Molecular clocks can be useful for dating evolutionary events like the separation of humans and chimpanzees. However, because the rates of molecular clocks vary from gene to gene, clock data should be interpreted cautiously. These rate differences can be attributed largely to differences in intensity of negative selection (which results in the elimination of harmful mutations) among different genes. The slowest molecular clock on record belongs to the histone genes, which encode the proteins around which DNA is wrapped to form chromatin (Chapters 3 and 13). These proteins are exceptionally similar in all organisms; only 2 amino acids (in a chain of about 100) distinguish plant and animal histones. Plants and animals last shared a common ancestor more than 1 billion years ago, which means, because each evolutionary lineage is separate, that there have been at least 2 billion years of evolution since they were in genetic contact. And yet the histones have hardly changed at all. Almost any amino acid change fatally disrupts the histone protein, preventing it from carrying out its proper function. Negative selection has thus been extremely effective in eliminating just about every amino acid–changing histone mutation over 2 billion years of evolution. The histone molecular clock is breathtakingly slow.

441

Other proteins are less subject to such rigorous negative selection. Occasional mutations may therefore become fixed, either through drift (if they are neutral) or selection (if beneficial). The extreme case of a fast molecular clock is that derived from a pseudogene, a gene that is no longer functional. Because all mutations in a pseudogene are by definition neutral—there is no function for a mutation to disrupt, so a mutation is neither deleterious nor beneficial—we expect to see a pseudogene’s molecular clock tick at a very fast rate. In the histone genes, virtually all mutations are selected against, constraining the rate of evolution; in pseudogenes, none is. Fig. 21.15 shows the varying rates of the molecular clock for different genes.

In the next chapter, we examine how genetic divergence between populations can lead to the evolution of new species.