Information regarding size, level of variability, molecular evolutionary models, and likelihood values from phylogenetic analyses for all mtDNA and nDNA genes can be found in Table 1.
Molecular evolutionary models are often applied to detect and quantify the type and the intensity of selective pressures acting on genes and on specific sites within them.
The expression profiles of each slimfast paralog inspired the molecular evolutionary models we used to test if branches leading to male-biased paralogs experienced accelerated rates of evolution.
In order to keep our molecular evolutionary models simple, we eliminated alignment columns with a CpG in any of the species.
As in the maximum likelihood and Bayesian analysis described before, the same ten data partitions and molecular evolutionary models were applied to estimate the posterior density of relative divergence times.
Recent advances in computer science and in the acquisition of new genetic sequences from a variety of organisms have opened up a wide spectrum of new possibilities in molecular evolutionary modeling.
This result, applied to the Poisson model of molecular evolution, was subsequently generalized by Su et al. [ 57] to apply to all standard symmetric molecular evolutionary models of nucleotide substitution up to and including the General Time Reversible model (GTR [ 58, 59]).
But because these works assume a character with binary states with equal substitution rates, the inconsistency conditions identified by assuming such a simplistic model cannot be directly applied to real-life molecular loci, which typically follow much more complex molecular evolutionary models and vary in rates of evolution.
Importantly, and unlike most probabilistic models currently used in molecular evolutionary studies, SC models are explicitly site-interdependent, and therefore, require complex Monte Carlo methods to be implemented and applied to empirical data [ 3, 4, 8].
Divergence times were estimated using the uncorrelated lognormal (UCLN) model of molecular evolutionary rate heterogeneity implemented in the computer program BEAST v. 1.8 [ 106, 107].
