DNA Sequence Variation

The development of techniques for isolating, restricting, and sequencing DNA in the 1970s and 1980s provided powerful tools for detecting, quantifying, and investigating genetic variation. The application of these techniques has provided a detailed view of molecular variation.

Restriction enzymes are one tool that can be used to detect genetic variation in DNA and examine patterns of genetic variation in nature. Each restriction enzyme recognizes and cuts a particular sequence of DNA nucleotides, known as that enzyme's restriction site (see Chapter 18). Variation in the presence of a restriction site is called a restriction fragment length polymorphism (RFLP; see Figure 18.26). Each restriction enzyme recognizes a limited number of nucleotide sites in a particular piece of DNA but, if a number of different restriction enzymes are used and the sites recognized by the enzymes are assumed to be random sequences, RFLPs can be used to estimate the amount of variation in the DNA and the proportion of nucleotides that differ between organisms.

Methods for determining the complete nucleotide sequences of DNA fragments (see p. 000 in Chapter 19) provide the most detailed evolutionary information, although they are both time consuming and expensive. DNA sequencing in evolutionary studies is therefore usually limited to a few individuals or to short sequences. Nevertheless, the high resolution of information provided by sequencing is often invaluable for understanding molecular processes that influence evolution and for determining phylogenies of closely related organisms. For example, DNA sequencing has been used to study the evolution of human immunodeficiency virus (HIV), the virus that causes AIDS. Like many other RNA viruses, HIV evolves rapidly, often changing its sequences within a single host over a period of several years. Evolutionary comparisons of HIV sequences in a dentist and seven of his patients who had AIDS demonstrated that five of the patients contracted AIDS from the dentist, whereas the other two patients probably acquired their HIV infection elsewhere.

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