Phylogenetic relationships in the Juncaceae inferred from nuclear ribosomal DNA internal transcribed spacer sequence data

The Juncaceae includes seven genera and ca. 440 species and is cosmopolitan in distribution. The bulk of the species diversity is found in Juncus (315 species) and Luzula (115 species). Here I present a phylogenetic study within Juncaceae that focuses on the large genus Juncus, using maximum parsimony, maximum likelihood, and Bayesian inference phylogenetic analyses of the nuclear ribosomal DNA internal transcribed spacer region (ITS), and samples the genera Distichia, Juncus, Luzula, and Oxychloe. The ITS data support the placement of Oxychloe with the other cushion plant genus Distichia well within the family, contrary to the placement as sister to the Cyperaceae in previous studies. Juncus is paraphyletic, with all of the other sampled Juncaceae genera nested within it. Luzula appears related to Juncus capitatus and Juncus trifidus, while the two cushion plant genera, Distichia and Oxychloe, are sister taxa and are nested within a clade of Juncus species from Juncus subgenus Juncus sections Juncotypus and Graminifolii. Leaf and inflorescence forms are homoplastic in the family and need to be more thoroughly quantified morphologically, anatomically, and developmentally to properly assess their patterns of evolution in the family. Chromosome patterns are complex, given the levels of aneuploidy/polyploidy in the family, but there appears to be a split between the Juncus-dominated clades, with diploid chromosome numbers generally in multiples of 10 or 20 and apparent aneuploid derivatives, and the Luzula clade, with diploid chromosome numbers generally in multiples of 6 or 12. This chromosome number difference might provide additional evidence for the placement of J. capitatus near Luzula, as this species has a 2n=18 chromosome compliment.