The molecular clock is a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged.The biomolecular data used for such calculations are usually nucleotide sequences for DNA or amino acid sequences for proteins.Sometimes referred to as node dating, node calibration is a method for phylogeny calibration that is done by placing fossil constraints at nodes.A node calibration fossil is the oldest discovered representative of that clade, which is used to constrain its minimum age.It is sometimes called a gene clock or an evolutionary clock.The notion of the existence of a so-called "molecular clock" was first attributed to Émile Zuckerkandl and Linus Pauling who, in 1962, noticed that the number of amino acid differences in hemoglobin between different lineages changes roughly linearly with time, as estimated from fossil evidence.They generalized this observation to assert that the rate of evolutionary change of any specified protein was approximately constant over time and over different lineages (based on the molecular clock hypothesis (MCH)).The genetic equidistance phenomenon was first noted in 1963 by Emanuel Margoliash, who wrote: "It appears that the number of residue differences between cytochrome c of any two species is mostly conditioned by the time elapsed since the lines of evolution leading to these two species originally diverged.
The molecular clock alone can only say that one time period is twice as long as another: it cannot assign concrete dates.
If this is correct, the cytochrome c of all mammals should be equally different from the cytochrome c of all birds.
Since fish diverges from the main stem of vertebrate evolution earlier than either birds or mammals, the cytochrome c of both mammals and birds should be equally different from the cytochrome c of fish.
Historical methods of clock calibration could only make use of a single fossil constraint (non-parametric rate smoothing),) allow for the use of multiple fossils to calibrate the molecular clock.
Simulation studies have shown that increasing the number of fossil constraints increases the accuracy of divergence time estimation.
The benchmarks for determining the mutation rate are often fossil or archaeological dates.