It remains unknown how common or significant epistatic fitness effects actually are. Hitchhiking occurs in two-locus selection models. Hitchhiking is a very simple concept, with potentially complex consequences. The easiest case to imagine is for neutral alleles to hitchhike by tight linkage to strongly selected alleles. Fixation of neutral alleles by hitchhiking may offer one possible explanation for rates of heterozygosity which are lower than expected by neutral theory.
Linkage disequilibrium can be advantageous, neutral, or disadvantageous.
Hitchhiking of neutral alleles is a simple example of a neutral effect for linkage disequilibrium. Hitchhiking of weakly deleterious alleles is a simple example of a deleterious effect for linkage disequilibrium. Stable mimetic polymorphism based on epistatic fitness interactions illustrates one possible advantage for linkage disequilibrium. See the next section below. If the effects of linkage disequilibrium are advantageous, then recombination may be harmful.