Allopolyploids are species whose increased complement of genetic material is the result of hybridization of two closely related species. Thus homeologous chromosomes in allopolyploids are equivalent, but not identical. These differences mean that the precise pattern of silencing and expression can have important phenotypic effects. Reciprocal silencing on the population level refers to the case where two populations are each descended from the same allopolyploid. In one population, one of the two equivalent locci (A) is expressed while the other (B) has been silenced, while in the other population the reciprocal pattern occurs, with B being expressed and A silenced. It is important to note that this refers to equivalent loci, specific locations within the genome, rather than the entire homeologous chromosome.
Reciprocal silencing on the population level has been proposed as a means of allopatric speciation following a polyploid event. Allopatric speciation occurs when two populations of the same species become spatially separated and accumulate enough genetic differences to lose the ability to interbreed. As redundant genes are silenced in allopolyploids there is the potential for rapid genetic differences to accumulate through reciprocal silencing. These differences can lead to the loss of ability to interbreed between separated populations at a faster rate than other methods of speciation, given the relative speed with which genes are silenced following a polyploid event. Faster still, redundant genes can be silenced through epigenetic means, although the importance of this phenomenon is not fully understood.