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