This technique is based on Allan Wilson and Vince Sarich's observation that rare spontaneous errors in DNA replication cause the mutations that drive molecular evolution, and that the accumulation of evolutionarily "neutral" differences between two sequences could be used to measure time, if the error rate of DNA replication could be calibrated. One method of calibrating the error rate was to use as references pairs of groups of living species whose date of speciation was already known from the fossil record.
Originally, it was assumed that the DNA replication error rate was constant--not just over time, but across all species and every part of a genome that you might want to compare. Because the enzymes that replicate DNA differ only very slightly between species, the assumption seemed reasonable a priori.
As molecular evidence has accumulated, the constant-rate assumption has proven false--or at least overly general. Molecular clock users are developing workaround solutions using a number of statistical approaches including maximum likelihood techniques.
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