Phylogenetic inferences from chloroplast chlB gene sequences of Nephrolepis exaltata (Filicopsida), Ephedra altissima (Gnetopsida), and diverse land plants.

The chloroplast chlB gene, involved in light-independent protochlorophyllide reduction, has been reported present in algae, in one bryophyte and some gymnosperms, but absent from various angiosperms. In this study, the complete or nearly complete chlB gene sequences from the fern Nephrolepis exaltata and the seed plant Ephedra altissima were determined. Comparison of five available land plant chlB sequences with a similar set of rbcL sequences, encoding the large subunit of ribulose 1,5-bisphosphate carboxylase, showed that the chlB rate of nonsynonymous substitution was about fourfold higher than for rbcL, while the chlB phylogeny resulted in a better resolution of the clades surveyed. The presence of chlB in other lineages of land plants was determined by amplification and sequencing of a chlB internal fragment, which was recovered from all the nonangiosperm taxa surveyed except Psilotum and Gnetum. The phylogenies derived from 23 land plant chlB sequences were largely congruent with the relationships inferred from other analyses. Neighbor-joining analysis supported the view that bryophytes are paraphyletic, with mosses as sister group to vascular plants. Within lycopodiophytes, Selaginella clustered with Lycopodium, but Isoetes was located basally to the other land plants. The various ferns surveyed were found to form a coherent group which derived after horsetails and which was sister group to seed plants. Our results strongly supported monophyly of the conifers-Ginkgo-cycads clade, where conifers were sister group to Ginkgo and cycads. The various phylogenies suggested an early divergence of the seed plant lineage leading to Ephedra.