scholarly journals Bayesian molecular clock dating of species divergences in the genomics era

2015 ◽  
Vol 17 (2) ◽  
pp. 71-80 ◽  
Author(s):  
Mario dos Reis ◽  
Philip C. J. Donoghue ◽  
Ziheng Yang
Keyword(s):  
Molecular Clock ◽  
Molecular Clock Dating

The fossil record of Phasmida (Insecta: Neoptera)

2000 ◽  
Vol 31 (4) ◽  
pp. 473-480 ◽  
Author(s):  
Erich Tilgner
Keyword(s):  
Dominican Republic ◽  
Molecular Clock ◽  
Fossil Record ◽  
Sister Group ◽  
Baltic Amber ◽  
Molecular Clock Dating

AbstractA review of the Phasmida fossil record is provided. No fossils of Timema Scudder are known. Euphasmida fossils include: Agathemera reclusa Scudder, Electrobaculum gracilis Sharov, Eophasma oregonense Sellick, Eophasma minor Sellick, Eophasmina manchesteri Sellick, Pseudoperla gracilipes Pictet, Pseudoperla lineata Pictet and various unclassified species from Grube Messel, Baltic amber, and Dominican Republic amber. The oldest documented Euphasmida fossils are 44-49 million years old; molecular clock dating underestimates the origin of the sister group Timema by at least 24 million years.

Molecular phylogenetics and molecular clock dating of Sapindales based on plastid rbcL, atpB and trnL-trnF DNA sequences

Taxon ◽  
2016 ◽  
Vol 65 (5) ◽  
pp. 1019-1036 ◽  
Author(s):  
Alexandra N. Muellner-Riehl ◽  
Andrea Weeks ◽  
Joshua W. Clayton ◽  
Sven Buerki ◽  
Lars Nauheimer ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Dna Sequences ◽  
Molecular Phylogenetics ◽  
Molecular Clock Dating

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

2005 ◽  
Vol 35 (3) ◽  
pp. 569-582 ◽  
Author(s):  
H. Peter Linder ◽  
Christopher R. Hardy ◽  
Frank Rutschmann
Keyword(s):  
Molecular Clock ◽  
Taxon Sampling ◽  
Molecular Clock Dating

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

2012 ◽  
Vol 63 (1) ◽  
pp. 15-27 ◽  
Author(s):  
Andrew H. Thornhill ◽  
Lindsay W. Popple ◽  
Richard J. Carter ◽  
Simon Y.W. Ho ◽  
Michael D. Crisp
Keyword(s):  
Comparative Study ◽  
Molecular Clock ◽  
Relaxed Molecular Clock ◽  
Molecular Clock Dating

scholarly journals Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution

2017 ◽  
Vol 284 (1857) ◽  
pp. 20170227 ◽  
Author(s):  
Rachel C. M. Warnock ◽  
Ziheng Yang ◽  
Philip C. J. Donoghue
Keyword(s):  
Molecular Clock ◽  
Sequence Data ◽  
Time Estimation ◽  
Divergence Times ◽  
Mechanistic Models ◽  
Sequence Evolution ◽  
High Coverage ◽  
Fossil Species ◽  
Fossil Preservation ◽  
Molecular Clock Dating

Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions.

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