RATES AND PATTERNS OF CHLOROPLAST DNA EVOLUTION

The chloroplast genome (cpDNA) of plants has been a focus of research in plant molecular evolution and systematics. Several features of this genome have facilitated molecular evolutionary analyses. First, the g enome is small and constitutes an abundant component of cellular DNA. Second, the chloroplast genome has been extensively characterized at t he molecular level providing the basic information to support comparat ive evolutionary research. And third, rates of nucleotide substitution are relatively slow and therefore provide the appropriate window of r esolution to study plant phylogeny at deep levels of evolution. Despit e a conservative rate of evolution and a relatively stable gene conten t, comparative molecular analyses reveal complex patterns of mutationa l change. Non-coding regions of cpDNA diverge through insertion/deleti on changes that are sometimes site dependent. Coding genes exhibit dif ferent patterns of codon bias that appear to violate the equilibrium a ssumptions of some evolutionary models. Rates of molecular change ofte n vary among plant families and orders in a manner that violates the a ssumption of a simple molecular clock. Finally, protein-coding genes e xhibit patterns of amino acid Change that appear to depend on protein structure, and these patterns may reveal subtle aspects of structure/f unction relationships. Only comparative studies of molecular sequences have the resolution to reveal this underlying complexity. A complete description of the complexity of molecular change is essential to a fu ll understanding of the mechanisms of evolutionary change and in the f ormulation of realistic models of mutational processes.