Previous studies of chloroplast DNA variation in the Asteraceae have resolved many systematic issues at higher taxonomic levels. However, major problems persist in resolving tribal relationships and the monophyly of the subfamily Lactucoideae. An expanded examination of chloroplast DNA variation in the Asteraceae is proposed using comparative restriction site mapping of 10 enzymes and DNA sequencing of two genes (rpoC2 and ndhF) from representative species in all currently recognized tribes in the family. These new data will be combined with those from previous chloroplast DNA studies to address both phylogenetic and molecular evolutionary questions. Integration of molecular and morphological data will produce a comprehensive phylogeny and classification of the Asteraceae. Fine scale restriction site and gene mapping will enable the first direct comparisons of the phylogenetic utility of restriction site mutations in coding and noncoding regions of the chloroplast genome. Similarly, the availability of DNA sequences of three genes (rbcL, rpoC2, ndhF) will provide much needed comparisons of the usefulness of different chloroplast genes for phylogenetic studies in angiosperms. Statistical analyses of restriction site and sequence data will be used to examine the patterns and rates of sequence evolution in the chloroplast genome. Identification of heterogeneity in the location of restriction site mutations will provide valuable information for character analysis in future molecular systematic studies in the Asteraceae and other angiosperm families. Furthermore, new insights will be gained into the rates and patterns of nucleotide substitutions within and between coding and noncoding sequences from three chloroplast genes with different functions and locations in the chloroplast genome.
