be replaceable at any one time. Although the elements of the set vary from time to time and from lineage to lineage, a total of 44 amino acids are permanently unreplaceable. Moreover, the number of different amino acids that can occur at any particular variable site is very small, limited to 2–4 alternatives. The conclusion is that molecular clocks have complex features that must be ascertained before drawing out inferences about the topology and timing of historical relationships.

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