Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data.

Trees inferred from DNA sequence data provide only limited insight into the phylogeny of seed plants because the living lineages (cycads, Ginkgo, conifers, gnetophytes, and angiosperms) represent fewer than half of the major lineages that have been detected in the fossil record. Nevertheless, phylogenetic trees of living seed plants inferred from sequence data can provide a test of relationships inferred in analyses that include fossils. So far, however, significant uncertainty persists because nucleotide data support several conflicting hypotheses. It is likely that improved sampling of gymnosperm diversity in nucleotide data sets will help alleviate some of the analytical issues encountered in the estimation of seed plant phylogeny, providing a more definitive test of morphological trees. Still, rigorous morphological analyses will be required to answer certain fundamental questions, such as the identity of the angiosperm sister group and the rooting of crown seed plants. Moreover, it will be important to identify approaches for incorporating insights from data that may be accurate but less likely than sequence data to generate results supported by high bootstrap values. How best to weigh evidence and distinguish among hypotheses when some types of data give high support values and others do not remains an important problem.