The chloroplast is an essential organelle derived from a cyanobacteria-like organism that was acquired as an endosymbiont by a remote ancestor of modern plants. The chloroplast's genome is a DNA molecule consisting of 150 kilobase pairs that encode 100 gene products. It has been completely sequenced in six very diverse plants and investigated for various purposes in several score species, yielding a tremendous wealth of information available for comparative evolutionary investigations. Clegg and his colleagues, in Chapter 11, uncover a complex evolutionary pattern. Some noncoding regions include hot spots for insertions and deletions and exhibit complex recombinational features. Selective drives in codon utilization have changed over evolutionary time. Patterns of amino acid replacements reflect functional constraints imposed by natural selection on protein configuration. Rates of evolution are quite variable from one order to another, although much of the variation can be accounted for by differences in generation time.
The constancy of evolutionary rates is the subject of Chapter 12. The Cu, Zn superoxide dismutase (SOD) seems to behave like a very erratic clock: the rate of amino acid replacement is 5 times faster among mammals than between fungi and animals. Walter M. Fitch and Francisco J. Ayala (19) analyze the amino acid sequences of several score species and show that SOD behaves like a fairly accurate clock by assuming a complex pattern in which different sets of amino acids have different probabilities of change that are nevertheless constant through time. The model for constancy requires that a set of only 28 amino acids
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.