The cycads have a central place in our understanding of the phylogenetic relationships of the seed plants. Their circumscription into two suborders (Zamiineae and the monofamilial Cycadineae) is supported by various molecular studies and is further confirmed here. We investigated higher-order relationships by sampling a large portion of the chloroplast genome for Bowenia, Cycas, Ceratozamia, Dioon, Encephalartos, Stangeria and Zamia, representing all the families, subfamilies and tribes in Stevenson’s (1992) treatment of the cycads. We obtained ~13.5 kb (unaligned) of DNA sequence data per taxon, spanning a diverse range of coding sequences, introns and intergenic spacers dispersed throughout the chloroplast genome. Our results are largely congruent with published molecular studies, and provide substantial support for most of the inferred backbone of cycad phylogeny. Dioon is strongly supported as the sistergroup of the remaining members of Zamiineae. Our findings also support the novel arrangement of Stangeria with subfamily Zamioideae (represented here by Zamia and Ceratozamia), as was recently noted by Bogner and Francisco-Ortega. The precise placement of Bowenia was not fully resolved, but its membership in Stangeriaceae was strongly rejected. In contrast to the other seed plants, cycad chloroplast genomes share two features of their molecular evolution with Ginkgo – a slower rate of evolution and an apparently elevated transition: transversion ratio. The question of cycad placement within the seed plants remains unresolved, and analyses based on different gene samplings, taxon samplings and phylogenetic optimality criteria provide different arrangements of the five living spermatophyte groups. Split-decomposition analysis suggests that there is conflicting signal in the seed-plant data, possibly a function of long-branch distortion. This conflict appears to be reduced by improving the taxon sampling. None of our analyses support a sistergroup relationship between Ginkgo and the cycads, but this possibility could not be rejected using parsimony-based parametric bootstrapping.

Key words: Bowenia, chloroplast phylogeny, Cycads, Ginkgo, SOWH test, Stangeria