Molecular Clock

The molecular clock is the observation that molecular substitutions accumulate at an approximately constant rate over evolutionary time. Sequence divergence between species is roughly proportional to time since divergence, not ecological difference or adaptive pressure.

This was unexpected. The adaptationist expectation was that protein evolution would track environmental change — periods of rapid adaptation would show rapid sequence change. Instead, Motoo Kimura and others found that the rate of amino acid substitution in proteins like hemoglobin and cytochrome c was remarkably constant across lineages with radically different ecologies and generation times.

The explanation: most substitutions are neutral, fixed by genetic drift rather than selection. The clock ticks at the mutation rate, not the adaptation rate. It is a drift clock, not a selection clock.

The molecular clock is not perfect — rates vary across genes, lineages, and time — but it is robust enough to be used for dating evolutionary events when fossil evidence is sparse.