Mutations are alterations in DNA. They create new genetic variation that allows evolutionary innovation. Most mutations are neutral--that is, they have no effect on the evolutionary process.

Most mutations occur in cells that will die when the organism dies. For example, a mutation in a muscle cell of an animal will be lost when that cell dies. Some of these somatic mutations may induce cancer, if the mutation causes the cell to lose control of cell division. Some somatic mutations in plants may persist if the part of the plant that contains the mutation is used for vegetative propagation. This is how the mutation for seedless oranges has persisted:

The original mutation produced a branch with seedless oranges, and pieces of the branch were grafted onto other orange trees, from which further grafts were propagated, until there are now many thousands of orange trees that produce fruit without seeds. But usually the only mutations that will be passed into future generations are the germ line mutations, which occur in eggs or sperm, or in the cells that produce eggs and sperm. Such a mutation may end up in a fertilized egg, from which an organism develops, and will be found in every cell, including the germ line cells, of the offspring.

Most germ line mutations are also neutral in their effect. This is because most of the DNA in eukaryotic cells does not encode genetic information. Mutations in the noncoding DNA usually do not matter, since the information in this DNA is not used to construct proteins. Mutations may accumulate in noncoding DNA, acting as a measure of evolutionary divergence.

Even within genes, many mutations are neutral. DNA encodes genetic information in codons. There are 64 possible codons but only 20 kinds of amino acids which these codons can specify. That is, in DNA language, there are 64 different words to specify only 20 different meanings. If a mutation occurs that changes one codon to another, without changing the amino acid that it specifies, the resulting protein will not be changed. This often occurs when a mutation changes the third base in the codon. Chloroplast DNA extracted from 20-million-year-old leaves of Taxodium and Magnolia and compared to modern chloroplast DNA indicate that most of the mutations of Magnolia, and all of the mutations in Taxodium, that occurred during the past 20 million years were in the third bases of codons. Mutations in the third base of a codon are not always neutral. If a mutation changes a codon from one that matches a common transfer RNA to one that matches an uncommon one, the efficiency of translation may be reduced.

Many mutations are almost neutral. If a mutation in a gene causes a different amino acid to be placed in a certain position in a protein, the protein will be changed--but perhaps not significantly. If one amino acid substitutes for another amino acid that is chemically similar (for example, if leucine substitutes for isoleucine), the protein shape may be almost identical to what it had previously been. Even a major amino acid change may have no effect on a protein if it occurs someplace out of the way--in a position that is on the outside of the protein and away from the active site, which is the location on the protein where the chemical reaction occurs. Many proteins exist in a great variety of forms known as isozymes. For example, cells of all organisms contain the protein cytochrome c. In all organisms, cytochrome c does the same job, but its structure is different in many different species. It therefore exists in hundreds of different forms, due to mutations. Often an isozyme from even a distantly related species can function well if inserted in place of an organism's normal enzyme. For example, many human genes work well when inserted into other animals such as mice. . .

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