Clonal interference

The coexistence of different beneficial genotypes in the same viral population implies that they have to outcompete each other in their way to fixation, ensuring that only the fittest one would be fixed at the end (Clarke et al. 1994). This phenomenon, known as clonal interference (Gerrish and Lenski 1998; Miralles et al. 1999, 2000), has several important implications for the evolutionary dynamics of RNA viruses.
(1) The probability of fixation of a given beneficial mutation decreases with both population size and mutation rate (i.e., the availability of beneficial mutations).
(2) As population size or mutation rate increases, adaptive substitutions result in larger fitness increases.
(3) The rate of adaptation is an increasing, but decelerating, function of both population size and mutation rate.
(4) Beneficial mutations that become transiently common but do not achieve fixation because of interfering beneficial mutations are relatively abundant.
(5) Transient polymorphisms may give rise to a "leapfrog" effect, where the most common genotype at a given moment might be less closely related to the immediately preceding one than with an earlier genotype. Consequently, adaptive substitutions appear as discrete, rare events, regardless of mutation rate or population size. They often do not occur simply as the result of a single mutation but instead represent the best of several competing mutations. Furthermore, in medium to large populations, the rate of fitness increase is hardly affected by changes in mutation rate. This consequence is of special relevance, since some authors have speculated that the high mutation rates of RNA viruses are maintained evolutionarily because of the great adaptive they bestow. However, when clonal interference is considered, this argument becomes questionable because increases in an already high mutation rates have little effect on adaptive capacity whereas decreases in mutation rate could come about with little or no decrease in the rate of adaptation and would benefit the population by slowing the accumulation of deleterious mutations.