(Q54998842)

15 June 2018

title

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era. (English)

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15 June 2018

author

Stephen A. Smith

series ordinal

1

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15 June 2018

Joseph W Brown

object named as

Joseph W Brown

series ordinal

2

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author name string

Joseph F Walker

series ordinal

3

1 reference

15 June 2018

language of work or name

English

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publication date

17 May 2018

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15 June 2018

published in

PLOS One

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15 June 2018

volume

13

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15 June 2018

issue

5

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15 June 2018

page(s)

e0197433

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15 June 2018

Creative Commons Attribution 4.0 International

copyright license

start time

17 May 2018

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Phyx: phylogenetic tools for unix

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

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

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Conceptual issues in Bayesian divergence time estimation.

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

A mixed relaxed clock model

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Advances in Time Estimation Methods for Molecular Data

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

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

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Fast Dating Using Least-Squares Criteria and Algorithms

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants.

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Can We Identify Genes with Increased Phylogenetic Reliability?

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

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

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

The Fossil Calibration Database-A New Resource for Divergence Dating

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Phylogenomic analyses data of the avian phylogenomics project

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Statistical binning enables an accurate coalescent-based estimation of the avian tree

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

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

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

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

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

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

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

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

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

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

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Phylogenomics resolves evolutionary relationships among ants, bees, and wasps

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Transcriptome sequences resolve deep relationships of the grape family

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Estimating divergence times in large molecular phylogenies

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

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

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Best practices for justifying fossil calibrations

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

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

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

INDELible: a flexible simulator of biological sequence evolution

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

BEAST: Bayesian evolutionary analysis by sampling trees

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

A general comparison of relaxed molecular clock models

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Inferring speciation times under an episodic molecular clock

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

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16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

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16 June 2018

1 reference

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

16 June 2018

1 reference

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Divergence time and evolutionary rate estimation with multilocus data

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

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16 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

16 June 2018

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13 August 2018

1 reference

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16 June 2018

1 reference

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16 June 2018

1 reference

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Testing for equality of evolutionary rates

16 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

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

16 June 2018

1 reference

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13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5957400

On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods

13 August 2018

1 reference

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13 August 2018

1 reference

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13 August 2018

1 reference

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Novel information theory-based measures for quantifying incongruence among phylogenetic trees

13 August 2018

1 reference

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

13 August 2018

1 reference

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treePL: divergence time estimation using penalized likelihood for large phylogenies

13 August 2018

1 reference

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

13 August 2018

1 reference

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13 August 2018

1 reference

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13 August 2018

1 reference

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Calibration of avian molecular clocks

13 August 2018

1 reference

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10.1371/JOURNAL.PONE.0197433

13 August 2018

Identifiers

DOI

1 reference

15 June 2018

PMCID

5957400

1 reference

15 June 2018

PubMed ID

29772020

1 reference

15 June 2018