Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae)

Four molecular data sets are available for the diploid intersterile genera of the cereal grain tribe Triticeae, and there are numerous differences among the four published trees. All six pairwise combinations of data sets were examined using tree comparisons, the incongruence length difference test, the Wilcoxon signed ranks test, and a permutation test. We describe some advantages, disadvantages, and properties of the different comparison methods. Test results provide no evidence for significant differences in the phylogenetic signal among the three nuclear data sets, with the exception of the placement of a single taxon. The chloroplast DNA restriction site data, however, support a significantly different tree, and the differences probably reflect a separate evolutionary history of the chloroplast genome.