Molecular clock

A molecular clock is a set of methods for inferring evolutionary timescales from changes in DNA, RNA or protein sequences. In its simplest form, the approach assumes that molecular substitutions accumulate at a constant rate. If two lineages have accumulated a measurable number of sequence differences, that amount can be related to elapsed time when the rate is known or estimated. In practice, observed sequence differences are not a direct stopwatch: they require evolutionary models and a phylogenetic framework, and genetic change can occur at different rates in different lineages.

Genetic data can indicate that one divergence is older or younger than another, but by themselves generally do not provide dates in calendar years. To estimate absolute ages, analyses need calibrations: independent time information associated with points in the evolutionary tree. Fossils are a widely used source, while ancient DNA or samples and carefully justified geological or climatic events may also inform dates. Calibration choices matter; fossils must be assigned appropriately within the tree, and geological-event calibrations require assumptions connecting the event with evolutionary divergence.

The strict or global clock model assumes a common evolutionary rate across lineages. Evolutionary rates can differ, so applying one constant rate indiscriminately can distort divergence estimates. Relaxed-clock methods allow rates to vary among branches, under alternative statistical assumptions. Some models allow nearby lineages to have related rates, while uncorrelated models treat branch rates differently. These approaches help represent biological variation, but they cannot simply infer time from sequence change without constraints: a long branch may reflect faster evolution, more elapsed time, or both.

Molecular-clock analyses are used to estimate when lineages diverged, investigate population histories and study the timing of evolutionary events. They have been applied to questions ranging from species diversification to the history of pathogens. Estimates should be interpreted as model-based results rather than exact timestamps. Their uncertainty can reflect sequence sampling, the evolutionary model, tree structure, rate variation and the quality and placement of calibrations. Biogeographic calibrations can be particularly problematic when the evolutionary event being dated is also used to test the effect of the same geological or climatic event, creating potential circularity.