Population genetics visualizes evolutionary dynamics as a process among genotypes. Phenotypes are represented only through empirical parameters. The quasispecies concept introduces the molecular mechanism of mutation. Optimization is seen as a process in genotype space. Populations optimize through adaptive walks.
Selective neutrality leads to random drift.
Understanding evolution will be always incomplete unless phenotypes are considered explicitly. At the current state of the art, almost all genotype-phenotype mappings are too complex to be analyzed and modeled. Only the most simple case of an evolutionary process, the optimization of RNA molecules in vitro, where genotypes and phenotypes are RNA sequences and structures, respectively, can be treated successfully. We derive a model based on a stochastic process which includes unfolding of genotypes to form phenotypes as well as their evaluation. Relations between genotypes and phenotypes are handled as mappings from sequence space onto the space of molecular structures.