Phylogeny of Setaria (Poaceae, Panicoideae, Paniceae) and Related Genera Based on the Chloroplast Gene ndhF

The genus Setaria is the largest genus in the so-called bristle clade, a monophyletic group of panicoid grasses distinguished by the presence of sterile branches, or bristles, in their inflorescences. The clade includes both foxtail millet and pearl millet, the latter an important cereal crop in dry parts of the world. Other members of the clade are weeds that are widespread agricultural pests. Previous molecular phylogenetic studies have suggested that Setaria might not be monophyletic but did not have a large enough sample of species to test this rigorously. In addition, taxonomic studies have suggested a close relationship between Setaria and Paspalidium, with some authors combining them into a single genus, but molecular studies included too few Paspalidium accessions for a meaningful conclusion. Accordingly, we have produced 77 new sequences of the chloroplast gene ndhF for 52 species not in previous analyses. These were added to available sequences for 35 species in 10 genera of the bristle clade and four outgroup taxa. We find that Setaria species fall into several moderately to strongly supported clades that correlate with geography but not with the existing subgeneric classification. Relationships among these clades and among other genera within the bristle clade are unclear. Constraint experiments using the approximately unbiased test reject the monophyly of Pennisetum, Setaria, and Setaria plus Paspalidium, as well as several other groupings, although the test may be overly sensitive and prone to Type I error. The more conservative Shimodaira-Hasegawa test fails to reject monophyly of any of the tested clades.