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The cliche has always been that in-breeding causes genetic diseases. A good example in history was the family prevalence of the genetic disease hemophilia in certain European royal families, who tended to marry other royals. Another example is the increased prevalence of genetic diseases such as Tay Sachs disease in certain Jewish populations, because they encouraged arranged marriages within the same ethnic population.
So how does in-breeding increase genetic diseases? The answer lies in the reduced genetic pool available. Although there is some truth that limited genetic populations increase the risk of inherited genetic diseases, the increased risk is probably not as high as people expect.
In-breeding does not actually cause any more genetic mutations than normal. However, if a genetic mutation occurs within a population, in-breeding will tend to promote that mutation to become more widely distributed. The typical genetic disease increased by in-breeding are recessive genetic diseases. Close relatives that marry may have a common ancestor who had one mutation of the recessive disease, but did not get any disease because they did not have the second mutation. Changes are higher than both of these close relatively may have the same mutation, and thus be "genetic carriers" for the recessive disease. If they produce children, these children are much more likely to actually have the full symptomatic version of the recessive disease.
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