018

issue

4

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10 July 2018

page(s)

863-869

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10 July 2018

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

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Dating Tips for Divergence-Time Estimation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Fast Dating Using Least-Squares Criteria and Algorithms

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

INSECT PHYLOGENOMICS. Response to Comment on "Phylogenomics resolves the timing and pattern of insect evolution".

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Measurably evolving pathogens in the genomic era

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Tree of life reveals clock-like speciation and diversification

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Do missing data influence the accuracy of divergence-time estimation with BEAST?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Phylogenomics resolves the timing and pattern of insect evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Molecular-clock methods for estimating evolutionary rates and timescales

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

The changing face of the molecular evolutionary clock

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Prospects for building large timetrees using molecular data with incomplete gene coverage among species

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

MEGA6: Molecular Evolutionary Genetics Analysis version 6.0

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Dating phylogenies with sequentially sampled tips

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

A total-evidence approach to dating with fossils, applied to the early radiation of the hymenoptera

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

An examination of phylogenetic models of substitution rate variation among lineages

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Birth-death prior on phylogeny and speed dating

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

A general comparison of relaxed molecular clock models

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Inferring speciation times under an episodic molecular clock

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Relaxed phylogenetics and dating with confidence

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Molecular clocks: four decades of evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Precision of molecular time estimates

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

PRIMARY STRUCTURE AND EVOLUTION OF CYTOCHROME C

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Comparison of mode estimation methods and application in molecular clock analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach

28 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

28 July 2018

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

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

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Estimation of primate speciation dates using local molecular clocks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

A molecular timescale for vertebrate evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Determining divergence times with a protein clock: update and reevaluation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Continental breakup and the ordinal diversification of birds and mammals

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Determining divergence times of the major kingdoms of living organisms with a protein clock

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Simple methods for testing the molecular evolutionary clock hypothesis.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Phylogenetic test of the molecular clock and linearized trees

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

The molecular clock may be an episodic clock

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Evolutionary Clock: Nonconstancy of Rate in Different Species

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Immunological Time Scale for Hominid Evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

The amino acid sequence of cytochrome c from Helix aspersa Müller (garden snail).

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Generation time and genomic evolution in primates

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Testing for equality of evolutionary rates

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Protein evolution and the molecular clock

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Evolutionary change in 5S RNA secondary structure and a phylogenic tree of 54 5S RNA species

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

The molecular evolution of cytochrome c in eukaryotes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5870647

Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times

28 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

Estimating divergence times in large phylogenetic trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

Phylogenetic dating with confidence intervals using mean path lengths

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

Evolutionary trees from DNA sequences: A maximum likelihood approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

Genomic clocks and evolutionary timescales

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

Converting distance to time: application to human evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

Science in Congress: Deceptive statistics—Response

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

A Bayesian phylogenetic method to estimate unknown sequence ages

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

treePL: divergence time estimation using penalized likelihood for large phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

Estimating divergence times in large molecular phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

Estimating the rate of evolution of the rate of molecular evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

Molecular Evidence for Deep Precambrian Divergences Among Metazoan Phyla

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

Evidence for higher rates of nucleotide substitution in rodents than in man

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSW026

21 January 2018

Identifiers

DOI

10.1093/MOLBEV/MSW026

1 reference

10 July 2018

PMC publication ID

5870647

1 reference

10 July 2018

PubMed publication ID

26882983

1 reference

10 July 2018