Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers

Phylogenetic relationships among the five groups of extant seed plants are presently quite unclear. For example, morphological studies consistently id entify the Gnetales as the extant sister group to angiosperms (the so-calle d "anthophyte" hypothesis), whereas a number of molecular studies recover g ymnosperm monophyly, and few agree with the morphology-based placement of G netales. To better resolve these and other unsettled issues, we have genera ted a new molecular data set of mitochondrial small subunit rRNA sequences, and have analyzed these data together with comparable data sets for the nu clear small subunit rRNA gene and the chloroplast rbcL gene. All nuclear an alyses strongly ally Gnetales with a monophyletic conifers, whereas all mit ochondrial analyses and those chloroplast analyses that take into account s aturation of third-codon position transitions actually place Gnetales withi n conifers, as the sister group to the Pinaceae, Combined analyses of all t hree genes strongly support this latter relationship, which to our knowledg e has never been suggested before, The combined analyses also strongly supp ort monophyly of extant gymnosperms, with cycads identified as the basal-mo st group of gymnosperms, Ginkgo as the next basal, and all conifers except for Pinaceae as sister to the Gnetales + Pinaceae clade. According to these findings, the Gnetales may be viewed as extremely divergent conifers, and the many morphological similarities between angiosperms and Gnetales (e.g., double fertilization and flower-like reproductive structures) arose indepe ndently.