We present a secondary structure model for the nuclear rDNA ITS region based on statistical analyses of covariation in 340 Asteraceae ITS sequences. The model includes novel structural motifs for ITS1 and ITS2 and supports some of the structural proposals of previous studies using thermodynamic criteria. The positional homology implied by the model provides a framework for molecular evolutionary studies and the first family-level phylogeny independent of chloroplast DNA data. The highly resolved ITS tree shows considerable congruence with the relationships among major lineages of the Asteraceae suggested by previous cpDNA studies. Combined analyses provide additional resolution and support for relationships in the family.

Key words: Asteraceae, ITS secondary structure, molecular evolution, sequence alignment