Sentence examples for using the strict molecular-clock from inspiring English sources

Two priors, the overall substitution rate (rgene gamma) and the rate-drift parameter (sigma2 gamma), were set at G (1, 7.9) and G (1, 1.0), respectively, using the strict molecular-clock assumption with a 75 MA constraint (a result of Azuma et al. [37]) on the divergence between Takifugu rubripes and Tetraodon nigroviridis.

So we roughly estimated the prior mean of the overall rate μ using the strict molecular clock with 295 Ma constraint to Gymnosperm/Angiosperm divergence time, and assigned the gamma prior G 4, 80) and G 4, 22) for this prior parameter in applying the nucleotide and codon substitution models, respectively.

This analysis was performed using the strict molecular clock model in BEAST.

To assess the relative fitness of the alternative clock relaxations, we calculated Bayes factors between each model using the strict molecular clock as a reference.

Furthermore, by using the strict molecular clock as a reference, they allow for a general comparison among any number of independent models [ 38].

Fossil-calibrated values were estimated using a Bayesian lognormal relaxed-clock model, while the substitution rate calibrated values were estimated using the strict molecular clock model using a fixed mean substitution rate of 1.30 X 10−8 subs/site/year.

The units for rate of evolution in the strict molecular clock model using the clock.rate parameter are substitutions per site per million years (Drummond et al. 2007).

[ 35, 36] explore the strict molecular clock assumption in these data using a Bayesian approach and find good support for a clock among the anthropoids, but not between the anthropoids and prosimians, nor within the prosimians.

A relaxed clock was used since a likelihood-ratio test performed as above rejected the strict molecular clock for all introns.

The settings used were the Yule tree prior, the HKY substitution model with four gamma categories and the strict molecular clock.

The relaxed molecular clock model also had a larger marginal likelihood according to the Bayes factors comparison (−2696.62 for the strict molecular clock compared to −2690.78 for the relaxed molecular clock).