The application of molecular methods to the study of plant evolution has provided a wealth of new information on evolutionary relationships. Most of this information has come from restriction site analyses of plant chloroplast DNAs (cpDNA). Direct sequence comparisons of cpDNA genes greatly extends the phylogenetic range of molecular analyses, while at the same time, revealing much about the processes of mutational change. We propose to continue our studies of cpDNA sequence evolution and to contrast patterns of cpDNA evolution to nuclear gene evolution. A major focus of our work is on rates of molecular evolution. We intend to continue our study on differential rates of evolution for chloroplast genes and to contrast cpDNA rates to nuclear gene rates in selected plant lineages. We also intend to expand our study of mutational """"""""hot spots"""""""" for addition/deletion change noncoding regions of cpDNA. We will use cpDNA sequence data to resolve questions about the origins and relationships of the monocot class. We have recently succeeded in sequencing part of a cpDNA gene from a miocene-aged leaf compression fossil, and we propose an expanded study of ancient DNA in plant species. Finally, we plan to characterize levels of nuclear gene diversity in pearl millet and to study the processes that generate and maintain molecular diversity.
