Studies of chloroplast DNA (cpDNA) variation have helped to clarify phylogenetic relationships in many plant groups. However, the most common types of cpDNA data cannot be applied to parasitic plant lineages that are completely non-photosynthetic. I propose to use a new source of data, sequences of nonphotosynthetic chloroplast genes, to investigate phylogenetic relationships in a family containing photosynthetic and nonphotosynthetic forms. Scrophulariaceae and Orobanchaceae are ideal for these studies because they contain plants with a wide range of parasitic behaviors, including some that are highly destructive to important crop plants. Additionally, plants in this group display remarkable variation in cpDNA structure and gene content associated with the loss of photosynthesis. A multiple approach involving gene sequencing and cpDNA mapping will examine the molecular phylogeny of this group and fully describe its variation in cpDNA structure and gene content. The study will focus on critical "transition" genera that unify the Scrophulariaceae with the (nonphotosynthetic) Orobanchaceae, but will include species in both groups plus outgroup taxa. Significant developments that should derive from this research include: (1) Efficient molecular systematic approaches that can be used within plant families, even "troublesome" ones that include nonphotosynthetic plants. (2) Opportunities to learn much about the phylogenetic relationships and character evolution within the most economically important group of parasitic plants. (3) A much deeper understanding of the dynamics and mechanisms of cpDNA molecular variation.
