relevant are those inherited via the genetic material. Population genetics, in a more formal sense, is the study of those variables that are responsible for changes in the frequency of alleles in populations. In essence, the theory is reductionistic because it makes simplified assumptions on the transformation laws, especially those related to development, that are operating within and between genotypic and phenotypic spaces (Lewontin, 1974). Such simplifications allow the estimation of allele frequencies of a given generation as a function (probabilistic and/or deterministic) of frequencies from previous generations, as well as a set of state variables, mostly including mutation, selection, migration, and random drift. The vast majority of these transformation laws are not considered by population genetics or, if considered, they are incorporated as linear transformations, i.e., the genes of the genotypic space map linearly on the phenotypic space. When applied, for instance, to a phenotypic trait such as fitness, linearity means that a change in a gene promotes a certain fitness change, and that the genotype is an array of independent units contributing to the fitness in an additive way. Mendelian laws are the only transformation laws formally incorporated to the core of the population genetics theory (Lewontin, 1974).
It seems likely that populations of organisms governed by simple transformation laws (specially epigenetic) will meet the theoretical predictions of population genetics much better than those organisms governed by unknown, but probably very complex, transformation laws. Therefore, RNA viruses should better meet the theoretical predictions of population genetics. As the number of their genes is small, the type and number of epistatic interactions among their products should be of minor relevance compared with organisms with larger genomes (Elena, 1999). Thus, epistasis is expected to be of minor importance in simple-genome RNA viruses (Elena, 1999).
The environment of an RNA virus has several components, all of which could have different effects on its adaptive process. The closest environmental component is formed by cytoplasmic components of the infected cell, but intercellular spaces within tissues, tissues within individual hosts, and the ecological environment where host species are living are other components that modulate the adaptive response of RNA viruses. The theoretical framework to understand the dynamics of haploid organisms can be found in a series of classic papers that appeared many years ago (Moran, 1957; Robson, 1957; Muller, 1964; Drobník and Dlouhá, 1966; Felsenstein, 1971; Karlin and McGregor, 1971; Cook and Nassar, 1972; Gillespie, 1973; Gladstein, 1973; Trajstman, 1973; Cannings, 1974, 1975; Haigh, 1978; Emigh, 1979a, b; Strobeck, 1979). These studies, together with more recent statistical procedures for testing the presence of positive Darwinian selection or neutrality at the nucleotide level