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The founder effect is the name given to describe one type of genetic drift. When a small population branches off from a larger one, it may not be genetically representative of the parent population. Certain alleles may be over- or under-represented. The different composition of the smaller population's gene pool disrupts the Hardy-Weinberg equilibrium. The result is a large number of a particular phenotype that may be rare or recessive in the parent population.

An example of the founder effect in action can be found in the Old Order Amish of Lancaster, Pennsylvania. The group was founded in the early 1770's. Since then, around 61 cases of a rare form of dwarfism/polydactylism have shown up in this population, a number almost equal to those occuring in the rest of the world. This condition is caused by a very rare recessive allele. However, one of the founders of the order must have carried it. It is estimated that of a population of around 17,000, about 13 percent of the population carries the allele. This much larger percentage was caused by the founder effect.

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