When the 2011 Edinburgh Festival Fringe begins on Friday, the theater-obsessed who make the pilgrimage to Scotland for this huge annual, multi-arts blowout can indulge their passion almost around the clock, assuming they have the stamina.
The upshot of these and many other studies is that instead of using cytochrome c simplistically as a molecular clock assumed to have a fixed substitution rate, other more reliable timing mechanisms have been used to link the variable substitution rate of cytochrome c to its structure and function and to particular episodes in primate evolution.
Runs were performed with an uncorrelated lognormal clock assuming constant population size (20,000,000 generations with the first 2,000,000 discarded as burn-in).
The likelihood ratio was then calculated as 2(lnL1-lnL2), where L1 is the null hypothesis (clock assumed), which is a subset or special case (in nested models) of the alternative hypothesis L2 (no clock assumed).
According to a molecular clock assuming rice and maize diverged 50 MYA [ 58], the TFIIAγ1 and TFIIAγ5 paralogs diverged about 54 ~76 MYA.
We followed previous work (Cui et al., 2013, Wagner et al., 2014) and applied a lognormal relaxed clock, assuming a constant population size.
In both approaches, the cox1 data set of the 162 sampled individuals was used applying an uncorrelated log-normal clock, assuming a coalescent model with constant population size as the best model fitting the data.
For each clade, the model suggested by jMODELTEST was used under a lognormal relaxed molecular clock (assuming a relaxed substitution rate of 1%) [ 87], and using an UPGMA-based (unweighted pair group method with arithmetic mean) starting tree.
Age of the major clades shown in Figure 3, estimated using a Bayesian non-correlated relaxed molecular clock assuming a Yule tree prior, or a coalescent constant population size model and alternative calibration rates.
For the maximum-likelihood trees, the experimental versions of the programs PROML (no assumption of molecular clock) and PROMLK (molecular clock assumed) from PHYLIP version 3.6a3 were used with the JTT evolutionary model and with the assumption of constant change rate between sites.
