Because the photosynthetic machinery requires many more gene functions than are specified on the cpDNA of plants and algae, it is assumed that many gene functions were transferred to the eukaryotic nuclear genome. The strong conservation of cpDNA gene content cited above indicates that most transfers of gene function from the chloroplast to the nuclear genome occurred early following the primordial endosymbiotic event. Among land plants, gene content is almost perfectly conserved, although a few recent transfers of function from the chloroplast to the nuclear genome have been demonstrated (Downie and Palmer 1991; Gantt et al., 1991).
Conservation of gene content and a relatively slow rate of nucleotide substitution in protein-coding genes has made the chloroplast genome an ideal focus for studies of plant evolutionary history (reviewed in Clegg, 1993). These efforts have culminated in the past year with the publication of a volume of papers that presents a detailed molecular phylogeny for seed plants (Chase et al., 1993). This effort has involved many laboratories that have together determined the DNA sequence for more than 750 copies (by latest count) of the cpDNA gene rbcL encoding the large subunit of ribulose-1,5-bisphosphate carboxylase (RuBisCo). The sequence data span the full range of plant diversity from algae to flowering plants. This very large collection of gene sequence data has allowed the reconstruction of plant evolutionary history at a level of detail that is unprecedented in molecular systematics.
Accurate phylogenies are of more than academic interest. They provide an organizing framework for addressing a host of other important questions about biological change. For example, questions about the origins of major morphological adaptions must be placed in a phylogenetic context to reconstruct the precise sequence of genetic (and molecular) changes that give rise to novel structures. The mutational processes that subsume biological change can be revealed in great detail through a phylogenetic analysis. And, questions about the frequency and mode of horizontal transfer of mobile genetic elements can only be addressed in a phylogenetic context. One can make a very long list of biological problems that are illuminated by phylogenetic analyses.
Despite their obvious utility, many important questions remain about the accuracy of molecular phylogenies. All methods of phylogenetic reconstruction assume a fairly high degree of statistical regularity in the underlying mutational dynamics. Our goal in this article is to analyze the tempo and mode of cpDNA evolution in greater depth. We will show that below the surface impression of conservation there are a variety of mutational processes that often violate assumptions of rate constancy and site independence of mutational change. To facilitate an analysis of patterns of cpDNA mutational change, we divide the