The Akirin1 and Akirin2 clades were defined as separate clusters and the coefficient of functional divergence and posterior probability for functional divergence at each site in the alignment were estimated using the Gu99 algorithm [ 28].
To estimate divergence times among lineages we used a coalescence approach that uses Bayesian inference and MCMC simulations to generate posterior probability values for divergence times as implemented in the program Beast[ 68].
Again, whether site j diverges across the DP is not known, so the full site likelihood is obtained by integrating against the Bernoulli probability distribution for divergence at the DP.
We recorded the maximum-likelihood estimate from the posterior probability distribution for divergence time, adjusted with a two year generation time [ 25] and its credibility interval based on the shortest parameter interval containing 90% of the area under the posterior distribution curve.
Instead, half (five out of ten) residues detected as high probability for functional divergence are located at the linker region between the EF and the SAM domain, or at the beginning of the SAM domain (see below, Fig. 5).
The coefficient of functional divergence and the posterior probability for the functional divergence were calculated for each position in the alignment.
Posterior probabilities for the divergence times are plotted in Figure 2A for both marker types.
Consequently, using complex eigenfrequencies and divergence velocities for every realization, the statistical responses of stochastic problem are obtained as expected values, standard deviations, probability density functions, and the probability of divergence occurrence.
A partial financial liberalization increases the probability of divergence from the de jure regime in the face of various shocks, but an increase in the level of financial reforms decreases the probability of divergence.
For instance, the posterior probabilities of divergence time between allopatric populations and between parapatric populations with significant migration rates were congruent.
