When an advantageous allele is naturally selected, the alleles linked to it also get selected. This evolutionary phenomenon is called genetic hitchhiking or genetic draft (1).
For example, when a new favorable mutation (X) occurs on chromosome 4 (figure), it gets selected and spreads across a population. This gene X carries along its linked genes P, Q and R. This effect of gene X on genes P, Q and R is called the hitchhiking effect (2).
The degree of this effect depends on the strength of the selectable gene, population size and number of genetic crossovers, with the hitchhiked genes being sustained during asexual reproduction (3) (4).
1. Smith, J.M. and J. Haigh, The hitch-hiking effect of a favourable gene. Genet Res, 1974. 23(1): p. 23-35. PMID 4407212
3. Kaplan, N.L., R.R. Hudson, and C.H. Langley, The "hitchhiking effect" revisited. Genetics, 1989. 123(4): p. 887-99. PMID 2612899
4. Gillespie, J.H., Is the population size of a species relevant to its evolution? Evolution, 2001. 55(11): p. 2161-9. PMID 11794777