title: Nucleotide variation at the runt locus in Drosophila melanogaster and Drosophila simulans.
abstract: Intra- and interspecific nucleotide variation for the major developmental gene runt in Drosophila was studied in D. melanogaster and D. simulans. The 1.5-kb protein-coding region and the 0.4-kb intron of the runt gene were sequenced for 11 alleles in each species. The D. melanogaster alleles originated from east Africa. Estimated parameters of intraspecific variation in D. melanogaster (exons: theta = 0.018, pi = 0.018; intron: theta = 0.014, pi = 0.014) and D. simulans (exons: theta = 0.007, pi = 0.005; intron: theta = 0.008, pi = 0.005) were below average for other X-linked genes, while divergence between species (exons: D = 0.094; intron: D = 0.069) fell within the normal range for both silent and replacement changes. This estimate for runt, along with published values for three other genes in regions of normal recombination, show east African D. melanogaster to be roughly twice as polymorphic as D. simulans. The majority of nucleotide variation, silent and replacement, in both species was found to be selectively neutral using various statistical tests (HKA, McDonald-Kreitman, Tajima, and Fu and Li tests). Monte Carlo simulations of the coalescent process significantly rejected a Wright-Fisher model with respect to an amino acid polymorphism and the distribution of polymorphic sites among the D. simulans lines. This indicated an old lineage and may reflect ancestral population substructuring in D. simulans.
authors.affiliation: Department of Ecology and Evolution, State University of New York at Stony Brook, USA. jlabate@iastate.edu
authors.forename: J A
authors.initials: JA
authors.lastname: Labate
authors.forename: C H
authors.initials: CH
authors.lastname: Biermann
authors.forename: W F
authors.initials: WF
authors.lastname: Eanes
mesh_terms: D000483:Alleles; D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics*; D004330:Drosophila / Q000235:genetics*; D029721:Drosophila Proteins; D004331:Drosophila melanogaster / Q000235:genetics*; D019143:Evolution, Molecular; D017344:Genes, Insect; D014644:Genetic Variation; D019476:Insect Proteins / Q000235:genetics*; D007438:Introns; D008969:Molecular Sequence Data; D009687:Nuclear Proteins; D011110:Polymorphism, Genetic; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D014157:Transcription Factors
chemical_list: D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D019476:Insect Proteins; D009687:Nuclear Proteins; D014157:Transcription Factors; C080833:run protein, Drosophila; D004247:DNA