Molecular clock

A molecular clock relates accumulated nucleotide substitutions to elapsed evolutionary time through an assumed rate. Two lineages evolving at the same constant rate $r$ for time $T$ have total expected substitution count $2rT$ per site before accounting for repeated changes obscured in endpoint sequences. Rate variation among sites or branches requires a more general clock model.

Use of dated fossil evidence to constrain evolutionary times. Geological age, phylogenetic placement, stem versus crown assignment and uncertainty all affect the constraint.

A calibration constraint allowing a small nonzero probability outside its principal range. It represents uncertainty but still needs biologically defensible tail probabilities.

A calibration constraint assigning zero probability to ages beyond a specified limit. Sequence data cannot overcome an excluded age under that prior.

A model allowing evolutionary rates to vary among branches. The distribution and dependence of rates affect inferred times and must be distinguished from absolute-time calibration.

A model assigning the same evolutionary rate to the relevant branches. Expected branch length is rate multiplied by duration; scaling times and inverse-scaling the rate preserves the sequence likelihood.