Phylogenetic relationships within Luzula DC. and Juncus L. (Juncaceae): A comparison of phylogenetic signals of trnL‐trnF intergenic spacer, trnL intron and rbcL plastome sequence data

Abstract Juncus and Luzula are the largest, almost cosmopolitan, genera in the Juncaceae. Relationships within Juncus and Luzula and among other genera of Juncaceae (Distichia, Marsippospermum, Oxychloë, Patosia and Rostkovia) remain incompletely resolved. RbcL sequence data resolved a part of the supraspecific phylogeny, but many clades remain polytomic. For this reason, the non‐coding cpDNA regions, trnL intron and trnL‐trnF intergenic spacer, were sequenced. We intended to create hypotheses of relationships within Juncaceae and to test the classification of the sections, but a primary goal to this study was to assess the relationships within Juncus and Luzula and to test for monophyly of groups recognized from rbcL data (especially the monophyly of genus Luzula and the Southern Hemisphere Clade (SHC)). Furthermore, we tested the influence of different rooting and ingroup composition on the tree topology. The parsimony analyses revealed several well‐supported lineages. The traditionally distinguished genus Luzula is monophyletic and Juncus is non‐monophyletic. Two subgenera of Luzula (Pterodes and Luzula) are non‐monophyletic, while subg. Marlenia forms a sister group to the whole Luzula clade (trnL‐F data set). Within Juncus, both subgenus Juncus and subgenus Agathryon are non‐monophyletic. SHC is clustered not only with the South African J. lomatophylus and J. capensis, but also together with members of the section Juncus, Caespitosi and Graminifolii. These sections form a well‐separated sister group to the SHC. Within the genera Juncus and Luzula, monophyly is demonstrated for a number of groups (e.g., Juncus section Stygiopsis, Luzula section Luzula) but questioned for others (e.g., Juncus section Graminifolii). The unusual, separate positioning of Juncus trifidus and J. monanthos were clarified by trnL‐trnF sequence data, but vary within the tree topology depending on outgroup selection and also due to LBA phenomenon.© The Willi Hennig Society 2006.