A molecular phylogeny of the subfamily Arundinoideae (Poaceae)

Includes bibliography.The subfamily Arundinoideae has long been considered to be an unnatural assemblage of genera, the relationships of which are obscure or unknown. Because morphological and anatomical data have, to date, been unable to elucidate relationships among these genera, sequence data from two chloroplast genes are used to elucidate relationships among 33 arundinoid genera. Sequence data from the variable, grass-specific insert in the rpoC2 gene is used to determine the relationships among 73 grass species from all currently recognised subfamilies. Phylogenetic analysis of this sequence data required the development of specialised alignment techniques based on testing assumptions of positional homology. Results of the analyses based on these alignments suggest that the Arundinoideae is divisible into four lineages, corresponding approximately to the tribes Danthonieae, Arundineae, Aristideae and Thysanolaeneae. Several arundinoid representatives are placed in other subfamilies. The rpoC2 sequence data was too variable to elucidate relationships at the tribal and subfamilial level. For this purpose, sequence data of the highly conserved rbcL gene was obtained from 22 taxa selected from the lineages identified by the rpoC2 study. Phylogenetic analysis of a total of 36 sequences resolved some of the relationships of the major clades, but other relationships were poorly supported. In an attempt to improve the resolution of these major clades, the rpoC2 and rbcL data sets were combined with restriction site data. These three data sets were analysed in a variety of combinations using both data combination and tree consensus methods to assess support of the phylogenetic relationships. Despite this, the resolution of the relationships among the Arundineae, Danthonieae, Aristideae and Chloridoideae was not resolved with any finality, although a (Arundineae (Danthonieae (Aristideae, Chloridoideae))) relationship is proposed as being most likely. The molecular phylogeny implies that eight grass subfamilies should be recognised. Two of these, the Danthonioideae and Aristidoideae, are new and the Arundinoideae is redelimited. Furthermore, new tribes in the subfamilies Centothecoideae (Thysanolaeneae) and Chloridoideae (Centropodieae) are proposed to accommodate lineages and taxa misplaced in the subfamily Arudinoideae as previously delimited