Seed Plant Relationships and the Systematic Position of Gnetales Based on Nuclear and Chloroplast DNA: Conflicting Data, Rooting Problems, and the Monophyly of Conifers

We investigated the systematic position of Gnetales and other seed plant groups using molecular data from 119 land plant species. More than 100 new sequences of rbcL, atpB, 26S, and 18S ribosomal DNA were analyzed together with available GenBank sequences. To evaluate thoroughly the phylogenetic information of each gene, the four data sets were analyzed both separately and combined using different character coding. We found no supported conflict between codon positions in the plastid sequences, but we found a more complex pattern, indicating conflict between transitions and transversions, within each position. Including all information, plastid data results in a “Gnetales basal” phylogeny, whereas nuclear data weakly supports anthophytes. When transitions are excluded, Gnetales associate with conifers. Our study does not answer all questions on seed plant phylogeny, but it does show conifers as monophyletic with high support, rejecting a close relationship between Gnetales and the conifer family Pinaceae. Nuclear and chloroplast data produced essentially identical phylogenies except for the position of the seed plant root, and a sister relationship between Gnetales and angiosperms could not be fully ruled out. These results strongly conflict with previously published analyses of mitochondrial data.