Chloroplast 16S rDNA Sequences and Phylogenetic Relationships of Fern Allies and Ferns

Abstract

Chloroplast 16S rDNA sequences from the charophyte algae Spirogyra and Coleo- chaete; the bryophytes Marchantia and Sphagnum; the allies Equisetum, Isoetes, Selaginella, Lycopodium, Tmesipteris and Psilotum; the eusporangiate ferns Angiopteris, Botrychium, and Ophioglossum; the leptosporangiate ferns Lydogium and Doodia; the gymnosperms Ephedra and Juniperus; and six angiosperms (two monocots and four dicots) were analyzed with the parsimony algorithm PAUP to infer phylogenetic relationships. The charophytes were the designated out- group and the bryophytes were at the base of the land plant clade. Relationships of most of the allies and Angiopteris were unresolved but a clade containing Psilotum + Tmesipteris (Psi- lotales) was sister to a clade composed of Botrychium and Ophioglossum (Ophioglossales). A leptosporangiate clade was strongly supported, and this clade grouped weakly with Angiop- teris. The Selaginella 16S rDNA sequence is apparently changing at a faster rate than the other sequences as evidenced by the extremely long branch associated with Selaginella. The effect of this long branch on the overall tree topology was tested by removing Selaginella from a subsequent analysis. Trees produced without Selaginella weakly supported the placement of Lycopodium at the base of the vascular plants clade but Isoetes grouped weakly with the seed plants. Removal of Selaginella also resulted in higher bootstrap values and decay indices for the majority of the clades. The determination of phylogenetic relationships of the fern allies, the Psi- lophyta, Lycophyta, and Sphenophyta, has proven to be elusive. Taxonomi- cally, the allies are generally considered to be positioned between the bryophytes and ferns but formal analyses of morphological and molecular data sets only partially resolve their relationships. In a cladistic analysis of mor- phological characters, Bremer et al. (1987) placed Psilotum at the base of vas- cular plants, the lycopsids branched off next, then Equisetum, and then the ferns. However, the portion of the clade containing the allies was con- structed with only four morphological characters and it is not reasonable to expect that a robust phylogeny containing highly divergent taxa can be pro- duced from such a small data set. Conversely, fossil evidence (Knoll and Roth- well, 1981; Stewart, 1983; Gensel and Andrews, 1984), characters relating to male gametogenesis (Garbary et. al., 1993), and chloroplast genome structures (Raubeson and Jansen, 1992) support the hypothesis that the lycophytes are at the base of the vascular land plant clade. Mishler et al. (1994) analyzed green plant molecular and morphological data sets separately and together, using parsimony algorithms. Some vascular land plants were included, with the allies represented by Equisetum, Lycopo- dium, Lycopodiella, and Selaginella. The analysis of general morphological characters placed the lycophytes sister to a clade containing Equisetum, ferns,