Molecular Clock: Technique to deduce the time in prehistory when two or more life forms diverged

It is based on comparing the detailed structure of key molecules. The method may be done for species, or any high data used for such calculations is often nucleotide sequences in genome analysis, or amino acid sequences for proteins such as haemoglobin. It is sometimes called a gene clock or evolutionary clock.

The key assumption behind the technique is that, in the long run, changes in molecular structure happen at a steady rate. Researchers such as Ayala have challenged this assumption. According to Ayala, these factors combine to limit the application of molecular clock models:

• Changing generation times: a mutation generally becomes fixed only from one generation to another. The shorter this timespan is, the more mutations can become fixed.
• Population size: apart from effects of small population size, genetic diversity will "bottom out" as populations become larger, and the fitness advantage of any one mutation becomes smaller.
• Species-specific differences due to differing metabolism, ecology, evolutionary history, etc.

Nevertheless, the method is now used widely in taxonomy and phylogeny.