Selection effects on a linked neutral locus

Selection changes the frequency of alleles at a linked locus as well as at those under selection if the population is not in linkage equilibrium. The magnitude of this frequency change depends on the tightness of the linkage, the selection intensity, and the deviation from linkage equilibrium. Allowing a population to mate randomly without selection brings the population closer to linkage equilibrium. This decreases the effect of selection on allelic frequencies at a linked neutral locus. However, if linkage is very tight it can take many generations to make a large difference in the effect of the linked locus. The loss due to undesirable changes in allelic frequencies at linked loci when the population is not in linkage equilibrium must be weighed against the time and effort saved by beginning intense selection for the primary trait in an early generation. Effects of selection intensity, linkage intensity, and delayed selection on changes in allelic frequency at a neutral linked locus are demonstrated.