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MBE Advance Access published online on July 28, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg197
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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Accepted June 11, 2003
© 2003 Society for Molecular Biology and Evolution

Original Articles

Evolutionary Rate Variation in Anthocyanin Pathway Genes

Yingqing Lu 1 and Mark D. Rausher 1*

1 Department of Biology, Box 90338, Duke University, Durham, NC 27708

* To whom correspondence should be addressed. E-mail: mrausher{at}duke.edu.


  Abstract

Over a broad taxonomic range, spanning monocots and dicots, upstream enzymes of the anthocyanin pigment pathway have evolved less rapidly than downstream enzymes. In this report it is shown 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, since the CHS-D gene exhibits higher synonymous substitution rates than the genes for the other two enzymes. Codon-based tests for positive selection suggest 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 than in CHS-D. Unlike the downstream genes, CHS-D also exhibits evidence of codon bias. Together, the evidence suggests that the difference in non-synonymous 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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