Recent work addressing the phylogeny of the extant conifers has yielded sharply conflicting views. For example, several studies have provided robust support for a sister-group relationship between Gnetales and Pinaceae, while others indicate that the extant conifers are monophyletic. To address these conflicts and clarify conifer relationships we sequenced a large portion of the plastid genome (spanning 15-17 conservative genes) from numerous seed plants, including 18 exemplar conifer taxa. The genes examined represent ca. one-ninth of the conifer plastid genome. Most analyses using different optimality criteria and data partitions produced similar results. These were are all largely congruent with the relationships proposed in a conifer-wide study by Stefanovic et al (1998) using 26S rDNA data, and the study of Cupressaceae s.l. by Gadek et al. (2000) using combined matK + rbcL sequences. We observed strong bootstrap support across almost all of our plastid-based phylogeny. These results suggest that the current level of character sampling is sufficient to reliably recover most aspects of higher-order relationship among the extant conifers. An unusual expansion in the open reading frame of one of the genes provides a structural synapomorphy linking Araucariaceae and Podocarpaceae. The conifers are consistently shown to be monophyletic among living seed plants, with Pinaceae indicated as the sister group of the other conifers, and with Araucariaceae-Podocarpaceae as the sister group of (Sciadopityaceae + Taxaceae + Cephalotaxaceae + Cupressaceae s.l.). The family Sciadopityaceae is the sister-group of the remaining taxa in the latter clade. Our results also suggest that the "Gnepine hypothesis" found in several recent molecular studies is a severe long-branch artifact that may be partly ameliorated by a sufficiently dense taxon sampling within the conifers. The likely parallel dissolution of several chloroplast NADH dehydrogenase genes in Pinaceae and Gnetales is also discussed.

Key words: Araucariaceae, Chloroplast, deep phylogeny, Gnepine, ndh genes, Podocarpaceae