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According to the mathematics of drift, when comparing divergent populations, most of the single-nucleotide differences can be assumed to have accumulated at the same rate as individuals with mutations are born.
This latter rate, it has been argued, is predictable from the error rate of the enzymes that carry out DNA replication ; these enzymes have been well studied and are highly conserved across all species.
Thus the neutral theory provides a rationale for the molecular clock, although the discovery of a molecular clock predates neutral theory.
The observed overdispersion of the molecular clock is not predicted by or compatible with neutral theory.

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