Genetic differences as seen within a species over spatial scales.

Either within or between subpopulations, the frequency of alleles and particularly the types of alleles that are present often vary from place to place. This is a consequence of what could be described as incomplete geographical barriers, that is, the ability but nonetheless relative inability of alleles to move rapidly over large distances.

Different locations can be subject to differences in mutation – that is, what alleles happen to arise – as well as variation that arise from a combination of differences in genetic drift and natural selection. Further, it is inefficiencies in migration of alleles from place to place that give rise to as well as maintains this genetic variation.

Should complete geographic barriers arise within populations already displaying geographic variation, then in a sense allopatric speciation will have been initiated in terms of geographic variation prior to this event. That is, different subpopulations found in different locations will differ prior to the imposition of these barriers and, presumably, further diverge genetically following the occurrence of absolute geographical isolation. See in particular also peripheral isolates.

Another way of looking at geographic isolation is that it reflects impediments to what is known as panmixis, or panmixia. That is, impediments to truly random mating as it can occur within a population. In other words, geographic variation cannot persist given panmixis and therefore geographic variation is one indication of a lack of panmixis within populations.