The Journal of Heredity 1986:77(4):226-235
© 1986 The American Genetic Association 77:226-235
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On the virtues and pitfalls of the molecular evolutionary clock
Dr. Ayala is professor of genetics, University of California, Davis, CA 95616. This lecture was delivered at the annual meeting of the Genetics Society of America, in Boston, on August 13, 1985. It is the twentieth in the series of Key lectures that was established by the American Genetic Association through funds bequeathed to the Association by Dr. Wilhelmine E. Key for the support of lectures in genetics. The author is very thankful to Drs. William A. Clemens, Walter M. Fitch, Richard Grantham, and Richard Holmquist for advice and discussions; to Dr. Alvaro Puga for providing his unpublished sequence of the cDNA for rat SOD; to Drs. Holmquist and Wilfried W. de Jong for copies of their manuscripts in press; and to Dr. Fitch for the amino acid differences between cytochrome c sequences. The efforts of Dr. Young Moo Lee who, with the collaboration of Mr. David J. Friedman, obtained in my laboratory the Drosophila melanogaster SOD sequence, deserve special mention as well as my appreciation
Abstract
"Informational" macromolecules—I.e., proteins and nucleic acids—have in their sequences a register of evolutionary history. Zuckerkandi and Pauling suggested in 1965 that these molecules might provide a "molecular clock" of evolution. The molecular clock would time evolutionary events and make it possible to reconstruct phylogenetic history—the branching relationships among lineages leading to modem species. Kimura's neutrality theory postulates that rates of molecular evolution are stochastically constant and, hence, that there is a molecular clock. A variety of tests have shown that molecular evolution does not behave like a stochastic clock. The variance in evolutionary rates is much too large and thus inconsistent with the neutrality theory. This, however, does not invalidate the clock, but rather leaves it without a theoretical foundation to anticipate its properties. Sequence comparisons show that molecular evolution is sufficiently regular to serve in many situations as a clock, but uncertainty concerning the properties of the clock (for example, about the circumstances that may yield large oscillations in substitution rates from time to time or from lineage to lineage) demands that it be used with caution. Few DNA or protein sequences are known from organisms that range from closely related, e.g., different mammals, to very remote, e.g., mammals and fungi. One example is cytochrome c, which has an acceptable clockwise behavior over the whole span, in spite of some irregularities. Another example is the copper-zinc superoxide dismutase (SOD), which behaves like a very erratic clock. The SOD average rate of amino acid substitution per 100 residues per 100 million years (MY) is 5.5 when fungi and animals are compared, 9.1 when comparisons are made between insects and mammals, and 27.8 when mammals are compared with each other. The question is which mode is more common over broad evolutionary spans: the regularity of cytochrome c or the capriciousness of SOD? Additional data sets will be required in order to obtain the answer and to develop expectations about the accuracy of the clock in particular instances. Untill such data exist, conclusions solely based on the molecular clock are potentially fraught with error.
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