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Our understanding of the history of life depends critically on knowledge of the ages of major clades.

The timing of land plant evolution is fundamental to the interpretation of earth history and macroevolution throughout the Phanerozoic.

Published shallow phylogenies (Black bass, Primate-sucking lice, 0.1 (95% of rates fall within 0.0082-0.0121 subs/site/Ma when σ = 0.1, for a mean rate of 0.01).

The independent rates relaxed clock model performed well at all levels of rate variation, although posterior intervals on times were significantly wider than for the strict clock.

The benchmarks for determining the mutation rate are often fossil or archaeological dates.

The molecular clock was first tested in 1962 on the haemoglobin protein variants of various animals, and is commonly used in molecular evolution to estimate times of speciation or radiation.

We examined whether: i) strict clock models are generally more appropriate in shallow phylogenies where rate variation is expected to be low, ii) the likelihood ratio test of the clock (LRT) reliably informs which model is appropriate for dating divergence times.

Strict and relaxed models were used to analyse sequences simulated under different levels of rate variation.

For example, the age of origin of the angiosperms has variously been related to the evolution of other plant lineages (e.g., ferns) (1) and biomes (e.g., tropical forests) (2), as well as to the major insect clades and their feeding habits (3–7), and even to the evolution of fungi (8, 9) and dinosaurs (10).

Relaxed molecular clock models allow divergence time dating and "relaxed phylogenetic" inference, in which a time tree is estimated in the face of unequal rates across lineages.

We present a new method for relaxing the assumption of a strict molecular clock using Markov chain Monte Carlo to implement Bayesian modeling averaging over random local molecular clocks.

We illustrate the method's utility on three example data sets involving mammal, primate and influenza evolution.

Finally, we explore methods to visualize the complex posterior distribution that results from inference under such models.




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