Submitted to: Molecular Phylogenetics and Evolution
Publication Type: Peer reviewed journal
Publication Acceptance Date: 3/6/2003
Publication Date: 11/1/2003
Citation: Rai, H.S., H.E. O'Brien, P.A. Reeves, R.G. Olmstead and S.W. Graham. 2003. Inference of higher-order relationships in the cycads from a large chloroplast data set. Molecular Phylogenetics and Evolution 29:350-359. Interpretive Summary: We investigated relationships among cycads, an ancient group of seed-bearing plants, by examining a large portion of the chloroplast genome from seven species chosen to exemplify our current understanding of taxonomic diversity in the order. The DNA regions that were considered span ~13.5 kb of unaligned data per taxon, and comprise a diverse range of coding sequences, introns and intergenic spacers dispersed throughout the plastid genome. Our results provide substantial support for most of the inferred backbone of cycad phylogeny, and weak evidence that the sister-group of the cycads among living seed plants is Ginkgo biloba. Cycas (representing Cycadaceae) is the sister-group of the remaining cycads; Dioon is part of the next most basal split. Two of the three commonly recognized families of cycads (Zamiaceae and Stangeriaceae) are not monophyletic; Stangeria is embedded within Zamiaceae, close to Zamia and Ceratozamia, and not closely allied to the other genus of Stangeriaceae, Bowenia. In contrast to the other seed plants, cycad chloroplast genomes share two features with Ginkgo: a reduced rate of evolution and an elevated transition:transversion ratio. We demonstrate that the latter aspect of their molecular evolution is unlikely to have affected inference of cycad relationships in the context of analyses of seed-plants.
Technical Abstract: The evolutionary relationships in many plant groups are not known. This study used a large amount of chloroplast DNA sequence data to reveal relationships in a particularily ancient order of non-flowering plants, the cycads (order Cycadales). The data provided strong support for the relationships found within the Cycadales, and suggested that Gingko biloba may be the closest extant relative of the cycads. The cycad chloroplast genome was found to be evolving much more slowly than that of flowering plants. Compared to flowering plants, cycad chloroplast DNA also exhibits a greater number of transitional changes (those that don't alter the amino acid sequence in the encoded protein) relative to transversional changes (those that do alter the amino acid sequence in the encoded protein). However, the differences in DNA evolution inferred between cycads and flowering plants were shown not to affect the estimatation of evolutionary relationships within the cycads.