Phylogenetic Relationships in Ephedra (Gnetales): Evidence from Nuclear and Chloroplast DNA Sequence Data

Sequences from the nuclear ribosomal internal transcribed spacer region 1 (nrDNA ITS1) and the plastid rps4 gene from the genus Ephedra (Ephedraceae, Gnetales) were obtained in order to infer phylogenetic relationships, character evolution, and historical biogeography in the genus. Within Ephedra the length of the nrDNA ITS1 varied from 1,081 to 1,143 basepairs (bp), in contrast to dramatically shorter lengths in the outgroups (Gnetum, Welwitschia, and Pinus). The rps4 locus varied in length from 645 to 661 bp in the same set of taxa. Both parsimony and maximum likelihood analyses of these sequences resulted in a well-resolved phylogeny that supports the monophyly of Ephedra, but not its subdivision into the traditional sections Ephedra, Asarca, and Alatae. The resulting phylogeny also indicates a derivation of the New World clade from among the Old World taxa. Among the Old World species three highly-supported monophyletic groups are recognized that are highly concordant with morphological evidence. The New World clade includes two main subclades of North and South American species that are strongly supported, while the position of two, mostly Mexican species E. pedunculata and E. compacta remains unresolved. Character reconstruction of ovulate strobilus types in Ephedra indicates that fleshy bracts are ancestral, with shifts to dry, winged bracts having occurred multiple times. Low levels of sequence divergence within the North American clade suggest either recent and rapid ecological radiation or highly conservative ribosomal DNA evolution within the clade. Ephedra L., the single genus of the family Ephedraceae (Gnetales), is a well-delimited genus of ca. 60 species that are distributed in deserts and other arid regions in both the Old and the New Worlds. Its unique combination of morphological and biochemical characters includes small, decussate or whorled, ephemeral leaves on photosynthetic stems (Kubitzki 1990), vessels and dimorphic tracheary elements (Carlquist 1996), ribbed pollen (Steeves and Barghoorn 1959), ovules with a single integument subtended by a pair of fleshy or wing-like bracts, and the presence of ephedrine and other alkaloids (Stapf 1889; Martens 1971; Takaso 1984; Caveney et al. 2001). The genus has generally been considered monophyletic (Price 1996; Huang 2000; Rydin et al. 2002), although this has not been tested rigorously. Chromosome numbers indicate a base number of x 5 7, with evidence of polyploidy and interspecific hybridization in both Old World and New World forms (Hunziker 1953; Pachomova 1971;