Asteraceae present special technical challenges for molecular phylogenetic studies. Less sequence divergence is generally observed between composites at all taxonomic levels than between comparable taxa in other families. Combining sequences from different loci into the same analysis increases the amount of phylogenetic signal and improves resolution in phylogenetic trees. As members of the Compositae Alliance continue to coordinate their efforts the motivation for combining DNA sequences from loci in different genomes will increase. However, the relatively recent radiation of the family suggests a greater probability of character incongruence between loci, because of differential lineage sorting and/or interspecific hybridization. Reported here is a preliminary molecular phylogenetic study of Heliantheae s. l. This complex exhibits typically low levels of intergeneric sequence divergence. Selected species in 16 genera were analyzed to test the feasibility of combining data. Sequences were determined or obtained for the variable 3 portion of the plastid locus ndhF and the nuclear ribosomal ITS region. Interlocus congruence was assessed with two methods both of which found significant congruence between nuclear and plastid trees. The data sets were then combined and analyzed together. The combined tree had a larger measure of signal content, higher resolution, and better support values for internal nodes than trees from either of the separate data sets.

Key words: Asteraceae, Heliantheae s. l., intergenomic incongruence, molecular phylogenetics