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So far we have only considered genes that affect a single phenotypic character. However, there are many examples showing that one gene can have multiple effects (pleiotropy) on the phenotype. For example, people with albinism lack pigment in their skin and hair, and also have crossed eyes at a higher frequency than pigmented individuals. This occurs because the gene that causes albinism can also cause defects in the nerve connections between the eyes and the brain. However, these two traits are not always linked, again showing the complexity of genetic interactions in determining phenotypes.

In laboratory mice, the recessive "mini-muscle" (MM) allele reduces hind limb muscle mass by 50%. Mice that are homozygous for the MM allele exhibit various pleiotropic effects, including an increase in muscle aerobic capacity, and larger hearts, livers, and spleens.

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