The founder effect is a dramatic decrease in genetic diversity caused through the formation of a small colony of individuals which remains isolated. The founder effect contributes to genetic drift, which causes certain genetic traits to vanish or become more abundant. Several human populations provide interesting sources of study for geneticists interested in the founder effect, as do numerous animal populations.

This concept was first widely discussed in 1952, when Ernst Mayr built on earlier theoretical work by others to come up with the idea of the founder effect. Mayr showed how small isolated populations can start to diverge from their larger parent populations, sometimes ultimately yielding a unique species. Since then, others have built on his work dramatically, performing long term studies of isolated communities and using advanced tools to analyze the genomes of organisms in these populations.

In a classic example of the founder effect, a small group splits off from a larger population, much as the Amish did during the Reformation. When a small group remains endogamous, meaning that people marry within the community, it can create a situation in which genetic diversity is extremely limited, because no new members are welcomed into the community. The founder effect is common among isolated religious communities and island populations, both of whom tend to be cut off from the larger population.

One effect of this phenomenon is the tendency for certain genetic traits to become concentrated. Because the founding community is so small, if one person carries a genetic mutation, that mutation can become amplified in the community. For example, the Amish have a much higher incidence of hexadactyly than the general population. The problems attributed to inbreeding are an example of the founder effect.

If a founder population is left alone long enough, it can diverge so radically from the parent population that it becomes an entirely new species. Charles Darwin noted this when he explored the animals of the Galapagos Islands, although he didn't understand the cause. Many people agree that the founder effect can be extremely problematic, because decreased genetic diversity can lead to an increase in the manifestation of genetic mutations. This is of special concern to biologists who are trying to save endangered species, as they must breed small starter populations in a responsible way to minimize the founder effect. This is one reason why conservation parks constantly trade animals.