Occasionally a gene on a single chromosome will be duplicated to create a pair of identical genes. Duplication may occur for any one of several reasons. One type of duplication occurs when the RNA transcript of a gene is "reverse transcribed" back into a DNA sequence and reinserted elsewhere in the genome (a process called retroposition), leading to a new, possibly functional copy of the gene in a new location and subject to different regulatory systems. This appears to have occurred with the human gene for phosphoglycerate kinase 2, which is involved in energy use in the cell.
More likely, a retroposed gene will be functionless, since it will not have the promoters and enhancers it needs for expression. Typically, one copy of a duplicated gene is either nonfunctional or accumulates mutations that render it so. After a long period of evolutionary time, the duplicate gene may acquire so many mutations that it may be difficult to see its relationship to its parent gene. Nonfunctional copies of previously functional genes are called pseudogenes.
Analysis of genomes shows that many gene copies are found lying next to each other, linked head to tail in an arrangement called a "tandem repeat." This may occur because of errors of the normal recombination machinery that is responsible for DNA repair and crossing over during meiosis. Tandem repeats are susceptible to amplification, which is the further increase in the number of copies. This can occur during crossing over. Normal crossing over pairs up identical segments on homologous chromosomes, and then exchanges them. If the chromosomes each have a tandem repeat, the crossover machinery may line up incorrectly, leaving one homologue with three gene copies and one with only one. Repeating this process over ensuing generations can lead to dozens of extra gene copies.
Duplication of much larger portions of a genome is also possible, including whole chromosomes (called chromosomal aberrations) and even the entire genome (called polyploidy). In each case, the number of copies of a gene increases. Such copies are usually removed by natural selection, but it is sometimes advantageous to have several gene copies, particularly for those genes that code for ribosomal RNAs. These are present in dozens or even hundreds of copies, allowing rapid production of new ribosomes during cell growth.
While gene duplication is a rare event in the short term, it is frequent enough in the long term to have been a central feature in the evolution of the genome of eukaryotic organisms. As with alleles, gene duplication frees up a gene copy to accumulate mutations with less selective penalty. Over time, such a gene may change its function slightly, or even acquire a new
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