Neutral Evolution of the Nonbinding Region of the Anthocyanin Regulatory Gene Ipmyb1 in IpomoeaSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY986823, AY986824, AY986825, AY986826, AY986827, AY986828, AY986829, AY986830, AY986831, AY986832, AY986833, AY986834, AY986835, AY986836, AY986837, AY986838, AY986839, AY986840, AY986841, AY986842, AY986843, AY986844, AY986845, AY986846, AY986847, AY986848, AY986849, AY986850, …

Plant transcription factors often contain domains that evolve very rapidly. Although it has been suggested that this rapid evolution may contribute substantially to phenotypic differentiation among species, this suggestion has seldom been tested explicitly. We tested the validity of this hypothesis by examining the rapidly evolving non-DNA-binding region of an R2R3-myb transcription factor that regulates anthocyanin expression in flowers of the genus Ipomoea. We first provide evidence that the W locus in Ipomoea purpurea, which determines whether flowers will be pigmented or white, corresponds to a myb gene segregating in southeastern U.S. populations for one functional allele and one nonfunctional allele. While the binding domain exhibits substantial selective constraint, the nonbinding region evolves at an average Ka/Ks ratio of 0.74. This elevated rate of evolution is due to relaxed constraint rather than to increased levels of positive selection. Despite this relaxed constraint, however, ∼20–25% of the codons, randomly distributed throughout the nonbinding region, are highly constrained, with the remainder evolving neutrally, indicating that the entire region performs important function(s). Our results provide little indication that rapid evolution in this regulatory gene is driven by natural selection or that it is responsible for floral-color differences among Ipomoea species.