Molecular Biology and Evolution 19:989-998 (2002)
© 2002 Society for Molecular Biology and Evolution
DNA Sequence Variation at a Duplicated Gene: Excess of Replacement Polymorphism and Extensive Haplotype Structure in the Drosophila melanogaster bicoid Region
,1
*Department Biologie II—Evolutionsbiologie, Universität München, Germany;
Department of Biology, University of Rochester, New York
The bicoid (bcd) gene of Drosophila has played an important role in understanding the system of developmental regulatory genes that controls segmentation in the fruit fly. Several studies in Drosophila and closely related insects suggest that bcd may be the result of a gene duplication in the Dipteran lineage. In addition, the presence of a large, conserved secondary structure in the 3' untranslated region (UTR) makes the bcd gene a good candidate for studying compensatory evolution and the relationship between RNA secondary structure and patterns of standing variation in natural populations. Despite these interesting aspects, a population-level analysis has until now not been performed on bcd. In this study, DNA sequence variation was examined for a 4-kb region of the bcd gene, including a portion of the 5' UTR, the entire coding region, and the 3' UTR, for 25 Drosophila melanogaster isofemale lines from Zimbabwe and one allele from D. simulans. Statistical tests revealed a significant excess of replacement polymorphisms in the D. melanogaster lineage that are clustered in two putative linker regions of the Bicoid protein. This result is consistent with a relaxation of selective constraints in these regions. In addition, we found a distinct haplotype structure and a significantly smaller number of haplotypes than predicted by the standard neutral model. It is unlikely that the haplotype structure is maintained by epistatic selection acting on the secondary structure in the 3' UTR or by the association of the bcd gene with polymorphic inversions. Instead, our two main observations, namely the occurrence of a haplotype structure and the excess of replacement polymorphisms, may indicate that the selective history of this gene is rather complex, involving both the relaxation of purifying selection in some parts of the protein and the action of positive selection in other parts of the gene region.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  P. R. Haddrill, K. R. Thornton, B. Charlesworth, and P. Andolfatto Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations Genome Res., June 1, 2005; 15(6): 790 - 799. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Nikoh, A. Duty, and G. Gibson Effects of Population Structure and Sex on Association Between Serotonin Receptors and Drosophila Heart Rate Genetics, December 1, 2004; 168(4): 1963 - 1974. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. S. Balakirev and F. J. Ayala Nucleotide Variation in the tinman and bagpipe Homeobox Genes of Drosophila melanogaster Genetics, April 1, 2004; 166(4): 1845 - 1856. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Clauss and T. Mitchell-Olds Functional Divergence in Tandemly Duplicated Arabidopsis thaliana Trypsin Inhibitor Genes Genetics, March 1, 2004; 166(3): 1419 - 1436. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Andolfatto and J. D. Wall Linkage Disequilibrium Patterns Across a Recombination Gradient in African Drosophila melanogaster Genetics, November 1, 2003; 165(3): 1289 - 1305. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Navarro-Sabate, M. Aguade, and C. Segarra Excess of Nonsynonymous Polymorphism at Acph-1 in Different Gene Arrangements of Drosophila subobscura Mol. Biol. Evol., November 1, 2003; 20(11): 1833 - 1843. [Abstract] [Full Text] [PDF]
|
|