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comparable to missense rates for a number of protein-coding genes. These results illustrate that evolutionary rates within group II introns vary and appear to be related to the functional importance of intron structural features.
The uniformitarian assumption plays a fundamental role in the science of molecular evolution, just as it did in the evolutionary paleontology of G. G. Simpson. We must assume that the kinds of mutational changes that we can demonstrate in ''microscopic detail" from comparative sequence analyses are the substance of molecular evolutionary change. When viewed in detail, the patterns of mutational change in the chloroplast genome are complex, and they belie the notion that the cpDNA is a staid and conservative molecule.
The use of cpDNA RELPs and cpDNA gene sequence data for phylogenetic inference has had an enormous impact on studies of plant phylogenetics and systematics. This has been facilitated by the belief that cpDNA-based mutational change is regular. By and large, the assumption of statistical regularity is adequate, and cpDNA data are an important addition to the previous evidence available to students of plant evolution. Nevertheless, it is important to investigate the ways that mutational change in this genome departs from the kinds of regularity assumed by most methods of phylogenetic inference. When this question is asked, we find that noncoding regions exhibit a number of mutational mechanisms. Some sites are clearly labile to small indel mutations, and in at least one case, large deletions also appear to be site dependent. Complex recombinational processes are also found to influence the evolution of at least some noncoding regions of cpDNA. Group II introns show a strong relationship between structure and probability of mutational change. Analyses of protein-coding genes also reveal complex patterns of mutational change. Finally, rates of nucleotide substitution are quite variable at the level of order and above. Current data suggest that much of the variation in evolutionary rate can be accounted for by the generation-time effect hypothesis, although this requires further investigation. There are also interesting patterns of codon bias. When land plant and algal genes are compared, it is evident that patterns of selection for codon utilization have changed over evolutionary time and that models that assume equilibrium nucleotide frequencies are likely to be violated. Patterns of amino acid replacement in the rbcL gene also reveal substantial variation in site-dependent probabilities of substitution. Taken in toto, these complexities in mutational change should motivate the development of more realistic algo-