Molecular clock dating

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A method that estimates when two lineages diverged by counting the sequence differences between their living descendants and converting that distance into time using a substitution rate. It is the only tool that can date events which left no rock at all, and it is the reason there is any figure for the origin of the eukaryotic cell or the split between the major animal phyla. Its weakness is structural and cannot be engineered away: the clock has no absolute scale of its own and must be calibrated against dated fossils, so it inherits every uncertainty in the fossil record it is used to correct, and substitution rates vary between genes, between lineages and over time. The consequence is a persistent and well-known disagreement — molecular estimates routinely place animal divergences tens of millions of years before the oldest accepted body fossils of those groups. Relaxed-clock models that let the rate vary along the tree narrowed the gap but did not close it, and whether the remaining difference is a real cryptic history or a systematic artefact of the method is still argued.

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