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Problem : What types of molecules make good molecular clocks?

Molecules that are present in a wide variety of organisms and that are under severe functional constraints make good molecular clocks.

Problem : Describe the hypothesis of neutral evolution.

This hypothesis states that most of the variability in molecular structure does not affect the molecule's functionality. Most of the variability occurs outside of the functional regions (regions that give a molecule its function) of the molecule. Changes that do not affect functionality (neutral substitutions) are not affected by natural selection. As a result, neutral substitutions occur at a regular rate through time.

Problem : How can the relatedness of two species be determined using a molecular clock?

Once a good molecular clock is identified. The sequences of the molecule in the different species must be compared. From this comparison we find the number of amino acid or nucleic acid bases that differ between the species. This number is then plotted against the rate at which the molecule is known to undergo neutral substitutions to determine the point at which two species last shared a common ancestor.

Problem : Why is a neutral substitution not acted on by natural selection.

A neutral substitution does not change the functionality of the molecule. Therefore, it does not change the fitness conveyed by that molecule.
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