Although molecular evolutionists are often interested in naturally evolved genes and proteins, molecular evolution can also be observed directly in the laboratory. Increasingly, evolutionary biologists are studying evolution experimentally. Because substitution rates are related to generation time rather than to absolute time, most of these experiments use unicellular organisms or viruses with short generations. Viruses, bacteria, and unicellular eukaryotes (such as the yeasts) can be cultured in large populations in the laboratory, and many of these organisms can evolve rapidly. In the case of some RNA viruses, the natural substitution rate may be as high as 1 substitution per 1,000 nucleotides per generation. Therefore in a virus of a few thousand nucleotides, one or more substitutions are expected (on average) every generation, and these changes can easily be determined by sequencing the entire viral genome (because of its small size). Generation time may be only tens of minutes (rather than years or decades, as in many animals), so biologists can directly observe substantial molecular evolution in a controlled population over the course of days, weeks, or months.

Experimental molecular evolutionary studies are used for a wide variety of purposes and have greatly expanded the ability of evolutionary biologists to test evolutionary concepts and principles. Biologists now routinely study evolution in the laboratory, and as we will see later in this chapter, they can use in vitro evolutionary techniques to produce novel molecules that perform new functions with industrial and pharmaceutical uses.