Donoghue DEB 9806937 Major evolutionary questions concerning the root of the phylogenetic tree of seed plants, of flowering plants, and a major lineage within flowering plants (the eudicots) have received considerable attention from evolutionary biologists, but have resisted convincing resolution. New approaches are, therefore, needed. The PIs propose a new strategy in which they will analyze a series of gene duplications in the phytochrome family of nuclear genes from members of each group to help solve this problem. Duplicate gene rooting relies on simultaneous phylogenetic analysis of genes that resulted from a gene duplication event that occurred along the branch subtending the plant group of interest. This procedure yields an unrooted gene network wherein two gene trees should be connected by a single branch, and the best rooted species tree is the one that is congruent with the two gene trees when the network is rooted along the connecting branch. Phytochrome genes are particularly well-suited for this approach because major duplications in the gene family apparently have occurred along the branches leading to each of the three main plant groups that we are interested in. Moreover, our preliminary analyses reveal a high level of agreement among duplicate gene trees, ample nucleotide variation, and considerable support for a number of critical branching events. We therefore are confident that this approach will provide insight into early branching events for each of the phylogenies in question. Additionally, these studies will elucidate the evolution of the phytochrome gene family in plants, and will highlight and elaborate the duplicate gene rooting procedure, which we hope will be of use in solving other difficult rooting problems.
