The HOLI domain could be accepted by M2a, indicating a positive selection pressure of HOLI domain during the molecular evolution process, whereas the ZnF_C4 domain was rejected.
In conclusion, our study shows that the binding characteristics, such as binding affinity, of modules selected from molecular libraries created on the CBM4-2 scanfold can be further improved by a molecular evolution process.
The tracing analysis of molecular evolution, a protein engineering approach employing the reconstruction of probable ancestral forms based on phylogenetic trees and their mutants, is a powerful approach that not only reveals the molecular evolution process and determinants of selection pressures, but also helps to study the structure-function relationships of proteins.
This does not imply that the rate of molecular evolution explains the process of diversification, because this complex and heterogeneous process can be influenced by many mechanisms such as hybridization [ 76], polyploidy [ 77], allopatric events [ 14], and the duplication of genes [ 30].
Analysis of many molecular phylogenies has also revealed correlations between substitution rates and clade size, suggesting a link between rates of molecular evolution and the process of diversification.
We employed the WAG+I+G model with four rate categories for proteins (this was the optimal model selected with ProtTest 1.3 [ 46]), and the GTR+I+G model with four rate categories for nucleotides, with normally distributed priors for the parameters in models of molecular evolution, a Yule process tree model, and default values for all other settings.
Because patterns of molecular evolution reflect long-term processes of mutation and selection in nature, interactions between recombination rate and genetic differentiation between species can be used to test the benefits of recombination.
Directed molecular evolution is a recursive process of controlled genetic diversification and functional screening.
However, the main aim is not simply to achieve the highest score, especially because the result will be fundamentally dependent on chance and not on special skills of the players, but to exercise students' knowledge on important aspects about the role of random processes in molecular evolution.
Thus the exact UPGMA solution carries practical implications for understanding of tree processes underlying molecular evolution.
