title: Nucleotide variation at the dopa decarboxylase (Ddc) gene in natural populations of Drosophila melanogaster.
abstract: We studied nucleotide sequence variation at the gene coding for dopa decarboxylase (Ddc) in seven populations of Drosophila melanogaster. Strength and pattern of linkage disequilibrium are somewhat distinct in the extensively sampled Spanish and Raleigh populations. In the Spanish population, a few sites are in strong positive association, whereas a large number of sites in the Raleigh population are associated nonrandomly but the association is not strong. Linkage disequilibrium analysis shows presence of two groups of haplotypes in the populations, each of which is fairly diverged, suggesting epistasis or inversion polymorphism. There is evidence of two forms of natural selection acting on Ddc. The McDonald-Kreitman test indicates a deficit of fixed amino acid differences between D. melanogaster and D. simulans, which may be due to negative selection. An excess of derived alleles at high frequency, significant according to the H-test, is consistent with the effect of hitchhiking. The hitchhiking may have been caused by directional selection downstream of the locus studied, as suggested by a gradual decrease of the polymorphism-to-divergence ratio. Altogether, the Ddc locus exhibits a complicated pattern of variation apparently due to several evolutionary forces. Such a complex pattern may be a result of an unusually high density of functionally important genes.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697-2525, USA. tatarenk@uci.edu
authors.forename: Andrey
authors.initials: A
authors.lastname: Tatarenkov
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Ayala
mesh_terms: D000483:Alleles; D000818:Animals; D001483:Base Sequence; D004296:Dopa Decarboxylase / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics*; D019143:Evolution, Molecular; D049810:Genetic Speciation; D005828:Genetics, Population; D005843:Geography; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D012689:Sequence Homology, Nucleic Acid
chemical_list: D004296:Dopa Decarboxylase