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MK Tickner, M Neitz, J Neitz; Extreme Polymorphism in L & M Photopigment Genes of Humans but Not Monkeys . Invest. Ophthalmol. Vis. Sci. 2002;43(13):3792.
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Purpose: There is evidence that the human X-chromosome photopigment gene locus has extreme diversity. This is remarkable because, overall, human gene diversity is exceedingly low. On average, the number of nucleotide differences between two human sequences drawn at random is fewer than 1 in 1,000. However, the differences are not distributed evenly. Most genes are relatively free of genetic polymorphism. Much of the diversity in the human genome is attributable to specific regions with more concentrated differences that are presumably attributable to unusually unstable genes or circumstances in which genetic variation has provided a selective advantage. Here, in order to quantify the degree of polymorphism of the L and M photopigment genes we calculated an index of nucleotide diversity (Pi). During evolution, the L and M pigment genes arose in a primate ancestor common to Old World (OW) monkeys and man. Thus, for comparison to humans we measured the diversity of monkey sequences. Methods: L and M pigment gene sequences were determined for ≷100 humans and ≷ 30 monkeys including 4 species. The index of nucleotide diversity (Pi) was calculated so that comparisons could be made between humans and monkeys and the photopigment genes could be compared with other loci in the human genome. Results: The coding sequence of the human L and M photopigment genes show extreme polymorphism. For example, considering only the non-silent polymorphisms we identified 23 different alleles of the human L gene. In exon 3, where the polymorphism is highest, Pi = 1.25%, more than ten times the average for the human genome. In contrast, the diversity of the same genes in monkeys is dramatically lower, with values of Pi that are lower than the overall average for the human genome. Conclusion: The human L and M pigment genes exhibit extreme nucleotide polymorphism. To our knowledge they are surpassed only by the major histocompatibility complex genes. This diversity is not observed in the monkey genes. The monkey and human genes have the same origin but something has occurred since the time the two lineages diverged to produce a dramatic difference in genetic diversity.
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