Literature DB >> 26688196

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

Mario dos Reis1,2, Philip C J Donoghue3, Ziheng Yang1.   

Abstract

Five decades have passed since the proposal of the molecular clock hypothesis, which states that the rate of evolution at the molecular level is constant through time and among species. This hypothesis has become a powerful tool in evolutionary biology, making it possible to use molecular sequences to estimate the geological ages of species divergence events. With recent advances in Bayesian clock dating methodology and the explosive accumulation of genetic sequence data, molecular clock dating has found widespread applications, from tracking virus pandemics and studying the macroevolutionary process of speciation and extinction to estimating a timescale for life on Earth.

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Year:  2015        PMID： 26688196     DOI： 10.1038/nrg.2015.8

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN： 1471-0056            Impact factor:   53.242


  119 in total

1.  Rise and fall of the Beringian steppe bison.

Authors:  Beth Shapiro; Alexei J Drummond; Andrew Rambaut; Michael C Wilson; Paul E Matheus; Andrei V Sher; Oliver G Pybus; M Thomas P Gilbert; Ian Barnes; Jonas Binladen; Eske Willerslev; Anders J Hansen; Gennady F Baryshnikov; James A Burns; Sergei Davydov; Jonathan C Driver; Duane G Froese; C Richard Harington; Grant Keddie; Pavel Kosintsev; Michael L Kunz; Larry D Martin; Robert O Stephenson; John Storer; Richard Tedford; Sergei Zimov; Alan Cooper
Journal:  Science       Date:  2004-11-26       Impact factor: 47.728

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

Authors:  Ziheng Yang; Bruce Rannala
Journal:  Mol Biol Evol       Date:  2005-09-21       Impact factor: 16.240

3.  A general comparison of relaxed molecular clock models.

Authors:  Thomas Lepage; David Bryant; Hervé Philippe; Nicolas Lartillot
Journal:  Mol Biol Evol       Date:  2007-09-21       Impact factor: 16.240

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

Authors:  Tracy A Heath; John P Huelsenbeck; Tanja Stadler
Journal:  Proc Natl Acad Sci U S A       Date:  2014-07-09       Impact factor: 11.205

Review 5.  Molecular-clock methods for estimating evolutionary rates and timescales.

Authors:  Simon Y W Ho; Sebastián Duchêne
Journal:  Mol Ecol       Date:  2014-10-30       Impact factor: 6.185

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

Authors:  R F Doolittle; D F Feng; S Tsang; G Cho; E Little
Journal:  Science       Date:  1996-01-26       Impact factor: 47.728

7.  Estimating the pattern of nucleotide substitution.

Authors:  Z Yang
Journal:  J Mol Evol       Date:  1994-07       Impact factor: 2.395

8.  The molecular clock may be an episodic clock.

Authors:  J H Gillespie
Journal:  Proc Natl Acad Sci U S A       Date:  1984-12       Impact factor: 11.205

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

Authors:  Alexei J Drummond; Marc A Suchard
Journal:  BMC Biol       Date:  2010-08-31       Impact factor: 7.431

10.  A revised dated phylogeny of the arachnid order Opiliones.

Authors:  Prashant P Sharma; Gonzalo Giribet
Journal:  Front Genet       Date:  2014-07-28       Impact factor: 4.599
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  77 in total

1.  Advances in Time Estimation Methods for Molecular Data.

Authors:  Sudhir Kumar; S Blair Hedges
Journal:  Mol Biol Evol       Date:  2016-02-16       Impact factor: 16.240

2.  A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth-Death Process.

Authors:  Arong Luo; David A Duchêne; Chi Zhang; Chao-Dong Zhu; Simon Y W Ho
Journal:  Syst Biol       Date:  2020-03-01       Impact factor: 15.683

Review 3.  Challenges in Species Tree Estimation Under the Multispecies Coalescent Model.

Authors:  Bo Xu; Ziheng Yang
Journal:  Genetics       Date:  2016-12       Impact factor: 4.562

4.  Reply to Hedges et al.: Accurate timetrees do indeed require accurate calibrations.

Authors:  Jennifer L Morris; Mark N Puttick; James W Clark; Dianne Edwards; Paul Kenrick; Silvia Pressel; Charles H Wellman; Ziheng Yang; Harald Schneider; Philip C J Donoghue
Journal:  Proc Natl Acad Sci U S A       Date:  2018-09-28       Impact factor: 11.205

5.  Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary.

Authors:  Liang Liu; Jin Zhang; Frank E Rheindt; Fumin Lei; Yanhua Qu; Yu Wang; Yu Zhang; Corwin Sullivan; Wenhui Nie; Jinhuan Wang; Fengtang Yang; Jinping Chen; Scott V Edwards; Jin Meng; Shaoyuan Wu
Journal:  Proc Natl Acad Sci U S A       Date:  2017-08-14       Impact factor: 11.205

Review 6.  Mammal madness: is the mammal tree of life not yet resolved?

Authors:  Nicole M Foley; Mark S Springer; Emma C Teeling
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2016-07-19       Impact factor: 6.237

7.  Origin of horsetails and the role of whole-genome duplication in plant macroevolution.

Authors:  James W Clark; Mark N Puttick; Philip C J Donoghue
Journal:  Proc Biol Sci       Date:  2019-10-30       Impact factor: 5.349

8.  Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation.

Authors:  Nathan S Upham; Jacob A Esselstyn; Walter Jetz
Journal:  PLoS Biol       Date:  2019-12-04       Impact factor: 8.029

9.  Genetic Stability and Evolution of the sigB Allele, Used for Listeria Sensu Stricto Subtyping and Phylogenetic Inference.

Authors:  Jingqiu Liao; Martin Wiedmann; Jasna Kovac
Journal:  Appl Environ Microbiol       Date:  2017-05-31       Impact factor: 4.792

10.  An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times.

Authors:  Konstantinos Angelis; Sandra Álvarez-Carretero; Mario Dos Reis; Ziheng Yang
Journal:  Syst Biol       Date:  2018-01-01       Impact factor: 15.683
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