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MBE Advance Access originally published online on July 28, 2003
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Mol. Biol. Evol. 20(11):1844-1853. 2003
DOI: 10.1093/molbev/msg197
© 2003 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

Evolutionary Rate Variation in Anthocyanin Pathway Genes

Yingqing Lu and Mark D. Rausher

Department of Biology, Duke University

E-mail: mrausher{at}duke.edu.

Over a broad taxonomic range that spans monocots and dicots, upstream enzymes of the anthocyanin pigment pathway have evolved less rapidly than downstream enzymes. In this article we show that this pattern is also evident within the genus Ipomoea. Specifically, the most upstream enzyme, chalcone synthase (CHS-D), evolves more slowly than the two most downstream enzymes, ancyocyanidin synthase (ANS) and UDP glucose flavonoid 3-oxy-glucosyltransferase (UFGT). This pattern appears not to be due to variation in mutation rates, because the CHS-D gene exhibits higher synonymous substitution rates than the genes for the other two enzymes. Codon-based tests for positive selection suggest that it has been negligible or absent in all three genes. In addition, the mean number of indel-creating events is four times as high in the downstream genes as in CHS-D. Unlike the downstream genes, CHS-D also exhibits evidence of codon bias. Together, the evidence suggests that the difference in nonsynonymous substitution rates between upstream and downstream genes is due to relaxed constraint on the downstream genes rather than a greater frequency of positively selected substitutions.

Key Words: anthocyanin pathway • nucleotide substitution rates • positive selection • codon usage • rate variation


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