Under normal conditions, most people can match any color in a test stimulus by adjusting the intensity of three superimposed colored light sources (blue, green, and red). The fact that only three colors are necesary to match all the colors perceived is a reflection of the fact that our sense of color is based on the relative levels of activity in three sets of cones with different absorption spectra. For about 2% of the male population and 0.03% of the female population, color vision is more limited. Only two colors of light are needed to match all the colors that these individuals can perceive; the third color is not seen. Sich dichromacy, or color blindness, is inherited as a recessive, sex-linked characteristic and exists in two forms: protanopia, in which all color matches can be achieved by using only green and blue light, and deuteranopia, using only blue and red. In another major class of color deficiencies all three wavelengths are needed, but the matches are made using values that are significantly different from those used by most people. Some of these anomalous trichromats require more red than normal to match other colors; others require more green than normal.

The genes that encode the red and green pigments in the cones of the retina lie adjacent to each other on the X chromosome and show a high degree of sequence homology. In contrast, the blue-sensitive pigment gene is found on chromosome 7 and is considerably different in its amino acid sequence. This suggests that the red and green pigment genes have evolved relatively recently. This genetic knowledge also explains why most color vision abnormalities involve the reg and green cone pigments, while the blue cone pigment remains relatively stable. Because they are located adjacent to each other on the X chromosome, crossing over during meiosis can result in an unequal distribution of the genes such that one chromosome contains multiple copies, while the other contains none. Crossing over can also result in hybrid genes that code for pigments with different absorption spectra.

Human dichromats lack one of the three cone pigments, either because the corresponding gene is missing or because it exists as a hybrid of the red and green pigment genes. For example, some deuteronopes lack the green pigment gene altogether; others have a hybrid gene that is thought to produce a redlike pigment in the "green" cones. Anomalous trichromats also possess hybrid genes, but these are thought to elaborate pigments whose spectral properties lie between those of the normal red and green pigments. Thus, although most anomalous trichromats have two distinct sets of long-wavelength cones (one normal, one hybrid), there is more overlap in their absorption spectra than in normal trichromats, and less of a difference in how the two sets of cones respond to a given wavelength.

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