The goals of this study were to elucidate phylogenetic relationships in Eleocharis (Cyperaceae) using the nuclear ribosomal internal transcribed spacer (ITS) region, and compare this phylogeny with three infrageneric classifications. Thirty Eleocharis species and eight outgroups were analyzed using maximum parsimony and maximum likelihood analyses. These analyses place Websteria within the Eleocharis clade. The sister group of Eleocharis has traditionally been inferred to be either members of the Abildgaardieae or Scirpeae. Theses analyses do not show strong support for Bulbostylis (Abildgaardieae) or Schoenoplectus (Scirpeae) as the sister lineage to Eleocharis. The ITS results are not entirely congruent with any of the classifications. There is support for a monophyletic Eleocharis subgenus Limnochloa and subgenus Zinserlingia sensu Gonzalez-Elizondo and Peterson, but many of the subdivisions of Eleocharis subgenus Eleocharis are para- or polyphyletic. Morphological characters inferred to have multiple origins by the TTS data, and qualitative traits such as texture, shape and color of nuts and scales, and share and texture of sheath apices have been used to define classification units in Eleocharis and this appears to have played a major role in the confusion surrounding relationships in the genus.
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