Relationships among the extant seed plants, angiosperms, conifers, cycads, ginkgos, and Gnetales, remain controversial. Recent molecular analyses refute the anthophyte hypothesis, which unites Gnetales and angiosperms, but disagree with respect to an alternative hypothesis. Different molecular trees suggest that Gnetales are sister to Pinaceae, to conifers, or to all other seed plants. These analyses are complicated by ancient divergence, variation in substitution rates among lineages, and extinctions. We analyzed a nine-locus dataset from 25 seed plants to infer relationships and to test for bias. The dataset included published sequences from the nuclear, chloroplast, and mitochondrial genomes and some unpublished phytochrome B sequences. Bayesian and parsimony analyses strongly support the gnepine hyothesis, in which Gnetales and Pinaceae are sister taxa. Moreover, Templeton tests reject the anthophyte hypothesis and the gnetifer hypothesis, in which Pinaceae are sister to conifers. However, results from parametric bootstrapping indicate bias in the data toward the gnepine tree. When mitochondrial atpA and plastid psaA are simulated on a gnetifer tree, analyses of the data infer gnepine trees. When these data are excluded from analyses, a gnetifer tree is inferred. Triplet likelihood ratio tests provide evidence that organellar sequences from Gnetales are evolving significantly faster than those from other seed plants, suggesting that bias toward the gnepine hypothesis might result from the very long branches to Gnetales. To test this, we used a maximum likelihood approach to identify the most rapidly evolving nucleotide sites and then excluded or down-weighted them in subsequent analyses. These analyses support the gnetifer hypothesis. Our results suggest that resolving deep divergences throughout the tree of life will require more than additional data from the rapidly expanding databases. Rather, they emphasize the need for careful analyses of the data to identify potential sources of conflict and bias.

Key words: Bayesian analyses, multigene dataset, parsimony, relative evolutionary rates, seed plant phylogeny, tests for bias