As the REs can be considerably larger than Mg, special care is taken to ensure convergence with respect to supercell size, and the binding of other large, non-RE solutes is calculated in the large supercells employed in the current work.
For sampling the posterior probability distributions and analyses of all model combinations (demographic and clock), ten Markov chain Monte Carlo (MCMC) chains of 100 million generations each were run to ensure convergence, with samples taken every 1,000 MCMC generations.
Thus, OCPG ensures convergence by providing near-optimal solutions.
LRAcluster set δ as 0.5, which ensures convergence for real applications in this study.
This was sufficient to ensure convergence within a single iteration.
Parameters were estimated using two independent runs of 10 million generations each (with a pre-run burn-in of 100,000 generations) to ensure convergence, checked with the program Tracer v1.4.
Please note that the OSEM3D reconstructions suffer more than others from severe noise; this is due to the long iteration scheme, applied to ensure convergence and consistency with the other reconstructions.
Additional ways of ensuring convergence could be explored with newer algorithms.
To ensure convergence of the solution with contact nonlinearity, displacement incrementation was controlled such that the maximum displacement increment during any increment was 1 nm.
Finally, Multidivtime analyses considering variance-covariance matrices from each gene partition were run twice ensure convergence, each one starting with a different random initial seed number.
