The reconstruction of seed plant relationships is recognized as one of the most difficult problems in plant systematics. A range of studies using various lines of evidence from morphology and molecules have given different and often strongly conflicting results. It is not clear, for example, whether the Gnetales represent the extant sister group of the flowering plants (the "anthophyte hypothesis"). Recent molecular studies suggest that they are instead closely related to (or even nested within) the conifers. The root of the seed plants, and the issue of gymnosperm monophyly, are likewise unclear. Long-branch attraction appears to be a major problem in seed plant phylogenetic inference, and may be partly responsible for the strongly discordant results from different studies. We have sampled large amounts of DNA sequence data from a variety of slowly evolving chloroplast genes, across taxa that span the major lineages of the seed plants, in order to try to explore these issues. The impact of long-branch attraction and of different levels of gene and taxon sampling on seed plant phylogenetic inference will be addressed.

Key words: angiosperms, chloroplast genes, Gnetales, long-branch attraction, phylogenetics, Seed plants