Definition
The molecular clock is the empirical observation, formalised in the 1960s, that genetic differences between species accumulate at an approximately steady average rate over time. If the rate can be calibrated against a known fossil date, then the number of differences between two sequences gives a time estimate for their last common ancestor.
In practice the clock is not perfectly even — substitution rates vary across genes, lineages, generation times, and population sizes. Modern molecular dating uses relaxed-clock models that allow rates to vary while constraining them with multiple fossil calibrations. The result is a probabilistic age range, not a single number.
Why it matters
How it works
Pick a pair of species, align homologous sequences, count substitutions per site. Divide by an estimate of the substitution rate per site per year (calibrated from fossils). The result is an estimate of years since the last common ancestor. Repeat across many genes to average out gene-specific variation; use Bayesian or maximum-likelihood software (BEAST, MrBayes) to propagate uncertainty.
For recent splits where ancient DNA exists, direct tip-dating uses radiocarbon ages of the fossils themselves as calibration points. This has firmed up the modern human, Neanderthal, and Denisovan split times to within a few tens of thousands of years.