The molecular clock relates the amount of sequence difference between species and the time since the species diverged.

The extent of genetic difference, or genetic divergence, between two species is a function of the time they have been genetically isolated from each other. The longer they have been apart, the greater the opportunity for mutation and fixation to occur in each population. This correlation between the time two species have been evolutionarily separated and the amount of genetic divergence between them is known as the molecular clock.

For a clock to function properly, it not only needs to keep time, but it also needs to be set. We set the clock using dates from the fossil record. For example, in a 1967 study, Vince Sarich and Allan Wilson determined from fossils that the lineages that gave rise to the Old and New World monkeys separated about 30 million years ago. Finding that the amount of genetic divergence between humans and chimpanzees was about one-fifth of that between Old and New World monkeys, they concluded that humans and chimpanzees had been separated one-fifth as long, or about 6 million years. Although this is the generally accepted number today, Sarich and Wilson’s result was revolutionary at the time, when it was thought that the two species had been separated for as long as 25 million years.