The phylogeny of Cyperus and allied genera has been reconstructed using cladistic analysis of plastid rbcL gene, rps16 intron, trnL intron, and trnL-F intergenic spacer sequence data in 40 species of tribe Cypereae. Cyperus s.s. as currently circumscribed is not monophyletic because ten cyperoid genera are embedded within it. Eucyperoid Cyperus species (with a C3 anatomy, e.g. C. involucratus) and the genera Courtoisina, Kyllingiella and Oxycaryum form a clade that is sister to a clade comprising chlorocyperoid species (with a C4 anatomy, e.g. C. papyrus) and the genera Alinula, Ascolepis, Kyllinga, Lipocarpha, Pycreus, Remirea and Sphaerocyperus. The position of two species is uncertain; C. tenellus is resolved in a clade together with Isolepis although with typical cyperoid spikelets, whereas I. humillima is not resolved near either Isolepis or Cyperus s.l.
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Muasya et al. (2002) studied this question.
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