The molecular clock has limited usefulness for estimating divergence times among species in part due to the saturation of dna sequences. this occurs because

a. dna sequences are unable to revert back to previous allelic states.
b. the variation in the substitution rate between closely related lineages prevents accurate estimation of divergence time.
c. variation in population sizes among lineages changes the effect of genetic drift.
d. in highly diverged lineages, substitutions will occur at sites that have been substituted previously

In highly diverged lineages, the substitutions process will occur at sites that have been substituted previously.

Explanation:

Molecular clock uses the mutation rate to reduce the time in prehistory when the life forms are diverged. The molecular clock uses the sequence of amino acids and nucleotide sequence for the DNA.  

This clock does not measure any time but the number of mutations, and other changes over certain time.  Sometimes its useful property might be limited due to the highly diverged lineages.

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