The disparity between rates of morphological and molecular evolution remains a key paradox in evolutionary genetics. A proposed resolution to this paradox has been the conjecture that morphological evolution proceeds via diversification in regulatory loci, and that phenotypic evolution may correlate better with regulatory gene divergence. This conjecture can be tested by examining rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive radiations. We have isolated homologues to the Arabidopsis APETALA3 (ASAP3͞TM6) and APETALA1 (ASAP1) floral regulatory genes and the CHLOROPHYLL A͞B BINDING PROTEIN9 (ASCAB9) photosynthetic structural gene from species in the Hawaiian silversword alliance, a premier example of plant adaptive radiation. We have compared rates of regulatory and structural gene evolution in the Hawaiian species to those in related species of North American tarweeds. Molecular evolutionary analyses indicate significant increases in nonsynonymous relative to synonymous nucleotide substitution rates in the ASAP3͞TM6 and ASAP1 regulatory genes in the rapidly evolving Hawaiian species. By contrast, no general increase is evident in neutral mutation rates for these loci in the Hawaiian species. An increase in nonsynonymous relative to synonymous nucleotide substitution rate is also evident in the ASCAB9 structural gene in the Hawaiian species, but not to the extent displayed in the regulatory loci. The significantly accelerated rates of regulatory gene evolution in the Hawaiian species may reflect the influence of allopolyploidy or of selection and adaptive divergence. The analyses suggest that accelerated rates of regulatory gene evolution may accompany rapid morphological diversification in adaptive radiations.floral regulatory loci ͉ MADS-box ͉ CAB9 ͉ Hawaiian silversword alliance R ates of morphological evolution are generally not correlated with rates of molecular evolution. This paradoxical observation was highlighted early by Wilson and coworkers (1-3), and subsequent molecular studies in species groups that have undergone recent adaptive radiations, such as African rift lake cichlids (4), columbines (5), and the Hawaiian silversword alliance (6), have documented marked incongruities in rates of morphological and molecular evolution. A proposed resolution to this paradox has been the conjecture that evolutionary changes in regulatory genes, rather than large-scale diversification in structural genes, may be responsible for interspecific variation in organismal morphologies (1)(2)(3)(7)(8)(9). This conjecture is reinforced by molecular developmental studies that indicate that dramatic shifts in organismal structure may arise from mutations at key regulatory loci (7-9). One test of this conjecture is to examine whether there is a significant acceleration in rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive radiations.The Hawaiian silversword alliance (Asteraceae: Heliantheae-Madiinae) is...