Novel strategies to study the role of mutation and nucleic acid structure in evolution

Natural selection processes tune genomes in the edge of the chaos imposed by mutation and drift, allowing an enduring exploration of fitter genetic networks within the constraints imposed by self-organization and the interactions of genotype and phenotype. Alternatively, evolution can be viewed from thermodynamic, kinetic or cybernetic perspectives. Regardless of insight, there is need to understand structure-function relationships at the molecular and holistic evolutionary levels. Strategies are here described that analyze genetic variation in time and trace the evolution of nucleic acid structure. Nucleic acid scanning techniques were used to measure sequence divergence and provide a direct inference of genome-wide mutation rate. This was tested for the first time in vegetatively propagating plants. The method is general and was also used in a study of mutational patterns in phytopathogenic fungi, showing there was a link between sequence and structural diversification of ribosomal gene spacers. In order to determine if this was a general phenomenon, the origin and diversification of nucleic acid secondary structure was traced using a cladistic method capable of producing rooted phylogenetic trees. Phylogenies reconstructed from primary and secondary RNA structure were congruent at all taxonomical levels, providing evidence of a strong link between phenotype and genotype favoring thermodynamic stability and dissipation of Gibbs free energy. Overall results suggest that thermodynamic principles are important driving forces of the evolutionary processes of the living world.