For each analysis, two independent Markov chain Monte Carlo (MCMC) runs of four Metropolis-coupled chains were performed with the gamma shape parameter, the proportion of invariable sites, base frequencies and substitution rates unlinked across partitions and assuming default priors.
Prior distributions on state frequencies, substitution rates, gamma distribution shape and the proportion of invariable sites were unlinked across all partitions and left at default values.
Bayesian analyses were performed with MrBayes 3.1.2 [ 51, 52] with the following priors: Dirichlet priors (1,1,1,1) for base frequencies and (1,1,1,1,1) for General Time Reversible (GTR) parameters scaled to the G-T rate, a uniform (0.05,50) and (0,1) priors for the gamma shape and the proportion of invariable sites (I), and an exponential (10.0) prior for branch lengths.
Otherwise, the Nanuk's wedge-like shape, down to the proportions of its wheels and the rake of its windshield, heavily echo those found on the Parcour.
When used, centrifugation is shown to alter the size and shape of agglomerates, increasing the proportion of chain agglomerates and reducing clusters.
The "mtRev" model of amino acids was selected and the gamma shape parameter and the proportion of invariable sites were determined using PhyML v.2.4.4 [ 63].
We generated 100 simulated datasets using Seq-Gen version 1.3.2 (Rambaut and Grassly 1997) of the same size as the original one, taking into account the T0 topology (including branch length), proportion of amino acid determined empirically, and parameter of the model from the constrained ML analysis including shape of the γ distribution and proportion of invariable sites.
The rate matrix, base frequencies, shape of the gamma distribution, and proportion of invariant sites were estimated before the ML analysis from a parsimony tree constructed from the data.
For ML analysis, the gamma shape parameter and the proportion of invariant sites were optimized.
Means and 95% confidence intervals for the gamma distribution shape parameter and the proportion of invariable sites (pI) were also estimated for each alignment that was analyzed.
The gamma shape parameter and the proportion of invariant sites were optimised during the searches.
