Potential of the 5′ and 3′ Ends of the Intergenic Spacer (IGS) of rDNA in the Cyperaceae: New Sequences for Lower‐Level Phylogenies in Sedges with an Example from <i>Uncinia</i> Pers.

In plants, the internal transcribed spacers (ITS; ca. 450 base pairs) of nuclear ribosomal DNA (rDNA) are the only well‐characterized nuclear sequences that are both easily amplified and appropriately variable for addressing relationships at lower taxonomic levels. In this study, we assess the utility of rDNA noncoding fragments from the external transcribed spacer 1 (ETS 1f) and from the 5′ end of the intergenic spacer ($$^{5^{\prime }}\mathrm{IGSf}\,$$) for reconstructing lower‐level relationships in the Cyperaceae. Phylogenetic analyses using the genus Uncinia (tribe Cariceae) as a model indicate that phylogenies inferred from ETS 1f and $$^{5^{\prime }}\mathrm{IGSf}\,$$ sequences are congruent with those derived from ITS. Although ITS and ETS 1f sequences evolve at similar rates, $$^{5^{\prime }}\mathrm{IGSf}\,$$ sequences evolve ca. 1.3 times faster. The combined analysis of all three regions (ca. 1414 bp) produced 3.6 times more informative characters than ITS and greater than 40 times more than trnT‐L and trnL‐F spacer data. Trees derived from combined analyses were the most robust and resolved. Infraspecific variation in the ETS 1f (0.0%–0.17%) and $$^{5^{\prime }}\mathrm{IGSf}\,$$ (0.0%) was extremely low, indicating that variation within species will not be a problem for phylogenetic analysis. Amplification experiments indicate that ETS 1f primers are universal for the Cyperaceae (ca. 5000 spp.) and Juncaceae (ca. 300 spp.), while $$^{5^{\prime }}\mathrm{IGSf}\,$$ primers are limited to tribe Cariceae (ca. 2300 spp.). Phylogenetic analyses suggest that sections Uncinia and Platyandrae are monophyletic but that series circumscriptions are largely artificial. A significant topological difference with key taxonomic and biogeographical implications between ITS and combined analyses stresses the importance of using all three noncoding regions to infer lower‐level phylogenies.